Mercurial > repos > iuc > mlst
diff mlst_list.xml @ 0:735872ff8222 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
author | iuc |
---|---|
date | Mon, 12 Dec 2016 15:07:38 -0500 |
parents | |
children | 8e8dc9a1e3e5 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mlst_list.xml Mon Dec 12 15:07:38 2016 -0500 @@ -0,0 +1,51 @@ +<tool id="mlst_list" name="MLST List" version="0.1.0"> + <requirements> + <requirement type="package" version="2.6">mlst</requirement> + </requirements> + + <version_command>mlst --version</version_command> + + <command detect_errors="exit_code"><![CDATA[ + mlst $list_type > "$report" + ]]></command> + + <inputs> + <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list" + help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" /> + </inputs> + + <outputs> + <data format="txt" name="report" label="${tool.name} - list of schemes"/> + </outputs> + + <tests> + <!-- Test the longlist option --> + <test> + <param name="list_type" value="true" /> + <output name="report" ftype="txt" file="output_longlist.txt" /> + </test> + + <!-- Test the list option --> + <test> + <param name="list_type" value="false" /> + <output name="report" ftype="txt" file="output_list.txt" /> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes. + + ]]></help> + + <citations> + <citation type="bibtex"> + @UNPUBLISHED{Seemann2016, + author = "Seemann T", + title = "ABRicate: mass screening of contigs for antiobiotic resistance genes", + year = "2016", + note = "https://github.com/tseemann/abricate"} + </citation> + </citations> +</tool>