Mercurial > repos > davidvanzessen > report_clonality_igg

annotate plotting_merged.xml @ 15:c6d0ee9b3d91 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 04 Dec 2014 10:53:23 -0500
parents 866d22e60e60
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
1 <tool id="report_clonality_igg" name="Report Clonality" version="1.0">
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
2 <description> </description>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
3 <command interpreter="bash">
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
4 r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
0
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
5 </command>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
6 <inputs>
10
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
7 <param name="in_file" format="tabular" type="data" label="Data to Process" />
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
8 <param name="clonaltype" type="select" label="Clonal Type Definition">
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
9 <option value="none">Dont remove duplicates based on clonaltype</option>
10
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
10 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
11 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
12 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
13 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
14 <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>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
15 </param>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
16
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
17 <param name="species" type="select" label="Species">
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
18 <option value="human">Human</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
19 <option value="mouse">Mouse</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
20 </param>
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
21
10
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
22 <param name="locus" type="select" label="Locus">
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
23 <option value="igh">IGH</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
24 <option value="igk">IGK</option>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
25 <option value="igl">IGL</option>
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
26 <option value="trb">TRB</option>
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
27 <option value="tra">TRA</option>
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
28 <option value="trg">TRG</option>
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
29 <option value="trd">TRD</option>
10
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
30 </param>
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
31
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
32 <param name="filterproductive" type="select" label="Filter out the unproductive sequences">
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
33 <option value="yes">Yes</option>
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
34 <option value="no">No</option>
10
06777331fbd8 Uploaded
davidvanzessen
parents: 0
diff changeset
35 </param>
0
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
36
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
37 </inputs>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
38 <outputs>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
39 <data format="html" name="out_file" />
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
40 </outputs>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
41 <help>
11
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
42 **INPUT**
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
43
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
44 One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
45
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
46 **OUTPUT**
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
47
866d22e60e60 Uploaded
davidvanzessen
parents: 10
diff changeset
48 It generates the following result:
0
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
49 </help>
08aa67564858 Uploaded
davidvanzessen
parents:
diff changeset
50 </tool>