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comparison mutation_analysis.xml @ 34:d436daae9d68 draft

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author davidvanzessen
date Thu, 18 Jun 2015 03:10:11 -0400
parents d84c9791d8c4
children 4b997f68d769
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33:ac9a4307861a 34:d436daae9d68
1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0"> 1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
2 <description></description> 2 <description></description>
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} 4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique
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="Identification method" help="" >
9 <option value="custom" selected="true">custom</option> 9 <option value="custom" selected="true">custom</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>
14 <option value="no" selected="true">no</option> 14 <option value="no" selected="true">no</option>
15 </param> 15 </param>
16 <param name="functionality" type="select" label="Functionality filter" help="" >
17 <option value="no_results" selected="true">Remove "No results"</option>
18 <option value="no_result_unproductive">Remove "No results" and "unproductive"</option>
19 <option value="dont_remove">Don't filter</option>
20 </param>
21
22 <param name="unique" type="select" label="Remove duplicates based on" help="" >
23 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
24 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
25 <option value="V_subclass">V + subclass</option>
26 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
27 <option value="AA.JUNCTION">AA.JUNCTION</option>
28 <option value="none">Don't remove duplicates</option>
29 </param>
30
16 </inputs> 31 </inputs>
17 <outputs> 32 <outputs>
18 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 33 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
19 </outputs> 34 </outputs>
20 <help> 35 <help>