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Build branch main with version main (5f6516e)

Browse Source 
Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements
This commit is contained in:
CI
2025-03-06 09:35:27 +00:00
parent 6f8d68b9cc
commit a518d2ead8
343 changed files with 40275 additions and 18530 deletions
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13
target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
View File

@@ -124,6 +124,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -234,16 +237,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bamtobed"
executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

164
target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
View File

@@ -2,7 +2,7 @@
# bedtools_bamtobed main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,72 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bamtobed main"
echo ""
echo "Converts BAM alignments to BED6 or BEDPE format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BAM file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output BED file."
echo ""
echo "Options:"
echo " --bedpe"
echo " type: boolean_true"
echo " Write BEDPE format. Requires BAM to be grouped or sorted by query."
echo ""
echo " --mate1"
echo " type: boolean_true"
echo " When writing BEDPE (-bedpe) format, always report mate one as the first"
echo " BEDPE \"block\"."
echo ""
echo " --bed12"
echo " type: boolean_true"
echo " Write \"blocked\" BED format (aka \"BED12\"). Forces -split."
echo " See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1"
echo ""
echo " --split"
echo " type: boolean_true"
echo " Report \"split\" BAM alignments as separate BED entries."
echo " Splits only on N CIGAR operations."
echo ""
echo " --splitD"
echo " type: boolean_true"
echo " Split alignments based on N and D CIGAR operators."
echo " Forces -split."
echo ""
echo " -ed, --edit_distance"
echo " type: boolean_true"
echo " Use BAM edit distance (NM tag) for BED score."
echo " - Default for BED is to use mapping quality."
echo " - Default for BEDPE is to use the minimum of"
echo " the two mapping qualities for the pair."
echo " - When -ed is used with -bedpe, the total edit"
echo " distance from the two mates is reported."
echo ""
echo " --tag"
echo " type: string"
echo " example: SM"
echo " Use other NUMERIC BAM alignment tag for BED score."
echo " Default for BED is to use mapping quality. Disallowed with BEDPE output."
echo ""
echo " --color"
echo " type: string"
echo " example: 250,250,250"
echo " An R,G,B string for the color used with BED12 format."
echo " Default is (255,0,0)."
echo ""
echo " --cigar"
echo " type: boolean_true"
echo " Add the CIGAR string to the BED entry as a 7th column."
}
# initialise variables
VIASH_MODE='run'
@@ -522,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed"
LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -639,6 +573,98 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bamtobed main"
echo ""
echo "Converts BAM alignments to BED6 or BEDPE format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BAM file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output BED file."
echo ""
echo "Options:"
echo " --bedpe"
echo " type: boolean_true"
echo " Write BEDPE format. Requires BAM to be grouped or sorted by query."
echo ""
echo " --mate1"
echo " type: boolean_true"
echo " When writing BEDPE (-bedpe) format, always report mate one as the first"
echo " BEDPE \"block\"."
echo ""
echo " --bed12"
echo " type: boolean_true"
echo " Write \"blocked\" BED format (aka \"BED12\"). Forces -split."
echo " See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1"
echo ""
echo " --split"
echo " type: boolean_true"
echo " Report \"split\" BAM alignments as separate BED entries."
echo " Splits only on N CIGAR operations."
echo ""
echo " --splitD"
echo " type: boolean_true"
echo " Split alignments based on N and D CIGAR operators."
echo " Forces -split."
echo ""
echo " -ed, --edit_distance"
echo " type: boolean_true"
echo " Use BAM edit distance (NM tag) for BED score."
echo " - Default for BED is to use mapping quality."
echo " - Default for BEDPE is to use the minimum of"
echo " the two mapping qualities for the pair."
echo " - When -ed is used with -bedpe, the total edit"
echo " distance from the two mates is reported."
echo ""
echo " --tag"
echo " type: string"
echo " example: SM"
echo " Use other NUMERIC BAM alignment tag for BED score."
echo " Default for BED is to use mapping quality. Disallowed with BEDPE output."
echo ""
echo " --color"
echo " type: string"
echo " example: 250,250,250"
echo " An R,G,B string for the color used with BED12 format."
echo " Default is (255,0,0)."
echo ""
echo " --cigar"
echo " type: boolean_true"
echo " Add the CIGAR string to the BED entry as a 7th column."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
View File

@@ -78,6 +78,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -186,16 +189,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bamtofastq"
executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

86
target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
View File

@@ -2,7 +2,7 @@
# bedtools_bamtofastq main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,33 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bamtofastq main"
echo ""
echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM"
echo "format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BAM file to be converted to FASTQ."
echo ""
echo "Outputs:"
echo " -fq, --fastq"
echo " type: file, required parameter, output, file must exist"
echo " Output FASTQ file."
echo ""
echo " -fq2, --fastq2"
echo " type: file, output, file must exist"
echo " FASTQ for second end. Used if BAM contains paired-end data."
echo " BAM should be sorted by query name is creating paired FASTQ."
echo ""
echo "Options:"
echo " --tags"
echo " type: boolean_true"
echo " Create FASTQ based on the mate info in the BAM R2 and Q2 tags."
}
# initialise variables
VIASH_MODE='run'
@@ -483,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -600,6 +573,59 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bamtofastq main"
echo ""
echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM"
echo "format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BAM file to be converted to FASTQ."
echo ""
echo "Outputs:"
echo " -fq, --fastq"
echo " type: file, required parameter, output, file must exist"
echo " Output FASTQ file."
echo ""
echo " -fq2, --fastq2"
echo " type: file, output, file must exist"
echo " FASTQ for second end. Used if BAM contains paired-end data."
echo " BAM should be sorted by query name is creating paired FASTQ."
echo ""
echo "Options:"
echo " --tags"
echo " type: boolean_true"
echo " Create FASTQ based on the mate info in the BAM R2 and Q2 tags."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
View File

@@ -67,6 +67,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -175,16 +178,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bed12tobed6"
executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

80
target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
View File

@@ -2,7 +2,7 @@
# bedtools_bed12tobed6 main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,30 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bed12tobed6 main"
echo ""
echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to"
echo "discrete BED6 features."
echo "For example, in the case of a gene with six exons, bed12ToBed6 would create six"
echo "separate BED6 features (i.e., one for each exon)."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BED12 file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output BED6 file to be written."
echo ""
echo "Options:"
echo " -n, --n_score"
echo " type: boolean_true"
echo " Force the score to be the (1-based) block number from the BED12."
}
# initialise variables
VIASH_MODE='run'
@@ -480,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -597,6 +573,56 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bed12tobed6 main"
echo ""
echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to"
echo "discrete BED6 features."
echo "For example, in the case of a gene with six exons, bed12ToBed6 would create six"
echo "separate BED6 features (i.e., one for each exon)."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input BED12 file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output BED6 file to be written."
echo ""
echo "Options:"
echo " -n, --n_score"
echo " type: boolean_true"
echo " Force the score to be the (1-based) block number from the BED12."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
View File

@@ -98,6 +98,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -213,16 +216,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_bedtobam"
executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

112
target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
View File

@@ -2,7 +2,7 @@
# bedtools_bedtobam main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,46 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bedtobam main"
echo ""
echo "Converts feature records (bed/gff/vcf) to BAM format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf)."
echo ""
echo " -g, --genome"
echo " type: file, required parameter, file must exist"
echo " Input genome file."
echo " NOTE: This is not a fasta file. This is a two-column tab-delimited file"
echo " where the first column is the chromosome name and the second their"
echo " sizes."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output BAM file to be written."
echo ""
echo "Options:"
echo " -mapq, --map_quality"
echo " type: integer"
echo " default: 255"
echo " min: 0"
echo " max: 255"
echo " Set the mappinq quality for the BAM records."
echo ""
echo " --bed12"
echo " type: boolean_true"
echo " The BED file is in BED12 format. The BAM CIGAR"
echo " string will reflect BED \"blocks\"."
echo ""
echo " -ubam, --uncompress_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
}
# initialise variables
VIASH_MODE='run'
@@ -496,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -613,6 +573,72 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_bedtobam main"
echo ""
echo "Converts feature records (bed/gff/vcf) to BAM format."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf)."
echo ""
echo " -g, --genome"
echo " type: file, required parameter, file must exist"
echo " Input genome file."
echo " NOTE: This is not a fasta file. This is a two-column tab-delimited file"
echo " where the first column is the chromosome name and the second their"
echo " sizes."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output BAM file to be written."
echo ""
echo "Options:"
echo " -mapq, --map_quality"
echo " type: integer"
echo " default: 255"
echo " min: 0"
echo " max: 255"
echo " Set the mappinq quality for the BAM records."
echo ""
echo " --bed12"
echo " type: boolean_true"
echo " The BED file is in BED12 format. The BAM CIGAR"
echo " string will reflect BED \"blocks\"."
echo ""
echo " -ubam, --uncompress_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
View File

@@ -226,6 +226,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -336,16 +339,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_genomecov"
executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

302
target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
View File

@@ -2,7 +2,7 @@
# bedtools_genomecov main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,141 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_genomecov main"
echo ""
echo "Compute the coverage of a feature file among a genome."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, file must exist"
echo " example: input.bed"
echo " The input file (BED/GFF/VCF) to be used."
echo ""
echo " -ibam, --input_bam"
echo " type: file, file must exist"
echo " The input file is in BAM format."
echo " Note: BAM _must_ be sorted by positions."
echo " '--genome' option is ignored if you use '--input_bam' option!"
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " The genome file to be used."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -d, --depth"
echo " type: boolean_true"
echo " Report the depth at each genome position (with one-based coordinates)."
echo " Default behavior is to report a histogram."
echo ""
echo " -dz, --depth_zero"
echo " type: boolean_true"
echo " Report the depth at each genome position (with zero-based coordinates)."
echo " Reports only non-zero positions."
echo " Default behavior is to report a histogram."
echo ""
echo " -bg, --bed_graph"
echo " type: boolean_true"
echo " Report depth in BedGraph format. For details, see:"
echo " genome.ucsc.edu/goldenPath/help/bedgraph.html"
echo ""
echo " -bga, --bed_graph_zero_coverage"
echo " type: boolean_true"
echo " Report depth in BedGraph format, as above (-bg)."
echo " However with this option, regions with zero"
echo " coverage are also reported. This allows one to"
echo " quickly extract all regions of a genome with 0"
echo " coverage by applying: \"grep -w 0\$\" to the output."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo " when computing coverage."
echo " For BAM files, this uses the CIGAR \"N\" and \"D\" operations"
echo " to infer the blocks for computing coverage."
echo " For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds"
echo " fields (i.e., columns 10,11,12)."
echo ""
echo " -ignoreD, --ignore_deletion"
echo " type: boolean_true"
echo " Ignore local deletions (CIGAR \"D\" operations) in BAM entries"
echo " when computing coverage."
echo ""
echo " --strand"
echo " type: string"
echo " choices: [ +, - ]"
echo " Calculate coverage of intervals from a specific strand."
echo " With BED files, requires at least 6 columns (strand is column 6)."
echo ""
echo " -pc, --pair_end_coverage"
echo " type: boolean_true"
echo " Calculate coverage of pair-end fragments."
echo " Works for BAM files only"
echo ""
echo " -fs, --fragment_size"
echo " type: boolean_true"
echo " Force to use provided fragment size instead of read length"
echo " Works for BAM files only"
echo ""
echo " --du"
echo " type: boolean_true"
echo " Change strand af the mate read (so both reads from the same strand)"
echo " useful for strand specific"
echo " Works for BAM files only"
echo ""
echo " -5, --five_prime"
echo " type: boolean_true"
echo " Calculate coverage of 5\" positions (instead of entire interval)."
echo ""
echo " -3, --three_prime"
echo " type: boolean_true"
echo " Calculate coverage of 3\" positions (instead of entire interval)."
echo ""
echo " --max"
echo " type: integer"
echo " min: 0"
echo " Combine all positions with a depth >= max into"
echo " a single bin in the histogram. Irrelevant"
echo " for -d and -bedGraph"
echo " - (INTEGER)"
echo ""
echo " --scale"
echo " type: double"
echo " min: 0.0"
echo " Scale the coverage by a constant factor."
echo " Each coverage value is multiplied by this factor before being reported."
echo " Useful for normalizing coverage by, e.g., reads per million (RPM)."
echo " - Default is 1.0; i.e., unscaled."
echo " - (FLOAT)"
echo ""
echo " --trackline"
echo " type: boolean_true"
echo " Adds a UCSC/Genome-Browser track line definition in the first line of"
echo " the output."
echo " - See here for more details about track line definition:"
echo " http://genome.ucsc.edu/goldenPath/help/bedgraph.html"
echo " - NOTE: When adding a trackline definition, the output BedGraph can be"
echo " easily"
echo " uploaded to the Genome Browser as a custom track,"
echo " BUT CAN NOT be converted into a BigWig file (w/o removing the"
echo " first line)."
echo ""
echo " --trackopts"
echo " type: string, multiple values allowed"
echo " Writes additional track line definition parameters in the first line."
echo " - Example:"
echo " -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'"
echo " Note the use of single-quotes if you have spaces in your parameters."
echo " - (TEXT)"
}
# initialise variables
VIASH_MODE='run'
@@ -591,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -708,6 +573,167 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_genomecov main"
echo ""
echo "Compute the coverage of a feature file among a genome."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, file must exist"
echo " example: input.bed"
echo " The input file (BED/GFF/VCF) to be used."
echo ""
echo " -ibam, --input_bam"
echo " type: file, file must exist"
echo " The input file is in BAM format."
echo " Note: BAM _must_ be sorted by positions."
echo " '--genome' option is ignored if you use '--input_bam' option!"
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " The genome file to be used."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -d, --depth"
echo " type: boolean_true"
echo " Report the depth at each genome position (with one-based coordinates)."
echo " Default behavior is to report a histogram."
echo ""
echo " -dz, --depth_zero"
echo " type: boolean_true"
echo " Report the depth at each genome position (with zero-based coordinates)."
echo " Reports only non-zero positions."
echo " Default behavior is to report a histogram."
echo ""
echo " -bg, --bed_graph"
echo " type: boolean_true"
echo " Report depth in BedGraph format. For details, see:"
echo " genome.ucsc.edu/goldenPath/help/bedgraph.html"
echo ""
echo " -bga, --bed_graph_zero_coverage"
echo " type: boolean_true"
echo " Report depth in BedGraph format, as above (-bg)."
echo " However with this option, regions with zero"
echo " coverage are also reported. This allows one to"
echo " quickly extract all regions of a genome with 0"
echo " coverage by applying: \"grep -w 0\$\" to the output."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo " when computing coverage."
echo " For BAM files, this uses the CIGAR \"N\" and \"D\" operations"
echo " to infer the blocks for computing coverage."
echo " For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds"
echo " fields (i.e., columns 10,11,12)."
echo ""
echo " -ignoreD, --ignore_deletion"
echo " type: boolean_true"
echo " Ignore local deletions (CIGAR \"D\" operations) in BAM entries"
echo " when computing coverage."
echo ""
echo " --strand"
echo " type: string"
echo " choices: [ +, - ]"
echo " Calculate coverage of intervals from a specific strand."
echo " With BED files, requires at least 6 columns (strand is column 6)."
echo ""
echo " -pc, --pair_end_coverage"
echo " type: boolean_true"
echo " Calculate coverage of pair-end fragments."
echo " Works for BAM files only"
echo ""
echo " -fs, --fragment_size"
echo " type: boolean_true"
echo " Force to use provided fragment size instead of read length"
echo " Works for BAM files only"
echo ""
echo " --du"
echo " type: boolean_true"
echo " Change strand af the mate read (so both reads from the same strand)"
echo " useful for strand specific"
echo " Works for BAM files only"
echo ""
echo " -5, --five_prime"
echo " type: boolean_true"
echo " Calculate coverage of 5\" positions (instead of entire interval)."
echo ""
echo " -3, --three_prime"
echo " type: boolean_true"
echo " Calculate coverage of 3\" positions (instead of entire interval)."
echo ""
echo " --max"
echo " type: integer"
echo " min: 0"
echo " Combine all positions with a depth >= max into"
echo " a single bin in the histogram. Irrelevant"
echo " for -d and -bedGraph"
echo " - (INTEGER)"
echo ""
echo " --scale"
echo " type: double"
echo " min: 0.0"
echo " Scale the coverage by a constant factor."
echo " Each coverage value is multiplied by this factor before being reported."
echo " Useful for normalizing coverage by, e.g., reads per million (RPM)."
echo " - Default is 1.0; i.e., unscaled."
echo " - (FLOAT)"
echo ""
echo " --trackline"
echo " type: boolean_true"
echo " Adds a UCSC/Genome-Browser track line definition in the first line of"
echo " the output."
echo " - See here for more details about track line definition:"
echo " http://genome.ucsc.edu/goldenPath/help/bedgraph.html"
echo " - NOTE: When adding a trackline definition, the output BedGraph can be"
echo " easily"
echo " uploaded to the Genome Browser as a custom track,"
echo " BUT CAN NOT be converted into a BigWig file (w/o removing the"
echo " first line)."
echo ""
echo " --trackopts"
echo " type: string, multiple values allowed"
echo " Writes additional track line definition parameters in the first line."
echo " - Example:"
echo " -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'"
echo " Note the use of single-quotes if you have spaces in your parameters."
echo " - (TEXT)"
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
View File

@@ -123,6 +123,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -231,16 +234,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

172
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
View File

@@ -2,7 +2,7 @@
# bedtools_getfasta main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,76 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_getfasta main"
echo ""
echo "Extract sequences from a FASTA file for each of the intervals defined in a"
echo "BED/GFF/VCF file."
echo ""
echo "Input arguments:"
echo " --input_fasta"
echo " type: file, file must exist"
echo " FASTA file containing sequences for each interval specified in the input"
echo " BED file."
echo " The headers in the input FASTA file must exactly match the chromosome"
echo " column in the BED file."
echo ""
echo " --input_bed"
echo " type: file, file must exist"
echo " BED file containing intervals to extract from the FASTA file."
echo " BED files containing a single region require a newline character"
echo " at the end of the line, otherwise a blank output file is produced."
echo ""
echo " --rna"
echo " type: boolean_true"
echo " The FASTA is RNA not DNA. Reverse complementation handled accordingly."
echo ""
echo "Run arguments:"
echo " -s, --strandedness"
echo " type: boolean_true"
echo " Force strandedness. If the feature occupies the antisense strand, the"
echo " output sequence will"
echo " be reverse complemented. By default strandedness is not taken into"
echo " account."
echo ""
echo "Output arguments:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output file where the output from the 'bedtools getfasta' commend will"
echo " be written to."
echo ""
echo " --tab"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited format instead of in FASTA"
echo " format."
echo ""
echo " --bed_out"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited BED format instead of in"
echo " FASTA format."
echo ""
echo " --name"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\" and"
echo " coordinate columns from the BED feature."
echo ""
echo " --name_only"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\""
echo " columns from the BED feature."
echo ""
echo " --split"
echo " type: boolean_true"
echo " When --input is in BED12 format, create a separate fasta entry for each"
echo " block in a BED12 record,"
echo " blocks being described in the 11th and 12th column of the BED."
echo ""
echo " --full_header"
echo " type: boolean_true"
echo " Use full fasta header. By default, only the word before the first space"
echo " or tab is used."
}
# initialise variables
VIASH_MODE='run'
@@ -526,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -643,6 +573,102 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_getfasta main"
echo ""
echo "Extract sequences from a FASTA file for each of the intervals defined in a"
echo "BED/GFF/VCF file."
echo ""
echo "Input arguments:"
echo " --input_fasta"
echo " type: file, file must exist"
echo " FASTA file containing sequences for each interval specified in the input"
echo " BED file."
echo " The headers in the input FASTA file must exactly match the chromosome"
echo " column in the BED file."
echo ""
echo " --input_bed"
echo " type: file, file must exist"
echo " BED file containing intervals to extract from the FASTA file."
echo " BED files containing a single region require a newline character"
echo " at the end of the line, otherwise a blank output file is produced."
echo ""
echo " --rna"
echo " type: boolean_true"
echo " The FASTA is RNA not DNA. Reverse complementation handled accordingly."
echo ""
echo "Run arguments:"
echo " -s, --strandedness"
echo " type: boolean_true"
echo " Force strandedness. If the feature occupies the antisense strand, the"
echo " output sequence will"
echo " be reverse complemented. By default strandedness is not taken into"
echo " account."
echo ""
echo "Output arguments:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output file where the output from the 'bedtools getfasta' commend will"
echo " be written to."
echo ""
echo " --tab"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited format instead of in FASTA"
echo " format."
echo ""
echo " --bed_out"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited BED format instead of in"
echo " FASTA format."
echo ""
echo " --name"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\" and"
echo " coordinate columns from the BED feature."
echo ""
echo " --name_only"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\""
echo " columns from the BED feature."
echo ""
echo " --split"
echo " type: boolean_true"
echo " When --input is in BED12 format, create a separate fasta entry for each"
echo " block in a BED12 record,"
echo " blocks being described in the 11th and 12th column of the BED."
echo ""
echo " --full_header"
echo " type: boolean_true"
echo " Use full fasta header. By default, only the word before the first space"
echo " or tab is used."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
View File

@@ -165,6 +165,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -272,16 +275,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_groupby"
executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

224
target/executable/bedtools/bedtools_groupby/bedtools_groupby
View File

@@ -2,7 +2,7 @@
# bedtools_groupby main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,102 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_groupby main"
echo ""
echo "Summarizes a dataset column based upon common column groupings."
echo "Akin to the SQL \"group by\" command."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input BED file to be used."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output groupby BED file."
echo ""
echo "Options:"
echo " -g, -grp, --groupby"
echo " type: string, required parameter"
echo " Specify the columns (1-based) for the grouping."
echo " The columns must be comma separated."
echo " - Default: 1,2,3"
echo ""
echo " -c, -opCols, --column"
echo " type: integer, required parameter"
echo " Specify the column (1-based) that should be summarized."
echo ""
echo " -o, -ops, --operation"
echo " type: string"
echo " Specify the operation that should be applied to opCol."
echo " Valid operations:"
echo " sum, count, count_distinct, min, max,"
echo " mean, median, mode, antimode,"
echo " stdev, sstdev (sample standard dev.),"
echo " collapse (i.e., print a comma separated list (duplicates allowed)),"
echo " distinct (i.e., print a comma separated list (NO duplicates"
echo " allowed)),"
echo " distinct_sort_num (as distinct, but sorted numerically, ascending),"
echo " distinct_sort_num_desc (as distinct, but sorted numerically,"
echo " descending),"
echo " concat (i.e., merge values into a single, non-delimited string),"
echo " freqdesc (i.e., print desc. list of values:freq)"
echo " freqasc (i.e., print asc. list of values:freq)"
echo " first (i.e., print first value)"
echo " last (i.e., print last value)"
echo " Default value: sum"
echo " If there is only column, but multiple operations, all operations will be"
echo " applied on that column. Likewise, if there is only one operation, but"
echo " multiple columns, that operation will be applied to all columns."
echo " Otherwise, the number of columns must match the the number of"
echo " operations,"
echo " and will be applied in respective order."
echo " E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
echo " the mean of column 4, and the count of column 6."
echo " The order of output columns will match the ordering given in the"
echo " command."
echo ""
echo " --full"
echo " type: boolean_true"
echo " Print all columns from input file. The first line in the group is used."
echo " Default: print only grouped columns."
echo ""
echo " --inheader"
echo " type: boolean_true"
echo " Input file has a header line - the first line will be ignored."
echo ""
echo " --outheader"
echo " type: boolean_true"
echo " Print header line in the output, detailing the column names."
echo " If the input file has headers (-inheader), the output file"
echo " will use the input's column names."
echo " If the input file has no headers, the output file"
echo " will use \"col_1\", \"col_2\", etc. as the column names."
echo ""
echo " --header"
echo " type: boolean_true"
echo " same as '-inheader -outheader'."
echo ""
echo " --ignorecase"
echo " type: boolean_true"
echo " Group values regardless of upper/lower case."
echo ""
echo " -prec, --precision"
echo " type: integer"
echo " default: 5"
echo " Sets the decimal precision for output."
echo ""
echo " -delim, --delimiter"
echo " type: string"
echo " default: ,"
echo " example: |"
echo " Specify a custom delimiter for the collapse operations."
}
# initialise variables
VIASH_MODE='run'
@@ -552,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -669,6 +573,128 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_groupby main"
echo ""
echo "Summarizes a dataset column based upon common column groupings."
echo "Akin to the SQL \"group by\" command."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input BED file to be used."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output groupby BED file."
echo ""
echo "Options:"
echo " -g, -grp, --groupby"
echo " type: string, required parameter"
echo " Specify the columns (1-based) for the grouping."
echo " The columns must be comma separated."
echo " - Default: 1,2,3"
echo ""
echo " -c, -opCols, --column"
echo " type: integer, required parameter"
echo " Specify the column (1-based) that should be summarized."
echo ""
echo " -o, -ops, --operation"
echo " type: string"
echo " Specify the operation that should be applied to opCol."
echo " Valid operations:"
echo " sum, count, count_distinct, min, max,"
echo " mean, median, mode, antimode,"
echo " stdev, sstdev (sample standard dev.),"
echo " collapse (i.e., print a comma separated list (duplicates allowed)),"
echo " distinct (i.e., print a comma separated list (NO duplicates"
echo " allowed)),"
echo " distinct_sort_num (as distinct, but sorted numerically, ascending),"
echo " distinct_sort_num_desc (as distinct, but sorted numerically,"
echo " descending),"
echo " concat (i.e., merge values into a single, non-delimited string),"
echo " freqdesc (i.e., print desc. list of values:freq)"
echo " freqasc (i.e., print asc. list of values:freq)"
echo " first (i.e., print first value)"
echo " last (i.e., print last value)"
echo " Default value: sum"
echo " If there is only column, but multiple operations, all operations will be"
echo " applied on that column. Likewise, if there is only one operation, but"
echo " multiple columns, that operation will be applied to all columns."
echo " Otherwise, the number of columns must match the the number of"
echo " operations,"
echo " and will be applied in respective order."
echo " E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
echo " the mean of column 4, and the count of column 6."
echo " The order of output columns will match the ordering given in the"
echo " command."
echo ""
echo " --full"
echo " type: boolean_true"
echo " Print all columns from input file. The first line in the group is used."
echo " Default: print only grouped columns."
echo ""
echo " --inheader"
echo " type: boolean_true"
echo " Input file has a header line - the first line will be ignored."
echo ""
echo " --outheader"
echo " type: boolean_true"
echo " Print header line in the output, detailing the column names."
echo " If the input file has headers (-inheader), the output file"
echo " will use the input's column names."
echo " If the input file has no headers, the output file"
echo " will use \"col_1\", \"col_2\", etc. as the column names."
echo ""
echo " --header"
echo " type: boolean_true"
echo " same as '-inheader -outheader'."
echo ""
echo " --ignorecase"
echo " type: boolean_true"
echo " Group values regardless of upper/lower case."
echo ""
echo " -prec, --precision"
echo " type: integer"
echo " default: 5"
echo " Sets the decimal precision for output."
echo ""
echo " -delim, --delimiter"
echo " type: string"
echo " default: ,"
echo " example: |"
echo " Specify a custom delimiter for the collapse operations."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
View File

@@ -301,6 +301,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -409,16 +412,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_intersect"
executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

386
target/executable/bedtools/bedtools_intersect/bedtools_intersect
View File

@@ -2,7 +2,7 @@
# bedtools_intersect main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,183 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_intersect main"
echo ""
echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
echo "features."
echo "Moreover, it allows one to have fine control as to how the intersections are"
echo "reported."
echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
echo ""
echo "Inputs:"
echo " -a, --input_a"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input file (BED/GFF/VCF/BAM) to be used as the -a file."
echo ""
echo " -b, --input_b"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: input_b.bed"
echo " The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -wa, --write_a"
echo " type: boolean_true"
echo " Write the original A entry for each overlap."
echo ""
echo " -wb, --write_b"
echo " type: boolean_true"
echo " Write the original B entry for each overlap."
echo " Useful for knowing _what_ A overlaps. Restricted by -f and -r."
echo ""
echo " -loj, --left_outer_join"
echo " type: boolean_true"
echo " Perform a \"left outer join\". That is, for each feature in A report each"
echo " overlap with B."
echo " If no overlaps are found, report a NULL feature for B."
echo ""
echo " -wo, --write_overlap"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " Only A features with overlap are reported."
echo ""
echo " -wao, --write_overlap_plus"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " However, A features w/o overlap are also reported with a NULL B"
echo " feature and overlap = 0."
echo ""
echo " -u, --report_A_if_no_overlap"
echo " type: boolean_true"
echo " Write the original A entry _if_ no overlap is found."
echo " - In other words, just report the fact >=1 hit was found."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -c, --number_of_overlaps_A"
echo " type: boolean_true"
echo " For each entry in A, report the number of overlaps with B."
echo " - Reports 0 for A entries that have no overlap with B."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -v, --report_no_overlaps_A"
echo " type: boolean_true"
echo " Only report those entries in A that have _no overlaps_ with B."
echo " - Similar to \"grep -v\" (an homage)."
echo ""
echo " -ubam, --uncompressed_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
echo ""
echo " -s, --same_strand"
echo " type: boolean_true"
echo " Require same strandedness. That is, only report hits in B."
echo " that overlap A on the _same_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -S, --opposite_strand"
echo " type: boolean_true"
echo " Require different strandedness. That is, only report hits in B"
echo " that overlap A on the _opposite_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -f, --min_overlap_A"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of A."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -F, --min_overlap_B"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of B."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -r, --reciprocal_overlap"
echo " type: boolean_true"
echo " Require that the fraction overlap be reciprocal for A AND B."
echo " - In other words, if -f is 0.90 and -r is used, this requires"
echo " that B overlap 90% of A and A _also_ overlaps 90% of B."
echo ""
echo " -e, --either_overlap"
echo " type: boolean_true"
echo " Require that the minimum fraction be satisfied for A OR B."
echo " - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
echo " that either 90% of A is covered OR 10% of B is covered."
echo " Without -e, both fractions would have to be satisfied."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " Provide a genome file to enforce consistent chromosome"
echo " sort order across input files. Only applies when used"
echo " with -sorted option."
echo ""
echo " --nonamecheck"
echo " type: boolean_true"
echo " For sorted data, don't throw an error if the file"
echo " has different naming conventions for the same chromosome"
echo " (e.g., \"chr1\" vs \"chr01\")."
echo ""
echo " --sorted"
echo " type: boolean_true"
echo " Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
echo ""
echo " --names"
echo " type: string"
echo " When using multiple databases, provide an alias"
echo " for each that will appear instead of a fileId when"
echo " also printing the DB record."
echo ""
echo " --filenames"
echo " type: boolean_true"
echo " When using multiple databases, show each complete filename instead of a"
echo " fileId when also printing the DB record."
echo ""
echo " --sortout"
echo " type: boolean_true"
echo " When using multiple databases, sort the output DB hits for each record."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " --nobuf, --no_buffer_output"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
echo ""
echo " --iobuf, --io_buffer_size"
echo " type: integer"
echo " Specify amount of memory to use for input buffer."
echo " Takes an integer argument. Optional suffixes K/M/G supported."
echo " Note: currently has no effect with compressed files."
}
# initialise variables
VIASH_MODE='run'
@@ -633,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -750,6 +573,209 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_intersect main"
echo ""
echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
echo "features."
echo "Moreover, it allows one to have fine control as to how the intersections are"
echo "reported."
echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
echo ""
echo "Inputs:"
echo " -a, --input_a"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input file (BED/GFF/VCF/BAM) to be used as the -a file."
echo ""
echo " -b, --input_b"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: input_b.bed"
echo " The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -wa, --write_a"
echo " type: boolean_true"
echo " Write the original A entry for each overlap."
echo ""
echo " -wb, --write_b"
echo " type: boolean_true"
echo " Write the original B entry for each overlap."
echo " Useful for knowing _what_ A overlaps. Restricted by -f and -r."
echo ""
echo " -loj, --left_outer_join"
echo " type: boolean_true"
echo " Perform a \"left outer join\". That is, for each feature in A report each"
echo " overlap with B."
echo " If no overlaps are found, report a NULL feature for B."
echo ""
echo " -wo, --write_overlap"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " Only A features with overlap are reported."
echo ""
echo " -wao, --write_overlap_plus"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " However, A features w/o overlap are also reported with a NULL B"
echo " feature and overlap = 0."
echo ""
echo " -u, --report_A_if_no_overlap"
echo " type: boolean_true"
echo " Write the original A entry _if_ no overlap is found."
echo " - In other words, just report the fact >=1 hit was found."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -c, --number_of_overlaps_A"
echo " type: boolean_true"
echo " For each entry in A, report the number of overlaps with B."
echo " - Reports 0 for A entries that have no overlap with B."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -v, --report_no_overlaps_A"
echo " type: boolean_true"
echo " Only report those entries in A that have _no overlaps_ with B."
echo " - Similar to \"grep -v\" (an homage)."
echo ""
echo " -ubam, --uncompressed_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
echo ""
echo " -s, --same_strand"
echo " type: boolean_true"
echo " Require same strandedness. That is, only report hits in B."
echo " that overlap A on the _same_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -S, --opposite_strand"
echo " type: boolean_true"
echo " Require different strandedness. That is, only report hits in B"
echo " that overlap A on the _opposite_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -f, --min_overlap_A"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of A."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -F, --min_overlap_B"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of B."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -r, --reciprocal_overlap"
echo " type: boolean_true"
echo " Require that the fraction overlap be reciprocal for A AND B."
echo " - In other words, if -f is 0.90 and -r is used, this requires"
echo " that B overlap 90% of A and A _also_ overlaps 90% of B."
echo ""
echo " -e, --either_overlap"
echo " type: boolean_true"
echo " Require that the minimum fraction be satisfied for A OR B."
echo " - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
echo " that either 90% of A is covered OR 10% of B is covered."
echo " Without -e, both fractions would have to be satisfied."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " Provide a genome file to enforce consistent chromosome"
echo " sort order across input files. Only applies when used"
echo " with -sorted option."
echo ""
echo " --nonamecheck"
echo " type: boolean_true"
echo " For sorted data, don't throw an error if the file"
echo " has different naming conventions for the same chromosome"
echo " (e.g., \"chr1\" vs \"chr01\")."
echo ""
echo " --sorted"
echo " type: boolean_true"
echo " Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
echo ""
echo " --names"
echo " type: string"
echo " When using multiple databases, provide an alias"
echo " for each that will appear instead of a fileId when"
echo " also printing the DB record."
echo ""
echo " --filenames"
echo " type: boolean_true"
echo " When using multiple databases, show each complete filename instead of a"
echo " fileId when also printing the DB record."
echo ""
echo " --sortout"
echo " type: boolean_true"
echo " When using multiple databases, sort the output DB hits for each record."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " --nobuf, --no_buffer_output"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
echo ""
echo " --iobuf, --io_buffer_size"
echo " type: integer"
echo " Specify amount of memory to use for input buffer."
echo " Takes an integer argument. Optional suffixes K/M/G supported."
echo " Note: currently has no effect with compressed files."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_links/.config.vsh.yaml
View File

@@ -100,6 +100,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -209,16 +212,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_links"
executable: "target/executable/bedtools/bedtools_links/bedtools_links"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

120
target/executable/bedtools/bedtools_links/bedtools_links
View File

@@ -2,7 +2,7 @@
# bedtools_links main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,50 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_links main"
echo ""
echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for"
echo "all features / intervals in a file."
echo "This is useful for cases when one wants to manually inspect through a large set"
echo "of annotations or features."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf)."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output HTML file to be written."
echo ""
echo "Options:"
echo " By default, the links created will point to human (hg18) UCSC browser."
echo " If you have a local mirror, you can override this behavior by supplying"
echo " the -base, -org, and -db options."
echo " For example, if the URL of your local mirror for mouse MM9 is called:"
echo " http://mymirror.myuniversity.edu, then you would use the following:"
echo " --base_url http://mymirror.myuniversity.edu"
echo " --organism mouse"
echo " --database mm9"
echo ""
echo " -base, --base_url"
echo " type: string"
echo " default: http://genome.ucsc.edu"
echo " The “basename” for the UCSC browser."
echo ""
echo " -org, --organism"
echo " type: string"
echo " default: human"
echo " The organism (e.g. mouse, human)."
echo ""
echo " -db, --database"
echo " type: string"
echo " default: hg18"
echo " The genome build."
}
# initialise variables
VIASH_MODE='run'
@@ -500,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -617,6 +573,76 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_links main"
echo ""
echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for"
echo "all features / intervals in a file."
echo "This is useful for cases when one wants to manually inspect through a large set"
echo "of annotations or features."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf)."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output HTML file to be written."
echo ""
echo "Options:"
echo " By default, the links created will point to human (hg18) UCSC browser."
echo " If you have a local mirror, you can override this behavior by supplying"
echo " the -base, -org, and -db options."
echo " For example, if the URL of your local mirror for mouse MM9 is called:"
echo " http://mymirror.myuniversity.edu, then you would use the following:"
echo " --base_url http://mymirror.myuniversity.edu"
echo " --organism mouse"
echo " --database mm9"
echo ""
echo " -base, --base_url"
echo " type: string"
echo " default: http://genome.ucsc.edu"
echo " The “basename” for the UCSC browser."
echo ""
echo " -org, --organism"
echo " type: string"
echo " default: human"
echo " The organism (e.g. mouse, human)."
echo ""
echo " -db, --database"
echo " type: string"
echo " default: hg18"
echo " The genome build."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_merge/.config.vsh.yaml
View File

@@ -174,6 +174,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -278,16 +281,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_merge"
executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

236
target/executable/bedtools/bedtools_merge/bedtools_merge
View File

@@ -2,7 +2,7 @@
# bedtools_merge main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,108 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_merge main"
echo ""
echo "Merges overlapping BED/GFF/VCF entries into a single interval."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (BED/GFF/VCF) to be merged."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " Output merged file BED to be written."
echo ""
echo "Options:"
echo " -s, --strand"
echo " type: boolean_true"
echo " Force strandedness. That is, only merge features"
echo " that are on the same strand."
echo " - By default, merging is done without respect to strand."
echo ""
echo " -S, --specific_strand"
echo " type: string"
echo " choices: [ +, - ]"
echo " Force merge for one specific strand only."
echo " Follow with + or - to force merge from only"
echo " the forward or reverse strand, respectively."
echo " - By default, merging is done without respect to strand."
echo ""
echo " -d, --distance"
echo " type: integer"
echo " Maximum distance between features allowed for features"
echo " to be merged."
echo " - Def. 0. That is, overlapping & book-ended features are merged."
echo " - (INTEGER)"
echo " - Note: negative values enforce the number of b.p. required for overlap."
echo ""
echo " -c, --columns"
echo " type: integer"
echo " Specify columns from the B file to map onto intervals in A."
echo " Default: 5."
echo " Multiple columns can be specified in a comma-delimited list."
echo ""
echo " -o, --operation"
echo " type: string"
echo " Specify the operation that should be applied to -c."
echo " Valid operations:"
echo " sum, min, max, absmin, absmax,"
echo " mean, median, mode, antimode"
echo " stdev, sstdev"
echo " collapse (i.e., print a delimited list (duplicates allowed)),"
echo " distinct (i.e., print a delimited list (NO duplicates allowed)),"
echo " distinct_sort_num (as distinct, sorted numerically, ascending),"
echo " distinct_sort_num_desc (as distinct, sorted numerically,"
echo " desscending),"
echo " distinct_only (delimited list of only unique values),"
echo " count"
echo " count_distinct (i.e., a count of the unique values in the column),"
echo " first (i.e., just the first value in the column),"
echo " last (i.e., just the last value in the column),"
echo " Default: sum"
echo " Multiple operations can be specified in a comma-delimited list."
echo " If there is only column, but multiple operations, all operations will be"
echo " applied on that column. Likewise, if there is only one operation, but"
echo " multiple columns, that operation will be applied to all columns."
echo " Otherwise, the number of columns must match the the number of"
echo " operations,"
echo " and will be applied in respective order."
echo " E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
echo " the mean of column 4, and the count of column 6."
echo " The order of output columns will match the ordering given in the"
echo " command."
echo ""
echo " -delim, --delimiter"
echo " type: string"
echo " default: ,"
echo " example: |"
echo " Specify a custom delimiter for the collapse operations."
echo ""
echo " -prec, --precision"
echo " type: integer"
echo " Sets the decimal precision for output (Default: 5)."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " -nobuf, --no_buffer"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
}
# initialise variables
VIASH_MODE='run'
@@ -558,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -675,6 +573,134 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_merge main"
echo ""
echo "Merges overlapping BED/GFF/VCF entries into a single interval."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (BED/GFF/VCF) to be merged."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " Output merged file BED to be written."
echo ""
echo "Options:"
echo " -s, --strand"
echo " type: boolean_true"
echo " Force strandedness. That is, only merge features"
echo " that are on the same strand."
echo " - By default, merging is done without respect to strand."
echo ""
echo " -S, --specific_strand"
echo " type: string"
echo " choices: [ +, - ]"
echo " Force merge for one specific strand only."
echo " Follow with + or - to force merge from only"
echo " the forward or reverse strand, respectively."
echo " - By default, merging is done without respect to strand."
echo ""
echo " -d, --distance"
echo " type: integer"
echo " Maximum distance between features allowed for features"
echo " to be merged."
echo " - Def. 0. That is, overlapping & book-ended features are merged."
echo " - (INTEGER)"
echo " - Note: negative values enforce the number of b.p. required for overlap."
echo ""
echo " -c, --columns"
echo " type: integer"
echo " Specify columns from the B file to map onto intervals in A."
echo " Default: 5."
echo " Multiple columns can be specified in a comma-delimited list."
echo ""
echo " -o, --operation"
echo " type: string"
echo " Specify the operation that should be applied to -c."
echo " Valid operations:"
echo " sum, min, max, absmin, absmax,"
echo " mean, median, mode, antimode"
echo " stdev, sstdev"
echo " collapse (i.e., print a delimited list (duplicates allowed)),"
echo " distinct (i.e., print a delimited list (NO duplicates allowed)),"
echo " distinct_sort_num (as distinct, sorted numerically, ascending),"
echo " distinct_sort_num_desc (as distinct, sorted numerically,"
echo " desscending),"
echo " distinct_only (delimited list of only unique values),"
echo " count"
echo " count_distinct (i.e., a count of the unique values in the column),"
echo " first (i.e., just the first value in the column),"
echo " last (i.e., just the last value in the column),"
echo " Default: sum"
echo " Multiple operations can be specified in a comma-delimited list."
echo " If there is only column, but multiple operations, all operations will be"
echo " applied on that column. Likewise, if there is only one operation, but"
echo " multiple columns, that operation will be applied to all columns."
echo " Otherwise, the number of columns must match the the number of"
echo " operations,"
echo " and will be applied in respective order."
echo " E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
echo " the mean of column 4, and the count of column 6."
echo " The order of output columns will match the ordering given in the"
echo " command."
echo ""
echo " -delim, --delimiter"
echo " type: string"
echo " default: ,"
echo " example: |"
echo " Specify a custom delimiter for the collapse operations."
echo ""
echo " -prec, --precision"
echo " type: integer"
echo " Sets the decimal precision for output (Default: 5)."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " -nobuf, --no_buffer"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''

13
target/executable/bedtools/bedtools_sort/.config.vsh.yaml
View File

@@ -114,6 +114,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -221,16 +224,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_sort"
executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

138
target/executable/bedtools/bedtools_sort/bedtools_sort
View File

@@ -2,7 +2,7 @@
# bedtools_sort main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,59 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_sort main"
echo ""
echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf) to be sorted."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output sorted file (bed/gff/vcf) to be written."
echo ""
echo "Options:"
echo " --sizeA"
echo " type: boolean_true"
echo " Sort by feature size in ascending order."
echo ""
echo " --sizeD"
echo " type: boolean_true"
echo " Sort by feature size in descending order."
echo ""
echo " --chrThenSizeA"
echo " type: boolean_true"
echo " Sort by chrom (asc), then feature size (asc)."
echo ""
echo " --chrThenSizeD"
echo " type: boolean_true"
echo " Sort by chrom (asc), then feature size (desc)."
echo ""
echo " --chrThenScoreA"
echo " type: boolean_true"
echo " Sort by chrom (asc), then score (asc)."
echo ""
echo " --chrThenScoreD"
echo " type: boolean_true"
echo " Sort by chrom (asc), then score (desc)."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " Sort according to the chromosomes declared in \"genome.txt\""
echo ""
echo " --faidx"
echo " type: file, file must exist"
echo " Sort according to the chromosomes declared in \"names.txt\""
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
}
# initialise variables
VIASH_MODE='run'
@@ -509,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -626,6 +573,85 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_sort main"
echo ""
echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input file (bed/gff/vcf) to be sorted."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, output, file must exist"
echo " Output sorted file (bed/gff/vcf) to be written."
echo ""
echo "Options:"
echo " --sizeA"
echo " type: boolean_true"
echo " Sort by feature size in ascending order."
echo ""
echo " --sizeD"
echo " type: boolean_true"
echo " Sort by feature size in descending order."
echo ""
echo " --chrThenSizeA"
echo " type: boolean_true"
echo " Sort by chrom (asc), then feature size (asc)."
echo ""
echo " --chrThenSizeD"
echo " type: boolean_true"
echo " Sort by chrom (asc), then feature size (desc)."
echo ""
echo " --chrThenScoreA"
echo " type: boolean_true"
echo " Sort by chrom (asc), then score (asc)."
echo ""
echo " --chrThenScoreD"
echo " type: boolean_true"
echo " Sort by chrom (asc), then score (desc)."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " Sort according to the chromosomes declared in \"genome.txt\""
echo ""
echo " --faidx"
echo " type: file, file must exist"
echo " Sort according to the chromosomes declared in \"names.txt\""
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''