Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
comparison complete_immunerepertoire.xml @ 0:7d97fa9a0423 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 09 May 2014 09:35:32 -0400 |
| parents | |
| children | 778a9d130904 |
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| -1:000000000000 | 0:7d97fa9a0423 |
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| 1 <tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0"> | |
| 2 <description> </description> | |
| 3 <command interpreter="bash"> | |
| 4 complete.sh | |
| 5 #for $i, $f in enumerate($patients) | |
| 6 ${f.id} | |
| 7 #for $j, $g in enumerate($f.samples) | |
| 8 ${g.sample} | |
| 9 #end for | |
| 10 #end for | |
| 11 "$clonaltype_select" $out_file $out_file.files_path $species $locus $selection | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <repeat name="patients" title="Patients" min="1" default="1"> | |
| 15 <repeat name="samples" title="Sample" min="1" default="1"> | |
| 16 <param name="sample" type="data" label="Sample to Process" /> | |
| 17 </repeat> | |
| 18 <param name="id" type="text" label="ID" /> | |
| 19 </repeat> | |
| 20 <param name="clonaltype_select" type="select" label="Clonal Type Definition"> | |
| 21 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> | |
| 22 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option> | |
| 23 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option> | |
| 24 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option> | |
| 25 <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> | |
| 26 </param> | |
| 27 | |
| 28 <param name="species" type="select" label="Species"> | |
| 29 <option value="human">Human</option> | |
| 30 <option value="mouse">Mouse</option> | |
| 31 </param> | |
| 32 | |
| 33 <param name="locus" type="select" label="Locus"> | |
| 34 <option value="igh">IGH</option> | |
| 35 <option value="igk">IGK</option> | |
| 36 <option value="igl">IGL</option> | |
| 37 </param> | |
| 38 | |
| 39 <param name="selection" type="select" label="Selection"> | |
| 40 <option value="unique">Unique (Based on clonaltype)</option> | |
| 41 <option value="all">All</option> | |
| 42 </param> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="html" name="out_file" /> | |
| 46 </outputs> | |
| 47 <help> | |
| 48 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. | |
| 49 </help> | |
| 50 <requirements> | |
| 51 <requirement type="package" version="1.0.0">igBlastn</requirement> | |
| 52 </requirements> | |
| 53 </tool> | |
| 54 |