Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 63:a7381fd96dad draft

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Uploaded
author davidvanzessen
date Fri, 25 Mar 2016 07:50:12 -0400
parents 79696e273853
children 88e0e7665086
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62:4262e880472d 63:a7381fd96dad
17 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option> 17 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option> 18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option> 19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
20 <option value="dont_filter">Don't filter</option> 20 <option value="dont_filter">Don't filter</option>
21 </param> 21 </param>
22 22 <param name="filter_uniques" type="select" label="Filter unique sequences">
23 <option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
24 <option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
27 <option value="no" selected="true">No</option>
28 </param>
23 <param name="unique" type="select" label="Remove duplicates based on" help="" > 29 <param name="unique" type="select" label="Remove duplicates based on" help="" >
24 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option> 30 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
25 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option> 31 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
26 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option> 32 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
27 <option value="AA.JUNCTION">AA.JUNCTION</option> 33 <option value="AA.JUNCTION">AA.JUNCTION</option>
31 <param name="naive_output" type="select" label="Output a file for naive analysis?"> 37 <param name="naive_output" type="select" label="Output a file for naive analysis?">
32 <option value="yes">Yes</option> 38 <option value="yes">Yes</option>
33 <option value="no" selected="true">No</option> 39 <option value="no" selected="true">No</option>
34 </param> 40 </param>
35 </conditional> 41 </conditional>
36 <param name="filter_uniques" type="select" label="Filter unique sequences" help="Filter out the sequences (based on CDR1, FR2, CDR2, FR3 and CDR3) that only occur once.">
37 <option value="yes">Yes</option>
38 <option value="no" selected="true">No</option>
39 <option value="keep">Keep uniques and filter out the duplicates</option>
40 </param>
41 </inputs> 42 </inputs>
42 <outputs> 43 <outputs>
43 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 44 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
44 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" > 45 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
45 <filter>naive_output_cond['naive_output'] == "yes"</filter> 46 <filter>naive_output_cond['naive_output'] == "yes"</filter>