annotate shm_csr.xml @ 5:012a738edf5a draft

Uploaded
author davidvanzessen
date Tue, 01 Nov 2016 10:15:37 -0400
parents faae21ba5c63
children 2ddb9a21f635
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
2 <description></description>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
3 <command interpreter="bash">
5
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
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 $fast
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
5 </command>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
6 <inputs>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
8 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
9 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
10 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
11 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
12 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
13 </param>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
14 <param name="functionality" type="select" label="Functionality filter" help="" >
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
15 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
16 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
17 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
18 </param>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
19 <param name="filter_uniques" type="select" label="Filter unique sequences" help="See below for an example.">
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
20 <option value="remove">Remove uniques (Based on nucleotide sequence + C)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
21 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
22 <option value="no" selected="true">No</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
23 </param>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
24 <param name="unique" type="select" label="Remove duplicates based on" help="" >
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
25 <option value="VGene,AA.JUNCTION,best_match" selected="true">Top.V.Gene, CDR3 (AA), C region</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
26 <option value="VGene,AA.JUNCTION">Top.V.Gene, CDR3 (AA)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
27 <option value="AA.JUNCTION,best_match">CDR3 (AA), C region</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
28 <option value="AA.JUNCTION">CDR3 (AA)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
29
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
30 <option value="VGene,CDR3.IMGT.seq,best_match" selected="true">Top.V.Gene, CDR3.nt.Seq, C region</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
31 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
32 <option value="CDR3.IMGT.seq,best_match">CDR3 (nt), C region</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
33 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
34 <option value="Sequence.ID">Don't remove duplicates</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
35 </param>
5
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
36 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
37 <option value="70_70" selected="true">>70% class and >70% subclass</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
38 <option value="60_55">>60% class and >55% subclass</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
39 <option value="70_0">>70% class</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
40 <option value="60_0">>60% class</option>
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
41 <option value="101_101">Do not assign (sub)class</option>
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
42 </param>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
43 <conditional name="naive_output_cond">
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
44 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
45 <option value="yes">Yes</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
46 <option value="no" selected="true">No</option>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
47 </param>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
48 </conditional>
5
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
49
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
50
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
51 <param name="fast" type="select" label="Fast" help="Skips generating the new ZIP files and Change-O/Baseline" >
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
52 <option value="yes">Yes</option>
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
53 <option value="no" selected="true">No</option>
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
54 </param>
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
55
012a738edf5a Uploaded
davidvanzessen
parents: 1
diff changeset
56
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
57 </inputs>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
58 <outputs>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
59 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
60 <data format="imgt_archive" name="naive_output_ca" label = "Naive CA input data from ${in_file.name}" >
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
61 <filter>naive_output_cond['naive_output'] == "yes"</filter>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
62 </data>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
63 <data format="imgt_archive" name="naive_output_cg" label = "Naive CG input data from ${in_file.name}" >
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
64 <filter>naive_output_cond['naive_output'] == "yes"</filter>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
65 </data>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
66 <data format="imgt_archive" name="naive_output_cm" label = "Naive CM input data from ${in_file.name}" >
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
67 <filter>naive_output_cond['naive_output'] == "yes"</filter>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
68 </data>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
69 </outputs>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
70 <citations>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
71 <citation type="doi">10.1093/nar/gks457</citation>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
72 <citation type="doi">10.1093/bioinformatics/btv359</citation>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
73 </citations>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
74 <help>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
75 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
76
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
77 +--------------------------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
78 | unique filter |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
79 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
80 | values | remove | keep |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
81 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
82 | A | A | A |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
83 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
84 | A | B | B |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
85 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
86 | B | D | C |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
87 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
88 | B | | D |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
89 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
90 | C | | |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
91 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
92 | D | | |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
93 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
94 | D | | |
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
95 +--------+--------+--------+
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
96
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
97 </help>
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
98 </tool>