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comparison shm_csr.xml @ 0:c33d93683a09 draft

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author davidvanzessen
date Thu, 13 Oct 2016 10:52:24 -0400
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1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
2 <description></description>
3 <command interpreter="bash">
4 wrapper.sh $in_file custom $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>
6 <inputs>
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
8 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
9 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
10 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
11 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
12 </param>
13 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
14 <option value="yes">yes</option>
15 <option value="no" selected="true">no</option>
16 </param>
17 <param name="functionality" type="select" label="Functionality filter" help="" >
18 <option value="productive" selected="true">Productive: Keep "productive" and "productive (see comment)"</option>
19 <option value="unproductive">Unproductive: Keep "unproductive" and "unproductive (see comment)"</option>
20 <option value="remove_unknown">Remove "unknown" and "unknown (see comment)"</option>
21 <option value="dont_filter">Don't filter</option>
22 </param>
23 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
24 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
25 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
26 <option value="no" selected="true">No</option>
27 </param>
28 <param name="unique" type="select" label="Remove duplicates based on" help="" >
29 <option value="VGene,AA.JUNCTION,best_match" selected="true">Top.V.Gene, CDR3 (AA), C region</option>
30 <option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3 (AA)</option>
31 <option value="AA.JUNCTION,best_match">CDR3 (AA), C region</option>
32 <option value="AA.JUNCTION">CDR3 (AA)</option>
33
34 <option value="VGene,CDR3.IMGT.seq,best_match" selected="true">Top.V.Gene, CDR3.nt.Seq, C region</option>
35 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
36 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option>
37 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
38 <option value="Sequence.ID">Don't remove duplicates</option>
39 </param>
40 <param name="class_filter" type="select" label="Class/Subclass filter" help="" >
41 <option value="70_70" selected="true">>70% class and >70% subclass</option>
42 <option value="60_55">>60% class and >55% subclass</option>
43 <option value="70_0">>70% class</option>
44 <option value="60_0">>60% class</option>
45 <option value="101_101">No class</option>
46 </param>
47 <conditional name="naive_output_cond">
48 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
49 <option value="yes">Yes</option>
50 <option value="no" selected="true">No</option>
51 </param>
52 </conditional>
53 </inputs>
54 <outputs>
55 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
56 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
57 <filter>naive_output_cond['naive_output'] == "yes"</filter>
58 </data>
59 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
60 <filter>naive_output_cond['naive_output'] == "yes"</filter>
61 </data>
62 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
63 <filter>naive_output_cond['naive_output'] == "yes"</filter>
64 </data>
65 </outputs>
66 <citations>
67 <citation type="doi">10.1093/nar/gks457</citation>
68 <citation type="doi">10.1093/bioinformatics/btv359</citation>
69 </citations>
70 <help>
71 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
72
73 +--------------------------+
74 | unique filter |
75 +--------+--------+--------+
76 | values | remove | keep |
77 +--------+--------+--------+
78 | A | A | A |
79 +--------+--------+--------+
80 | A | B | B |
81 +--------+--------+--------+
82 | B | D | C |
83 +--------+--------+--------+
84 | B | | D |
85 +--------+--------+--------+
86 | C | | |
87 +--------+--------+--------+
88 | D | | |
89 +--------+--------+--------+
90 | D | | |
91 +--------+--------+--------+
92
93 </help>
94 </tool>