Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 69:7acdcd5c52ef draft

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Uploaded
author davidvanzessen
date Fri, 22 Apr 2016 05:07:10 -0400
parents 88e0e7665086
children 0513b46178c4
comparison
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68:3636d5aaa127 69:7acdcd5c52ef
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 $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="Identification method" help="" >
9 <option value="custom" selected="true">custom</option> 9 <option value="custom" selected="true">custom</option>
45 </param> 45 </param>
46 </conditional> 46 </conditional>
47 </inputs> 47 </inputs>
48 <outputs> 48 <outputs>
49 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 49 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
50 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" > 50 <data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
51 <filter>naive_output_cond['naive_output'] == "yes"</filter>
52 </data>
53 <data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
54 <filter>naive_output_cond['naive_output'] == "yes"</filter>
55 </data>
56 <data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
51 <filter>naive_output_cond['naive_output'] == "yes"</filter> 57 <filter>naive_output_cond['naive_output'] == "yes"</filter>
52 </data> 58 </data>
53 </outputs> 59 </outputs>
54 <help> 60 <help>
55 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. 61 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.