CI
833a44f68a
Build pipeline: viash-hub.biobox.main-rgg5q
Source commit: 4aa0a893d2
Source message: Add agat convert bed2gff (#97)
* add config
* add help
* add script
* add test data and expected output file
* add script to get test data
* add tests
* update changelog
* fix path to test data
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
172 lines
7.4 KiB
JSON
172 lines
7.4 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "agat_convert_bed2gff",
|
|
"description": "The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"inputs" : {
|
|
"title": "Inputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"bed": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted",
|
|
"help_text": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted."
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"outputs" : {
|
|
"title": "Outputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file",
|
|
"help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT."
|
|
,
|
|
"default": "$id.$key.output.gff"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"arguments" : {
|
|
"title": "Arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"source": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file",
|
|
"help_text": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"primary_tag": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file",
|
|
"help_text": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"inflate_off": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_false`, default: `true`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag)",
|
|
"help_text": "Type: `boolean_false`, default: `true`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.\n"
|
|
,
|
|
"default": "True"
|
|
}
|
|
|
|
|
|
,
|
|
"inflate_type": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon]",
|
|
"help_text": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"verbose": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_true`, default: `false`. add verbosity",
|
|
"help_text": "Type: `boolean_true`, default: `false`. add verbosity"
|
|
,
|
|
"default": "False"
|
|
}
|
|
|
|
|
|
,
|
|
"config": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file",
|
|
"help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n"
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"nextflow input-output arguments" : {
|
|
"title": "Nextflow input-output arguments",
|
|
"type": "object",
|
|
"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.",
|
|
"properties": {
|
|
|
|
|
|
"publish_dir": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
|
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"param_list": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
|
"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.",
|
|
"hidden": true
|
|
|
|
}
|
|
|
|
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
|
|
{
|
|
"$ref": "#/definitions/inputs"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/outputs"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|