Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg

comparison complete_immunerepertoire.xml @ 7:a9053212a462 draft

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author davidvanzessen
date Mon, 05 Jan 2015 09:30:08 -0500
parents 0dafe2f9ceb8
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6:8b46fca04595 7:a9053212a462
6 ${f.id} 6 ${f.id}
7 #for $j, $g in enumerate($f.samples) 7 #for $j, $g in enumerate($f.samples)
8 ${g.sample} 8 ${g.sample}
9 #end for 9 #end for
10 #end for 10 #end for
11 " $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection 11 " $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <repeat name="patients" title="Patients" min="1" default="1"> 14 <repeat name="patients" title="Patients" min="1" default="1">
15 <repeat name="samples" title="Sample" min="1" default="1"> 15 <repeat name="samples" title="Sample" min="1" default="1">
16 <param name="sample" type="data" label="Sample to Process" /> 16 <param name="sample" type="data" label="Sample to Process" />
17 </repeat> 17 </repeat>
18 <param name="id" type="text" label="ID" /> 18 <param name="id" type="text" label="ID" />
19 </repeat> 19 </repeat>
20 <param name="clonaltype_select" type="select" label="Clonal Type Definition"> 20 <param name="clonaltype" type="select" label="Clonal Type Definition">
21 <option value="none">Don't remove duplicates based on clonaltype</option>
21 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option> 22 <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,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">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.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 <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>
37 <option value="trb">TRB</option> 38 <option value="trb">TRB</option>
38 <option value="tra">TRA</option> 39 <option value="tra">TRA</option>
39 <option value="trg">TRG</option> 40 <option value="trg">TRG</option>
40 <option value="trd">TRD</option> 41 <option value="trd">TRD</option>
41 </param> 42 </param>
42 43
43 <param name="selection" type="select" label="Selection"> 44 <param name="filterproductive" type="select" label="Filter out the unproductive sequences">
44 <option value="unique">Unique (Based on clonaltype)</option> 45 <option value="yes">Yes</option>
45 <option value="all">All</option> 46 <option value="no">No</option>
46 </param> 47 </param>
47 </inputs> 48 </inputs>
48 <outputs> 49 <outputs>
49 <data format="html" name="out_file" /> 50 <data format="html" name="out_file" />
50 </outputs> 51 </outputs>
51 <help> 52 <help>
52 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. 53 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.
53 </help> 54 </help>
54 </tool> 55 </tool>
55