CI
7645430e58
Build pipeline: viash-hub.biobox.v0.1-8mh8l
Source commit: b84b29747d
Source message: Bump version to v0.1.0
208 lines
8.6 KiB
JSON
208 lines
8.6 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "bedtools_getfasta",
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"description": "Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.",
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"type": "object",
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"definitions": {
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"input arguments" : {
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"title": "Input arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"input_fasta": {
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"type":
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"string",
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"description": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file",
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"help_text": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file.\nThe headers in the input FASTA file must exactly match the chromosome column in the BED file.\n"
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}
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,
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"input_bed": {
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"type":
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"string",
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"description": "Type: `file`. BED file containing intervals to extract from the FASTA file",
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"help_text": "Type: `file`. BED file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n"
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}
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,
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"rna": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA",
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"help_text": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n"
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,
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"default": "False"
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}
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}
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},
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"run arguments" : {
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"title": "Run arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"strandedness": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Force strandedness",
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"help_text": "Type: `boolean_true`, default: `false`. Force strandedness. If the feature occupies the antisense strand, the output sequence will\nbe reverse complemented. By default strandedness is not taken into account.\n"
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,
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"default": "False"
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}
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}
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},
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"output arguments" : {
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"title": "Output arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type":
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"string",
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"description": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to",
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"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n"
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,
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"default": "$id.$key.output.output"
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}
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,
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"tab": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format",
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"help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format.\n"
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,
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"default": "False"
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}
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,
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"bed_out": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format",
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"help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format.\n"
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,
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"default": "False"
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}
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,
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"name": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature",
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"help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature.\n"
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,
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"default": "False"
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}
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,
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"name_only": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature",
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"help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature.\n"
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,
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"default": "False"
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}
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,
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"split": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED",
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"help_text": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED.\n"
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,
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"default": "False"
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}
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,
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"full_header": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Use full fasta header",
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"help_text": "Type: `boolean_true`, default: `false`. Use full fasta header. By default, only the word before the first space or tab is used.\n"
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,
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"default": "False"
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}
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}
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},
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"nextflow input-output arguments" : {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
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"properties": {
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"publish_dir": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/input arguments"
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},
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{
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"$ref": "#/definitions/run arguments"
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},
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{
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"$ref": "#/definitions/output arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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