Mercurial > repos > mgarnier > pangenome_cog_analysis
view pangenomeCogAnalysis.xml @ 2:0428ce25da81 draft
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author | mgarnier |
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date | Fri, 02 Jul 2021 14:53:33 +0000 |
parents | 731fb6cb324b |
children | 27c5a6f2301c |
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<tool id="pangenome_cog_analysis" name="Pangenome COG Analysis" version="1.0"> <description>Provide statistics from pangenome matrix and COG annotations </description> <!-- <requirements> <requirement type="package" version=""></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__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4 $output5 ]]></command> <inputs> <param format="tabular" name="input" type="data" label="Pangenome Matrix" help="Headers must be: Cluster,genes_strain1,genes_strain2..."/> <param format="tabular" name="input2" type="data" label="Strains group file (example species information)" help="Headers must be: strain1,groupinfo"/> <param type="data" name="input_files" format="txt" multiple="true" label="Collection of COG files" help="Each files must be named with the same strain name as defined in Strain group file. Headers must be Gene,COG,COGcategory"/> <param type="data" name="gff_files" format="gff3" multiple="true" label="Collection of GFF files for preparing Circos track" help="Not necessarily annotations from all strains, only those that you want to be represented as Circos tracks"/> <!--<param format="tabular" name="input_files" type="data" multiple="true" label="Annotation files"/>--> </inputs> <outputs> <data format="txt" name="output" label="List of group-specific clusters"/> <data format="tabular" name="output2" label="COG category count average per group"/> <data format="tabular" name="output3" label="Detailed COG category count values per group"/> <data format="tabular" name="output4" label="COG category count average"/> <data format="tabular" name="output5" label="Core-genes coordinates"/> </outputs> </tool>