Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 114:e7b550d52eb7 draft

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Uploaded
author davidvanzessen
date Tue, 09 Aug 2016 07:20:41 -0400
parents ade5cf6fd2dc
children 626a956f3811
comparison
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113:b84477f57318 114:e7b550d52eb7
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_ca $naive_output_cg $naive_output_cm $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 $empty_region_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="Method of identification of C region" help="" > 8 <param name="method" type="select" label="Method of identification of C region" help="" >
9 <option value="custom" selected="true">custom</option> 9 <option value="custom" selected="true">custom</option>
26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option> 26 <option value="keep_c">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
27 <option value="no" selected="true">No</option> 27 <option value="no" selected="true">No</option>
28 </param> 28 </param>
29 <param name="unique" type="select" label="Remove duplicates based on" help="" > 29 <param name="unique" type="select" label="Remove duplicates based on" help="" >
30 <option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option> 30 <option value="AA.JUNCTION_V_subclass" selected="true">Top.V.Gene, CDR3.Seq, C region</option>
31 <option value="AA.JUNCTION_subclass">CDR3.Seq + C region</option> 31 <option value="AA.JUNCTION_subclass">CDR3.Seq, C region</option>
32 <option value="AA.JUNCTION_V">CDR3.seq + Top.V.Gene</option> 32 <option value="AA.JUNCTION_V">CDR3.seq, Top.V.Gene</option>
33 <option value="AA.JUNCTION">CDR3.seq</option> 33 <option value="AA.JUNCTION">CDR3.seq</option>
34 <option value="none">Don't remove duplicates</option> 34 <option value="none">Don't remove duplicates</option>
35 </param> 35 </param>
36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" > 36 <param name="class_filter" type="select" label="Class/Subclass filter" help="" >
37 <option value="70_70" selected="true">>70% class and >70% subclass</option> 37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
38 <option value="60_55" selected="true">>60% class and >55% subclass</option> 38 <option value="60_55">>60% class and >55% subclass</option>
39 <option value="70_0">>70% class</option> 39 <option value="70_0">>70% class</option>
40 <option value="60_0">>60% class</option> 40 <option value="60_0">>60% class</option>
41 </param> 41 </param>
42 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
43 <option value="FR1" selected="true">FR1 : exclude empty CDR1,FR2,CDR2,FR3</option>
44 <option value="CDR1">CDR1: exclude empty FR2,CDR2,FR3</option>
45 <option value="FR2">FR2: exclude empty,CDR2,FR3</option>
46 </param>
42 <conditional name="naive_output_cond"> 47 <conditional name="naive_output_cond">
43 <param name="naive_output" type="select" label="Output a file for naive analysis?"> 48 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
44 <option value="yes">Yes</option> 49 <option value="yes">Yes</option>
45 <option value="no" selected="true">No</option> 50 <option value="no" selected="true">No</option>
46 </param> 51 </param>
47 </conditional> 52 </conditional>
48 </inputs> 53 </inputs>
49 <outputs> 54 <outputs>
50 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/> 55 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
51 <data format="tabular" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" > 56 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
52 <filter>naive_output_cond['naive_output'] == "yes"</filter> 57 <filter>naive_output_cond['naive_output'] == "yes"</filter>
53 </data> 58 </data>
54 <data format="tabular" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" > 59 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
55 <filter>naive_output_cond['naive_output'] == "yes"</filter> 60 <filter>naive_output_cond['naive_output'] == "yes"</filter>
56 </data> 61 </data>
57 <data format="tabular" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" > 62 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
58 <filter>naive_output_cond['naive_output'] == "yes"</filter> 63 <filter>naive_output_cond['naive_output'] == "yes"</filter>
59 </data> 64 </data>
60 </outputs> 65 </outputs>
61 <help> 66 <help>
62 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. 67 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.