Mercurial > repos > dereeper > pgap
view PGAP.xml @ 11:e0c913351502 draft default tip
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author | dereeper |
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date | Thu, 01 Jul 2021 12:22:53 +0000 (2021-07-01) |
parents | f33df1459a4b |
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<tool id="PGAP" name="PGAP" version="1.0"> <description>Pan-Genome Analysis Pipeline </description> <requirements> <requirement type="package" version="2.2.26">blast-legacy</requirement> <requirement type="package" version="7.480">mafft</requirement> <requirement type="package" version="14.137">mcl</requirement> <requirement type="package" version="3.697">phylip</requirement> <requirement type="package" version="1.7.2">perl-bioperl</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__}/PGAP_wrapper2.pl -g $input_files -p $proteins -l $named_input_files -o $output >>$logfile 2>&1 ]]></command> <inputs> <param format="fasta" name="input_files" type="data" multiple="true" label="Coding genes FASTA files"/> <param format="fasta" name="proteins" type="data" multiple="true" label="Protein FASTA files"/> </inputs> <outputs> <data format="txt" name="output" label="Pangenome presence absence matrix"/> <data format="txt" name="logfile" label="Logfile"/> </outputs> </tool>