annotate extractSplitReads_BwaMem.xml @ 1:a20ac5d90c16 draft default tip

planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
author hepcat72
date Fri, 10 Aug 2018 13:15:57 -0400
parents 839c219ab0aa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
a20ac5d90c16 planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents: 0
diff changeset
1 <tool id="extractSplitReads_BwaMem"
0
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
2 name="Extract Split Reads"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
3 version="0.1.0">
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
4
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
5 <description>from bwaMEM (part of lumpy-sv)</description>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
6
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
7 <requirements>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
8 <requirement type="package" version="0.2.14a">lumpy-sv</requirement>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
9 </requirements>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
10
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
11 <version_command>extractSplitReads_BwaMem | grep ^extractSplitReads_BwaMem | cut -d v -f 2</version_command>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
12
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
13 <command detect_errors="aggressive">
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
14 <![CDATA[
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
15 extractSplitReads_BwaMem
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
16 -i '$input'
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
17 -n $numSplits
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
18 $includeDups
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
19 -m $minNonOverlap
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
20 > '$output'
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
21 ]]>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
22 </command>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
23
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
24 <inputs>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
25
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
26 <param format="sam" name="input" type="data" label="Sam alignment file" argument="--infile"/>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
27
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
28 <param name="numSplits"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
29 label="numSplits"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
30 argument="--numSplits"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
31
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
32 type="integer"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
33 value="2"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
34
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
35 help="The maximum number of split-read mappings to allow per read. Reads with more are excluded." />
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
36
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
37 <param name="includeDups"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
38 label="includeDups"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
39 argument="--includeDups"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
40
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
41 type="boolean"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
42 truevalue="--includeDups"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
43 falsevalue=""
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
44 checked="no"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
45 value="false"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
46
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
47 help="Include alignments marked as duplicates." />
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
48
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
49 <param name="minNonOverlap"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
50 label="minNonOverlap"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
51 argument="--minNonOverlap"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
52
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
53 type="integer"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
54 value="20"
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
55
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
56 help="Minimum non-overlap between split alignments on the query." />
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
57
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
58 </inputs>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
59 <outputs>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
60 <data format="sam" name="output" />
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
61 </outputs>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
62
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
63 <tests>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
64 <test>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
65 <param name="input" value="JS01-BWA-MEM.splitters.sam"/>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
66 <output name="output" file="JS01-BWA-MEM.splitters.out.sam"/>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
67 </test>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
68 <test>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
69 <param name="input" value="pe.pos_sorted.sam"/>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
70 <output name="output" file="pe.pos_sorted.out.sam"/>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
71 </test>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
72 </tests>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
73
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
74 <help>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
75 <![CDATA[
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
76
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
77 Usage: `extractSplitReads_BwaMem -i <file>`
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
78
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
79 extractSplitReads_BwaMem v0.1.0
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
80
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
81 Author: Ira Hall
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
82
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
83 Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
84
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
85 Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
86
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
87
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
88 Options:
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
89 -h, --help show this help message and exit
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
90 -i FILE, --inFile=FILE
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
91 A SAM file or standard input (-i stdin).
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
92 -n INT, --numSplits=INT
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
93 The maximum number of split-read mappings to allow per
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
94 read. Reads with more are excluded. Default=2
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
95 -d, --includeDups Include alignments marked as duplicates. Default=False
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
96 -m INT, --minNonOverlap=INT
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
97 minimum non-overlap between split alignments on the
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
98 query (default=20)
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
99
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
100 ]]>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
101 </help>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
102
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
103 <citations>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
104 <citation type="doi">doi:10.1186/gb-2014-15-6-r84</citation>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
105 </citations>
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
106
839c219ab0aa planemo upload commit 0066847e0ac19632c3091ac3148069de3bb3855f-dirty
hepcat72
parents:
diff changeset
107 </tool>