Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 52:d3542f87a304 draft

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author davidvanzessen
date Fri, 29 Jan 2016 08:11:31 -0500
parents 099cc1254f74
children 79696e273853
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51:d4e72eeea640 52:d3542f87a304
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 $naive_output 4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1} $functionality $unique $naive_output $filter_uniques
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>
31 <param name="naive_output" type="select" label="Output a file for naive analysis?"> 31 <param name="naive_output" type="select" label="Output a file for naive analysis?">
32 <option value="yes">Yes</option> 32 <option value="yes">Yes</option>
33 <option value="no" selected="true">No</option> 33 <option value="no" selected="true">No</option>
34 </param> 34 </param>
35 </conditional> 35 </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 </param>
36 </inputs> 40 </inputs>
37 <outputs> 41 <outputs>
38 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 42 <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}" > 43 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
40 <filter>naive_output_cond['naive_output'] == "yes"</filter> 44 <filter>naive_output_cond['naive_output'] == "yes"</filter>