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comparison mutation_analysis.xml @ 47:099cc1254f74 draft

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author davidvanzessen
date Mon, 09 Nov 2015 07:21:09 -0500
parents 42e39033514b
children d3542f87a304
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46:42e39033514b 47:099cc1254f74
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} $functionality $unique 4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output
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>
25 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option> 25 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
26 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option> 26 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
27 <option value="AA.JUNCTION">AA.JUNCTION</option> 27 <option value="AA.JUNCTION">AA.JUNCTION</option>
28 <option value="none">Don't remove duplicates</option> 28 <option value="none">Don't remove duplicates</option>
29 </param> 29 </param>
30 30 <conditional name="naive_output_cond">
31 <param name="naive_output" type="select" label="Output a file for naive analysis?">
32 <option value="yes">Yes</option>
33 <option value="no" selected="true">No</option>
34 </param>
35 </conditional>
31 </inputs> 36 </inputs>
32 <outputs> 37 <outputs>
33 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 38 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
39 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
40 <filter>naive_output_cond['naive_output'] == "yes"</filter>
41 </data>
34 </outputs> 42 </outputs>
35 <help> 43 <help>
36 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. 44 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
37 </help> 45 </help>
38 <requirements> 46 <requirements>