Mercurial > repos > devteam > samtool_filter2

annotate samtool_filter2.xml @ 9:649a225999a5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 0d0561efe21c89202c258f4ecc5083cb84a137ba"
author iuc
date Sun, 24 Nov 2019 13:40:05 -0500
parents a7add3e93cc5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8+galaxy1">
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
2 <description>files on FLAG MAPQ RG LN or by region</description>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
3 <requirements>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
4 <requirement type="package" version="1.8">samtools</requirement>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
5 </requirements>
8
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
6 <macros>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
7 <xml name="flag_options">
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
8 <option value="0x0001">Read is paired</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
9 <option value="0x0002">Read is mapped in a proper pair</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
10 <option value="0x0004">The read is unmapped</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
11 <option value="0x0008">The mate is unmapped</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
12 <option value="0x0010">Read is mapped to the reverse strand of the reference</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
13 <option value="0x0020">Mate is mapped to the reverse strand of the reference</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
14 <option value="0x0040">Read is the first in a pair</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
15 <option value="0x0080">Read is the second in a pair</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
16 <option value="0x0100">The alignment of this read is not primary</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
17 <option value="0x0200">The read fails platform/vendor quality checks</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
18 <option value="0x0400">The read is a PCR or optical duplicate</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
19 <option value="0x0800">Supplementary alignment</option>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
20 </xml>
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
21 </macros>
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
22 <command detect_errors="exit_code"><![CDATA[
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
23 ##set up input files, regions requires input.bam and input.bai
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
24 #if $input1.is_of_type('bam')
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
25 #set $input = 'input.bam'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
26 ln -s '$input1' $input &&
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
27 ln -s '$input1.metadata.bam_index' input.bai &&
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
28 #elif $input1.is_of_type('sam')
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
29 #set $input = 'input.sam'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
30 ln -s '$input1' $input &&
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
31 #end if
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
32 samtools view
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
33 $possibly_select_inverse '$output1'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
34 $header
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
35
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
36 #if $input1.is_of_type('sam')
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
37 -S
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
38 #end if
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
39
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
40 #if str($outputtype) == 'bam'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
41 -b
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
42 #end if
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
43
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
44 #if str($mapq)
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
45 -q $mapq
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
46 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
47 #if $flag.filter == 'yes'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
48 #if str($flag.reqBits) != 'None'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
49 #set $reqs = str($flag.reqBits).split(',')
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
50 #set $reqFlag = 0
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
51 #for $xn in $reqs:
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
52 #set $reqFlag += int($xn, 16)
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
53 #end for
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
54 -f $hex($reqFlag)
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
55 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
56 #if str($flag.skipBits) != 'None'
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
57 #set $skips = str($flag.skipBits).split(',')
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
58 #set $skipFlag = 0
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
59 #for $xn in $skips:
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
60 #set $skipFlag += int(xn,16)
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
61 #end for
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
62 -F $hex($skipFlag)
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
63 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
64 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
65 #if str($read_group).strip()
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
66 -r '$read_group'
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
67 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
68 #if str($library).strip()
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
69 -l '$library'
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
70 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
71 #if $bed_file
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
72 -L '$bed_file'
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
73 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
74 $input
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
75 #if str($regions).strip() and $input1.is_of_type('bam')
6
dc6ff68ea5e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
devteam
parents: 5
diff changeset
76 #for region in str($regions).split():
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
77 '$region'
6
dc6ff68ea5e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4
devteam
parents: 5
diff changeset
78 #end for
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
79 #end if
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
80 ]]></command>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
81 <inputs>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
82 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
83 <param name="header" type="select" label="Header in output">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
84 <option value="-h">Include header</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
85 <option value="">Exclude header</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
86 <option value="-H">Only the header</option>
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
87 </param>
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
88 <param name="mapq" type="integer" min="0" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
89 <conditional name="flag">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
90 <param name="filter" type="select" label="Filter on bitwise flag">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
91 <option value="no">no</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
92 <option value="yes">yes</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
93 </param>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
94 <when value="no"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
95 <when value="yes">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
96 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)">
8
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
97 <expand macro="flag_options" />
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
98 </param>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
99 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)">
8
a7add3e93cc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
iuc
parents: 7
diff changeset
100 <expand macro="flag_options" />
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
101 </param>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
102 </when>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
103 </conditional>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
104 <param name="library" type="text" value="" label="Select alignments from Library"
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
105 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
106 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
107 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
108 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED file" help="(-L)"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
109 <param name="possibly_select_inverse" type="boolean" truevalue="-U" falsevalue="-o" checked="false" label="Use inverse selection" help="Select the opposite of the listed chromosomes" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
110 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
111 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
112 <param name="outputtype" type="select" label="Select the output format">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
113 <option value="bam">BAM (-b)</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
114 <option value="sam">SAM</option>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
115 </param>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
116 </inputs>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
117 <outputs>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
118 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
119 <change_format>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
120 <when input="outputtype" value="bam" format="bam" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
121 </change_format>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
122 </data>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
123 </outputs>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
124 <tests>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
125 <test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
126 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
127 <param name="header" value=""/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
128 <param name="filter" value="yes"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
129 <param name="reqBits" value="0x0080"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
130 <param name="outputtype" value="sam"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
131 <output name="output1">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
132 <assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
133 <has_text text="141" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
134 <not_has_text text="77" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
135 </assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
136 </output>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
137 </test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
138 <test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
139 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
140 <param name="header" value=""/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
141 <param name="filter" value="no"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
142 <param name="read_group" value="rg1"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
143 <param name="outputtype" value="sam"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
144 <output name="output1">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
145 <assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
146 <has_text text="rg1" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
147 <not_has_text text="rg2" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
148 </assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
149 </output>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
150 </test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
151 <test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
152 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
153 <param name="header" value=""/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
154 <param name="filter" value="yes"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
155 <param name="skipBits" value="0x0008"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
156 <param name="mapq" value="250"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
157 <param name="outputtype" value="sam"/>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
158 <output name="output1">
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
159 <assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
160 <has_text text="both_reads_align_clip_marked" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
161 <not_has_text text="both_reads_present_only_first_aligns" />
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
162 </assert_contents>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
163 </output>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
164 </test>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
165 </tests>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
166 <help><![CDATA[
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
167 **What it does**
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
168
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
169 This tool uses the samtools view command in SAMtools_ toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
170
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
171 **Input**
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
172
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
173 Input is either a SAM or BAM file.
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
174
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
175 **Output**
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
176
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
177 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
178
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
179 **Options**
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
180
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
181 Filtering by read group or library requires headers in the input SAM or BAM file.
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
182
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
183 If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions.
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
184 A region can be presented, for example, in the following format::
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
185
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
186 chr2 (the whole chr2)
1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
187 chr2:1000000 (region starting from 1,000,000bp)
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
devteam
parents: 0
diff changeset
188 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
189
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
190 Note: The coordinate is 1-based.
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
191
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
192 Multiple regions may be specified, separated by a space character::
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
193
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
194 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
195
5
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
devteam
parents: 4
diff changeset
196 .. _SAMtools: http://www.htslib.org/
7
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
197 ]]></help>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
198 <citations>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
199 <citation type="doi">10.1093/bioinformatics/btp352</citation>
56c31114ad4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 24d5defd0880276f60d3d2f6abed9a00fa57eb0e
iuc
parents: 6
diff changeset
200 </citations>
0
2d4ae2f8231e Imported from capsule None
devteam
parents:
diff changeset
201 </tool>