Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 110:ade5cf6fd2dc draft

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Uploaded
author davidvanzessen
date Tue, 02 Aug 2016 08:30:23 -0400
parents e39176ccddc8
children e7b550d52eb7
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109:0096cd454380 110:ade5cf6fd2dc
3 <command interpreter="bash"> 3 <command interpreter="bash">
4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter 4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" /> 7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
8 <param name="method" type="select" label="Identification method" help="" > 8 <param name="method" type="select" label="Method of identification of C region" help="" >
9 <option value="custom" selected="true">custom</option> 9 <option value="custom" selected="true">custom</option>
10 <option value="blastn">blastn</option> 10 <option value="blastn">blastn</option>
11 </param> 11 </param>
12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" > 12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
13 <option value="yes">yes</option> 13 <option value="yes">yes</option>
25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</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> 26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
27 <option value="no" selected="true">No</option> 27 <option value="no" selected="true">No</option>
28 </param> 28 </param>
29 <param name="unique" type="select" label="Remove duplicates based on" help="" > 29 <param name="unique" type="select" label="Remove duplicates based on" help="" >
30 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option> 30 <option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option>
31 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option> 31 <option value="AA.JUNCTION_subclass">CDR3.Seq + C region</option>
32 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option> 32 <option value="AA.JUNCTION_V">CDR3.seq + Top.V.Gene</option>
33 <option value="AA.JUNCTION">AA.JUNCTION</option> 33 <option value="AA.JUNCTION">CDR3.seq</option>
34 <option value="none">Don't remove duplicates</option> 34 <option value="none">Don't remove duplicates</option>
35 </param> 35 </param>
36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" > 36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" >
37 <option value="70_70" selected="true">>70% class and >70% subclass</option> 37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
38 <option value="60_55" selected="true">>60% class and >55% subclass</option> 38 <option value="60_55" selected="true">>60% class and >55% subclass</option>