Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline
view combined.xml @ 3:2b1d3d6843e8 draft
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author | davidvanzessen |
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date | Fri, 22 Nov 2013 08:12:46 -0500 |
parents | 4e3df2384422 |
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<tool id="immunerepertoirecombined" name="Immunerepertoire combined" version="1.0"> <description>pipeline</description> <command interpreter="bash"> combined.sh #for $i, $f in enumerate($files) ${f.file} ${f.id} #end for "$clonaltype_select" $out_file $out_file.files_path </command> <inputs> <repeat name="files" title="File" min="1" default="1"> <param name="file" format="fasta" type="data" label="Data to Process" /> <param name="id" type="text" label="ID" /> </repeat> <param name="clonaltype_select" type="select" label="Clonal Type Definition"> <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option> </param> </inputs> <outputs> <data format="html" name="out_file" /> </outputs> <help> The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them. </help> <requirements> <requirement type="package" version="1.0.0">igBlastn</requirement> </requirements> </tool>