update config: add requirements, add keyword, update --config & --out…

…put description

src/agat/agat_sp_prokka_infer_name_from_attributes/config.vsh.yaml

@@ -3,7 +3,8 @@ namespace: agat
 description: |
   The script aims to fill a Name attribute based on <gene> attribute in a
   prokka gff annotation file. If no gene attribute is present it take if
-  from the <inference> attribute.keywords: [gene annotations, GFF conversion]
+  from the <inference> attribute.
+keywords: [gene annotations, GFF conversion, prokka]
 links:
   homepage: https://github.com/NBISweden/AGAT
   documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_Prokka_inferNameFromAttributes.html
@@ -12,6 +13,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
@@ -29,7 +32,7 @@ argument_groups:
     arguments:
       - name: --output
         alternatives: [-o, --out, --outfile]
-        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        description: Output GFF file.
         type: file
         direction: output
         required: true
@@ -43,7 +46,7 @@ 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