Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.xml @ 66:88e0e7665086 draft

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author davidvanzessen
date Wed, 06 Apr 2016 05:54:13 -0400
parents a7381fd96dad
children 7acdcd5c52ef
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65:ae8b721a2964 66:88e0e7665086
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 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
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>
17 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option> 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> 18 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option> 19 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
20 <option value="dont_filter">Don't filter</option> 20 <option value="dont_filter">Don't filter</option>
21 </param> 21 </param>
22 <param name="filter_uniques" type="select" label="Filter unique sequences"> 22 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
23 <option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option> 23 <option value="yes">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option>
24 <option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option> 24 <option value="yes_c">Remove uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3 + C)</option>
25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</option> 25 <option value="keep">Keep uniques (CDR1 + FR2 + CDR2 + FR3 + CDR3)</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>
30 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option> 30 <option value="AA.JUNCTION_V_subclass" selected="true">AA.JUNCTION + V + subclass</option>
31 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option> 31 <option value="AA.JUNCTION_subclass">AA.JUNCTION + subclass</option>
32 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option> 32 <option value="AA.JUNCTION_V">AA.JUNCTION + V</option>
33 <option value="AA.JUNCTION">AA.JUNCTION</option> 33 <option value="AA.JUNCTION">AA.JUNCTION</option>
34 <option value="none">Don't remove duplicates</option> 34 <option value="none">Don't remove duplicates</option>
35 </param>
36 <param name="class_filter" type="select" label="Class/Sublass filter" help="" >
37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
38 <option value="70_0">>70% class</option>
39 <option value="60_0">>60% class</option>
35 </param> 40 </param>
36 <conditional name="naive_output_cond"> 41 <conditional name="naive_output_cond">
37 <param name="naive_output" type="select" label="Output a file for naive analysis?"> 42 <param name="naive_output" type="select" label="Output a file for naive analysis?">
38 <option value="yes">Yes</option> 43 <option value="yes">Yes</option>
39 <option value="no" selected="true">No</option> 44 <option value="no" selected="true">No</option>
45 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" > 50 <data format="tabular" name="naive_output" label = "Naive input data from ${in_file.name}" >
46 <filter>naive_output_cond['naive_output'] == "yes"</filter> 51 <filter>naive_output_cond['naive_output'] == "yes"</filter>
47 </data> 52 </data>
48 </outputs> 53 </outputs>
49 <help> 54 <help>
50 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis. 55 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
56
57 +--------------------------+
58 | unique filter |
59 +--------+--------+--------+
60 | values | remove | keep |
61 +--------+--------+--------+
62 | A | A | A |
63 +--------+--------+--------+
64 | A | B | B |
65 +--------+--------+--------+
66 | B | D | C |
67 +--------+--------+--------+
68 | B | | D |
69 +--------+--------+--------+
70 | C | | |
71 +--------+--------+--------+
72 | D | | |
73 +--------+--------+--------+
74 | D | | |
75 +--------+--------+--------+
76
51 </help> 77 </help>
52 <requirements> 78 <requirements>
53 <requirement type="package" version="1.0">blastn</requirement> 79 <requirement type="package" version="1.0">blastn</requirement>
54 </requirements> 80 </requirements>
55 </tool> 81 </tool>