Mercurial > repos > davidvanzessen > shm_csr

annotate shm_csr.xml @ 94:84e9e5c8c101 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
author rhpvorderman
date Fri, 24 Mar 2023 16:58:28 +0000
parents 8fcf31272f6e
children d63eff357515
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.0" profile="16.04">
89
3c9d4d976c47 "planemo upload commit 8b702d0cf8f2355307eb8f95989f3d2488b2c963"
rhpvorderman
parents: 88
diff changeset
2 <description></description>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
3 <requirements>
84
4db34e32dd47 "planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
rhpvorderman
parents: 83
diff changeset
4 <requirement type="package" version="3.7.1">python</requirement>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
5 <requirement type="package" version="0.4.4">changeo</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
6 <!--Biopython should be set at a version at the release of changeo 0.4.4.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
7 Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.-->
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
8 <requirement type="package" version="1.72">biopython</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
9 <requirement type="package" version="1.2.0">xlrd</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
10 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
11 <requirement type="package" version="1.4.3">r-reshape2</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
12 <requirement type="package" version="0.5.0">r-scales</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
13 <requirement type="package" version="3.4_5">r-seqinr</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
14 <requirement type="package" version="1.11.4">r-data.table</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
15 <requirement type="package" version="6.0">unzip</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
16 <requirement type="package" version="4.4.18">bash</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
17 <requirement type="package" version="1.34">tar</requirement>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
18 <requirement type="package" version="5.39">file</requirement>
90
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 89
diff changeset
19 <requirement type="package" version="4.6.0">findutils</requirement>
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 89
diff changeset
20 <requirement type="package" version="1.07.1">bc</requirement>
6809c63d9161 "planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents: 89
diff changeset
21 <requirement type="package" version="0.83">font-ttf-ubuntu</requirement>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
22 </requirements>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
23 <command interpreter="bash">
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
24 <![CDATA[
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
25 #set $input=$in_file.name
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
26 ln -s "$in_file" "$input" &&
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
27 #if str ( $filter_unique.filter_unique_select ) == "remove":
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
28 $__tool_directory__/wrapper.sh "$input"
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
29 custom $out_file $out_file.files_path
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
30 "${in_file.name}" "-" $functionality $unique
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
31 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
32 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
33 $naive_output_igm_naive_memory
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
34 $filter_unique.filter_unique_select
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
35 $filter_unique.filter_unique_clone_count
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
36 $class_filter_cond.class_filter
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
37 $empty_region_filter
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
38 $fast
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
39 #else:
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
40 $__tool_directory__/wrapper.sh
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
41 "$input" custom
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
42 $out_file $out_file.files_path
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
43 "${in_file.name}" "-" $functionality $unique
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
44 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
45 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
46 $naive_output_igm_naive_memory
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
47 $filter_unique.filter_unique_select
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
48 2
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
49 $class_filter_cond.class_filter
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
50 $empty_region_filter
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
51 $fast
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
52 #end if
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
53 ]]>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
54 </command>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
55 <inputs>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
56 <param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" />
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
57 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
58 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
59 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
60 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
61 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
62 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
63 <param name="functionality" type="select" label="Functionality filter" help="" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
64 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
65 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
66 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
67 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
68 <conditional name="filter_unique">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
69 <param name="filter_unique_select" type="select" label="Filter unique sequences" help="See below for an example.">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
70 <option value="remove" selected="true">Remove uniques (Based on nucleotide sequence + C)</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
71 <option value="remove_vjaa">Remove uniques (Based on V+J+CDR3 (AA))</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
72 <option value="keep">Keep uniques (Based on nucleotide sequence + C)</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
73 <option value="no">No</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
74 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
75 <when value="remove">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
76 <param name="filter_unique_clone_count" size="4" type="integer" label="How many sequences should be in a group to keep 1 of them" value="2" min="2"/>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
77 </when>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
78 <when value="keep"></when>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
79 <when value="no"></when>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
80 </conditional>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
81 <param name="unique" type="select" label="Remove duplicates based on" help="" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
82 <option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
83 <option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option>
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
84 <option value="VGene,JGene,CDR3.IMGT.AA">Top.V.Gene, Top.J.Gene, CDR3 (AA)</option>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
85 <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
86 <option value="CDR3.IMGT.AA">CDR3 (AA)</option>
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
87
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
88 <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3 (nt), C region</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
89 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
90 <option value="VGene,JGene,CDR3.IMGT.seq">Top.V.Gene, Top.J.Gene, CDR3 (nt)</option>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
91 <option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
92 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
93 <option value="VGene,DGene,JGene,CDR3.IMGT.seq">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3 (nt)</option>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
94 <option value="Sequence.ID" selected="true">Don't remove duplicates</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
95 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
96 <conditional name="class_filter_cond">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
97 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
98 <option value="70_70" selected="true">>70% class and >70% subclass</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
99 <option value="60_55">>60% class and >55% subclass</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
100 <option value="70_0">>70% class</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
101 <option value="60_0">>60% class</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
102 <option value="19_0">>19% class</option>
93
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
103 <option value="101_101_all">Do not assign (sub)class</option>
8fcf31272f6e planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
rhpvorderman
parents: 92
diff changeset
104 <option value="101_101_IGM">Everything is IGM</option>
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
105 <option value="101_101_IGA">Everything is IGA</option>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
106 <option value="101_101_IGG">Everything is IGG</option>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
107 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
108 </conditional>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
109 <conditional name="naive_output_cond">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
110 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
111 <option value="yes">Yes</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
112 <option value="no" selected="true">No</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
113 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
114 <when value="yes"></when>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
115 <when value="no"></when>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
116 </conditional>
92
cf8ad181628f planemo upload commit 36be3b053802693392f935e6619ba3f2b1704e3c
rhpvorderman
parents: 91
diff changeset
117 <param name="fast" type="select" label="Fast" help="Skips Change-O/Baseline" >
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
118 <option value="yes">Yes</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
119 <option value="no" selected="true">No</option>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
120 </param>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
121 </inputs>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
122 <outputs>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
123 <data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
124 <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
125 <filter>naive_output_cond['naive_output'] == "yes"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
126 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
127 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
128 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
129 </data>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
130 <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
131 <filter>naive_output_cond['naive_output'] == "yes"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
132 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
133 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
134 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
135 </data>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
136 <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
137 <filter>naive_output_cond['naive_output'] == "yes"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
138 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
139 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
140 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
141 </data>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
142 <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
143 <filter>naive_output_cond['naive_output'] == "yes"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
144 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
94
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
145 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
146 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
147 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
148 </data>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
149 <data format="imgt archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}">
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
150 <filter>naive_output_cond['naive_output'] == "yes"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
151 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
152 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
153 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
154 </data>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
155 <data format="imgt archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}">
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
156 <filter>naive_output_cond['naive_output'] == "yes"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
157 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
158 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
84e9e5c8c101 "planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140"
rhpvorderman
parents: 93
diff changeset
159 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
83
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
160 </data>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
161 <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" >
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
162 <filter>naive_output_cond['naive_output'] == "yes"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
163 <filter>class_filter_cond['class_filter'] == "101_101"</filter>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
164 </data>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
165 </outputs>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
166 <tests>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
167 <test>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
168 <param name="fast" value="yes"/>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
169 <output name="out_file" file="test1.html"/>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
170 </test>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
171 </tests>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
172 <help>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
173 <![CDATA[
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
174 **References**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
175
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
176 Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying selection in high-throughput Immunoglobulin sequencing data sets. In *Nucleic Acids Research, 40 (17), pp. e134–e134.* [`doi:10.1093/nar/gks457`_]
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
177
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
178 .. _doi:10.1093/nar/gks457: http://dx.doi.org/10.1093/nar/gks457
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
179
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
180 Gupta, Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria, Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. *In Bioinformatics, 31 (20), pp. 3356–3358.* [`doi:10.1093/bioinformatics/btv359`_]
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
181
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
182 .. _doi:10.1093/bioinformatics/btv359: http://dx.doi.org/10.1093/bioinformatics/btv359
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
183
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
184 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
185
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
186 **Input files**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
187
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
188 IMGT/HighV-QUEST .zip and .txz are accepted as input files. The file to be analysed can be selected using the dropdown menu.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
189
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
190 .. class:: infomark
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
191
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
192 Note: Files can be uploaded by using “get data” and “upload file” and selecting “IMGT archive“ as a file type. Special characters should be prevented in the file names of the uploaded samples as these can give errors when running the immune repertoire pipeline. Underscores are allowed in the file names.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
193
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
194 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
195
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
196 **Sequence starts at**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
197
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
198 Identifies the region which will be included in the analysis (analysed region)
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
199
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
200 - Sequences which are missing a gene region (FR1/CDR1 etc) in the analysed region are excluded.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
201 - Sequences containing an ambiguous base in the analysed region or the CDR3 are excluded.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
202 - All other filtering/analysis is based on the analysed region.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
203
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
204 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
205
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
206 **Functionality filter**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
207
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
208 Allows filtering on productive rearrangements, unproductive rearrangements or both based on the assignment provided by IMGT.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
209
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
210 **Filter unique sequences**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
211
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
212 *Remove unique:*
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
213
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
214
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
215 This filter consists of two different steps.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
216
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
217 Step 1: removes all sequences of which the nucleotide sequence in the “analysed region” and the CDR3 (see sequence starts at filter) occurs only once. (Sub)classes are not taken into account in this filter step.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
218
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
219 Step 2: removes all duplicate sequences (sequences with the exact same nucleotide sequence in the analysed region, the CDR3 and the same (sub)class).
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
220
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
221 .. class:: infomark
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
222
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
223 This means that sequences with the same nucleotide sequence but a different (sub)class will be included in the results of both (sub)classes.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
224
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
225 *Keep unique:*
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
226
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
227 Removes all duplicate sequences (sequences with the exact same nucleotide sequence in the analysed region and the same (sub)class).
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
228
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
229 Example of the sequences that are included using either the “remove unique filter” or the “keep unique filter”
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
230
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
231 +--------------------------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
232 | unique filter |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
233 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
234 | values | remove | keep |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
235 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
236 | A | A | A |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
237 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
238 | A | B | B |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
239 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
240 | B | D | C |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
241 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
242 | B | | D |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
243 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
244 | C | | |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
245 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
246 | D | | |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
247 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
248 | D | | |
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
249 +--------+--------+--------+
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
250
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
251 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
252
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
253 **Remove duplicates based on**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
254
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
255 Allows the selection of a single sequence per clone. Different definitions of a clone can be chosen.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
256
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
257 .. class:: infomark
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
258
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
259 Note: The first sequence (in the data set) of each clone is always included in the analysis. When the first matched sequence is unmatched (no subclass assigned) the first matched sequence will be included. This means that altering the data order (by for instance sorting) can change the sequence which is included in the analysis and therefore slightly influences the results.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
260
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
261 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
262
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
263 **Human Class/Subclass filter**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
264
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
265 .. class:: warningmark
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
266
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
267 Note: This filter should only be applied when analysing human IGH data in which a (sub)class specific sequence is present. Otherwise please select the do not assign (sub)class option to prevent errors when running the pipeline.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
268
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
269 The class percentage is based on the ‘chunk hit percentage’ (see below). The subclass percentage is based on the ‘nt hit percentage’ (see below).
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
270
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
271 The SHM & CSR pipeline identifies human Cµ, Cα, Cγ and Cε constant genes by dividing the reference sequences for the subclasses (NG_001019) in 8 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are then individually aligned in the right order to each input sequence. This alignment is used to calculate the chunck hit percentage and the nt hit percentage.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
272
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
273 *Chunk hit percentage*: The percentage of the chunks that is aligned
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
274
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
275 *Nt hit percentage*: The percentage of chunks covering the subclass specific nucleotide match with the different subclasses. The most stringent filter for the subclass is 70% ‘nt hit percentage’ which means that 5 out of 7 subclass specific nucleotides for Cα or 6 out of 8 subclass specific nucleotides of Cγ should match with the specific subclass.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
276 The option “>25% class” can be chosen when you only are interested in the class (Cα/Cγ/Cµ/Cɛ) of your sequences and the length of your sequence is not long enough to assign the subclasses.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
277
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
278 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
279
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
280 **Output new IMGT archives per class into your history?**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
281
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
282 If yes is selected, additional output files (one for each class) will be added to the history which contain information of the sequences that passed the selected filtering criteria. These files are in the same format as the IMGT/HighV-QUEST output files and therefore are also compatible with many other analysis programs, such as the Immune repertoire pipeline.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
283
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
284 -----
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
285
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
286 **Execute**
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
287
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
288 Upon pressing execute a new analysis is added to your history (right side of the page). Initially this analysis will be grey, after initiating the analysis colour of the analysis in the history will change to yellow. When the analysis is finished it will turn green in the history. Now the analysis can be opened by clicking on the eye icon on the analysis of interest. When an analysis turns red an error has occurred when running the analysis. If you click on the analysis title additional information can be found on the analysis. In addition a bug icon appears. Here more information on the error can be found.
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
289
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
290 ]]>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
291 </help>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
292 <citations>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
293 <citation type="doi">10.1093/nar/gks457</citation>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
294 <citation type="doi">10.1093/bioinformatics/btv359</citation>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
295 </citations>
729738462297 "planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
rhpvorderman
parents: 81
diff changeset
296 </tool>