Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
view complete_immunerepertoire.xml @ 0:7d97fa9a0423 draft
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author | davidvanzessen |
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date | Fri, 09 May 2014 09:35:32 -0400 |
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children | 778a9d130904 |
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<tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0"> <description> </description> <command interpreter="bash"> complete.sh #for $i, $f in enumerate($patients) ${f.id} #for $j, $g in enumerate($f.samples) ${g.sample} #end for #end for "$clonaltype_select" $out_file $out_file.files_path $species $locus $selection </command> <inputs> <repeat name="patients" title="Patients" min="1" default="1"> <repeat name="samples" title="Sample" min="1" default="1"> <param name="sample" type="data" label="Sample to Process" /> </repeat> <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> <param name="species" type="select" label="Species"> <option value="human">Human</option> <option value="mouse">Mouse</option> </param> <param name="locus" type="select" label="Locus"> <option value="igh">IGH</option> <option value="igk">IGK</option> <option value="igl">IGL</option> </param> <param name="selection" type="select" label="Selection"> <option value="unique">Unique (Based on clonaltype)</option> <option value="all">All</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>