|
0
|
1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
|
|
|
2 <description></description>
|
|
|
3 <command interpreter="bash">
|
|
34
|
4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique
|
|
0
|
5 </command>
|
|
|
6 <inputs>
|
|
|
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
|
|
19
|
8 <param name="method" type="select" label="Identification method" help="" >
|
|
|
9 <option value="custom" selected="true">custom</option>
|
|
|
10 <option value="blastn">blastn</option>
|
|
|
11 </param>
|
|
22
|
12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
|
|
|
13 <option value="yes">yes</option>
|
|
|
14 <option value="no" selected="true">no</option>
|
|
|
15 </param>
|
|
34
|
16 <param name="functionality" type="select" label="Functionality filter" help="" >
|
|
37
|
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>
|
|
38
|
19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
|
|
37
|
20 <option value="dont_filter">Don't filter</option>
|
|
34
|
21 </param>
|
|
|
22
|
|
|
23 <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>
|
|
|
25 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
|
|
|
26 <option value="V_subclass">V + subclass</option>
|
|
|
27 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
|
|
|
28 <option value="AA.JUNCTION">AA.JUNCTION</option>
|
|
|
29 <option value="none">Don't remove duplicates</option>
|
|
|
30 </param>
|
|
|
31
|
|
0
|
32 </inputs>
|
|
|
33 <outputs>
|
|
|
34 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
|
|
|
35 </outputs>
|
|
|
36 <help>
|
|
12
|
37 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
|
|
0
|
38 </help>
|
|
45
|
39 <!--<requirements>
|
|
14
|
40 <requirement type="package" version="1.0">blastn</requirement>
|
|
45
|
41 </requirements>-->
|
|
0
|
42 </tool>
|
