From 602f8b17888d25007496ff780d64a58cb71733cf Mon Sep 17 00:00:00 2001 From: Leila011 Date: Mon, 19 Aug 2024 16:17:11 +0200 Subject: [PATCH] update config: add requirements, add keyword, update --config & --output description --- .../config.vsh.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/agat/agat_sp_prokka_infer_name_from_attributes/config.vsh.yaml b/src/agat/agat_sp_prokka_infer_name_from_attributes/config.vsh.yaml index 11bef360..2bff1aa0 100644 --- a/src/agat/agat_sp_prokka_infer_name_from_attributes/config.vsh.yaml +++ b/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 attribute in a prokka gff annotation file. If no gene attribute is present it take if - from the attribute.keywords: [gene annotations, GFF conversion] + from the 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