update config: format description, add requirements, add keywords, up…

…date --config description

src/agat/agat_convert_sp_gff2bed/config.vsh.yaml

@@ -8,22 +8,25 @@ description: |
   in column 7 and 8 accordingly.
 
   ### Definition of the bed format: 
+
   #### Definition of the BED format:
-  1. **chrom** - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
-  2. **chromStart** - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
-  3. **chromEnd** - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
+
+    1. **chrom** - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
+    2. **chromStart** - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
+    3. **chromEnd** - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
 
   #### OPTIONAL fields:
-  4. **name** - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
-  5. **score** - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
-  6. **strand** - Defines the strand - either '+' or '-'.
-  7. **thickStart** - The starting position at which the feature is drawn thickly.
-  8. **thickEnd** - The ending position at which the feature is drawn thickly.
-  9. **itemRgb** - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RGB value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
-  10. **blockCount** - The number of blocks (exons) in the BED line.
-  11. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
-  12. **blockStarts** - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
-keywords: [gene annotations, GTF conversion]
+
+    4. **name** - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
+    5. **score** - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray).
+    6. **strand** - Defines the strand - either '+' or '-'.
+    7. **thickStart** - The starting position at which the feature is drawn thickly.
+    8. **thickEnd** - The ending position at which the feature is drawn thickly.
+    9. **itemRgb** - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RGB value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
+    10. **blockCount** - The number of blocks (exons) in the BED line.
+    11. **blockSizes** - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
+    12. **blockStarts** - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
+keywords: [gene annotations, GTF conversion, BED]
 links:
   homepage: https://github.com/NBISweden/AGAT
   documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2bed.html
@@ -32,6 +35,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
@@ -50,7 +55,7 @@ argument_groups:
       - name: --output
         alternatives: [--outfile, --out, -o]
         description: |
-          File where the result will be written. If no output file is specified, the output will be written to STDOUT.
+          File where the result will be written.
         type: file
         direction: output
         required: true
@@ -76,7 +81,7 @@ argument_groups:
       - name: --config
         alternatives: [-c]
         description: |
-          Input AGAT config file. By default, AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original 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).
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
         type: file
         required: false
         example: custom_agat_config.yaml