Mercurial > repos > mgarnier > catchsequence
diff catchsequence/catchsequence.xml @ 0:c30eb2050ef5 draft default tip
Uploaded
author | mgarnier |
---|---|
date | Thu, 26 Aug 2021 13:41:33 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/catchsequence/catchsequence.xml Thu Aug 26 13:41:33 2021 +0000 @@ -0,0 +1,46 @@ +<tool id="catchsequence" name="Catch Sequence" version="0.1.0"> + <description>Catch sequence for BioloMICS import</description> +<requirements> + <requirement type="package" version="1.0.1">abricate</requirement> + <requirement type="package" version="2.19.0">mlst</requirement> + <!--<requirement type="package" version="6.6.0">emboss</requirement> + <requirement type="package" version="1.3.2">pandas</requirement>--> +</requirements> + + +<command detect_errors="aggressive"><![CDATA[ + +#import re + ## Creates symlinks for each input file based on the Galaxy 'element_identifier' + ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat') + #set $named_input_files = '' + #for $input_file in $input_files + ## Add single quotes around each input file identifier + #set $_input_file = "'{}'".format($input_file.element_identifier) + ln -s '${input_file}' ${_input_file} && + #set $named_input_files = $named_input_files + ' ' + $_input_file + #end for + + + perl '$__tool_directory__/catchsequence.pl' $named_input_files > "$output" + + + +]]></command> + <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output" --> + <!-- ./nuclescore.sh ${named_input_files} > "$output" --> + +<inputs> + <param type="data" name="input_files" format="fasta" multiple="true" label="Genome fasta files"/> + <!-- <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> --> +</inputs> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + +<help> +No documentation + </help> + +</tool>