From 21e23b49385018bbab2811f897a77206247f001f Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 14:13:28 +0200
Subject: [PATCH] improve config: add requirements, add keywords, format
 description,..

---
 src/agat/agat_sp_statistics/config.vsh.yaml | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/agat/agat_sp_statistics/config.vsh.yaml b/src/agat/agat_sp_statistics/config.vsh.yaml
index 09b68779..ec6cdf90 100644
--- a/src/agat/agat_sp_statistics/config.vsh.yaml
+++ b/src/agat/agat_sp_statistics/config.vsh.yaml
@@ -1,14 +1,15 @@
 name: agat_sp_statistics
 namespace: agat
 description: |
-  The script provides exhaustive statistics of a gft/gff file. /!\ If you
-  have isoforms in your file, even if correct, some values calculated
+  The script provides exhaustive statistics of a gft/gff file. 
+  
+  If you have isoforms in your file, even if correct, some values calculated
   might sounds incoherent: e.g. total length mRNA can be superior than the
   genome size. Because all isoforms length is added... It is why by
   default we always compute the statistics twice when there are isoforms,
   once with the isoforms, once without (In that case we keep the longest
   isoform per locus).
-keywords: [gene annotations]
+keywords: [gene annotations, statistics, gff]
 links:
   homepage: https://github.com/NBISweden/AGAT
   documentation: https://agat.readthedocs.io/en/latest/tools/agat_sp_statistics.html
@@ -17,6 +18,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+ - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
@@ -36,7 +39,7 @@ argument_groups:
       - name: --output
         alternatives: [-o]
         description: |
-          File where will be written the result. If no output file is specified, the output will be written to STDOUT.
+          File where will be written the result.
         type: file
         direction: output
         required: true
@@ -65,7 +68,7 @@ argument_groups:
       - name: --config
         alternatives: [-c]
         description: |
-          String - 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).
+          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