|
0
|
1 <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0">
|
|
|
2 <description></description>
|
|
|
3 <command interpreter="bash">
|
|
1
|
4 wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $filter_uniques $class_filter $empty_region_filter
|
|
0
|
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="" >
|
|
1
|
9 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
|
|
0
|
10 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
|
|
|
11 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
|
|
|
12 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
|
|
|
13 </param>
|
|
|
14 <param name="functionality" type="select" label="Functionality filter" help="" >
|
|
1
|
15 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
|
|
|
16 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
|
|
|
17 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
|
|
0
|
18 </param>
|
|
|
19 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
|
|
|
20 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
|
|
|
21 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
|
|
|
22 <option value="no" selected="true">No</option>
|
|
|
23 </param>
|
|
|
24 <param name="unique" type="select" label="Remove duplicates based on" help="" >
|
|
|
25 <option value="VGene,AA.JUNCTION,best_match" selected="true">Top.V.Gene, CDR3 (AA), C region</option>
|
|
|
26 <option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3 (AA)</option>
|
|
|
27 <option value="AA.JUNCTION,best_match">CDR3 (AA), C region</option>
|
|
|
28 <option value="AA.JUNCTION">CDR3 (AA)</option>
|
|
|
29
|
|
|
30 <option value="VGene,CDR3.IMGT.seq,best_match" selected="true">Top.V.Gene, CDR3.nt.Seq, C region</option>
|
|
|
31 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
|
|
|
32 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option>
|
|
|
33 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
|
|
|
34 <option value="Sequence.ID">Don't remove duplicates</option>
|
|
|
35 </param>
|
|
|
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>
|
|
|
38 <option value="60_55">>60% class and >55% subclass</option>
|
|
|
39 <option value="70_0">>70% class</option>
|
|
|
40 <option value="60_0">>60% class</option>
|
|
1
|
41 <option value="101_101">Do not assign (sub)class</option>
|
|
0
|
42 </param>
|
|
|
43 <conditional name="naive_output_cond">
|
|
|
44 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
|
|
|
45 <option value="yes">Yes</option>
|
|
|
46 <option value="no" selected="true">No</option>
|
|
|
47 </param>
|
|
|
48 </conditional>
|
|
|
49 </inputs>
|
|
|
50 <outputs>
|
|
|
51 <data format="html" name="out_file" label = "SHM & CSR on ${in_file.name}"/>
|
|
|
52 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
|
|
|
53 <filter>naive_output_cond['naive_output'] == "yes"</filter>
|
|
|
54 </data>
|
|
|
55 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
|
|
|
56 <filter>naive_output_cond['naive_output'] == "yes"</filter>
|
|
|
57 </data>
|
|
|
58 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
|
|
|
59 <filter>naive_output_cond['naive_output'] == "yes"</filter>
|
|
|
60 </data>
|
|
|
61 </outputs>
|
|
|
62 <citations>
|
|
|
63 <citation type="doi">10.1093/nar/gks457</citation>
|
|
|
64 <citation type="doi">10.1093/bioinformatics/btv359</citation>
|
|
|
65 </citations>
|
|
|
66 <help>
|
|
|
67 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
|
|
|
68
|
|
|
69 +--------------------------+
|
|
|
70 | unique filter |
|
|
|
71 +--------+--------+--------+
|
|
|
72 | values | remove | keep |
|
|
|
73 +--------+--------+--------+
|
|
|
74 | A | A | A |
|
|
|
75 +--------+--------+--------+
|
|
|
76 | A | B | B |
|
|
|
77 +--------+--------+--------+
|
|
|
78 | B | D | C |
|
|
|
79 +--------+--------+--------+
|
|
|
80 | B | | D |
|
|
|
81 +--------+--------+--------+
|
|
|
82 | C | | |
|
|
|
83 +--------+--------+--------+
|
|
|
84 | D | | |
|
|
|
85 +--------+--------+--------+
|
|
|
86 | D | | |
|
|
|
87 +--------+--------+--------+
|
|
|
88
|
|
|
89 </help>
|
|
|
90 </tool>
|
