samtool_filter2: samtool_filter2.xml annotate

annotate samtool_filter2.xml @ 6:dc6ff68ea5e8 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4

author	devteam
date	Thu, 05 Oct 2017 10:31:42 -0400
parents	b7aa423007bf
children	56c31114ad4a

rev	line source
3 c31a37f6d48a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828 devteam parents: 2 diff changeset	1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	2 <description>files on FLAG MAPQ RG LN or by region</description>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	3 <requirements>
3 c31a37f6d48a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828 devteam parents: 2 diff changeset	4 <requirement type="package" version="1.2">samtools</requirement>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	5 </requirements>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	6 <stdio>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	7 <exit_code range="1:" />
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	8 </stdio>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	9 <command>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	10 <![CDATA[
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	11 ##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	12 #if $input1.is_of_type('bam')
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	13 #set $input = 'input.bam'
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	14 ln -s '$input1' $input &&
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	15 ln -s '$input1.metadata.bam_index' input.bai &&
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	16 #elif $input1.is_of_type('sam')
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	17 #set $input = 'input.sam'
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	18 ln -s '$input1' $input &&
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	19 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	20 samtools view $possibly_select_inverse '$output1' $header
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	21
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	22 #if $input1.is_of_type('sam')
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	23 -S
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	24 #end if
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	25
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	26 #if str($outputtype) == 'bam'
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	27 -b
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	28 #end if
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	29
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	30 #if str($mapq)
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	31 -q $mapq
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	32 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	33 #if $flag.filter == 'yes'
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	34 #if str($flag.reqBits) != 'None'
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	35 #set $reqs = str($flag.reqBits).split(',')
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	36 #set $reqFlag = 0
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	37 #for $xn in $reqs:
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	38 #set $reqFlag += int($xn, 16)
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	39 #end for
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	40 -f $hex($reqFlag)
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	41 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	42 #if str($flag.skipBits) != 'None'
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	43 #set $skips = str($flag.skipBits).split(',')
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	44 #set $skipFlag = 0
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	45 #for $xn in $skips:
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	46 #set $skipFlag += int(xn,16)
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	47 #end for
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	48 -F $hex($skipFlag)
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	49 #end if
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	50 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	51 #if str($read_group).strip()
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	52 -r '$read_group'
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	53 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	54 #if str($library).strip()
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	55 -l '$library'
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	56 #end if
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	57 #if $bed_file
b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	58 -L '$bed_file'
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	59 #end if
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	60 $input
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	61 #if str($regions).strip() and $input1.is_of_type('bam')
6 dc6ff68ea5e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4 devteam parents: 5 diff changeset	62 #for region in str($regions).split():
dc6ff68ea5e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4 devteam parents: 5 diff changeset	63 '$region'
dc6ff68ea5e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit a97efd3ee05c6e27ff8294f66ea975445966d9c4 devteam parents: 5 diff changeset	64 #end for
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	65 #end if
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	66 ## need to redirect stderr message so galaxy does not think this failed
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	67 2>&1
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	68 ]]>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	69 </command>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	70 <inputs>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	71 <param name="input1" type="data" format="sam,bam" label="SAM or BAM file to filter" />
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	72 <param name="header" type="select" label="Header in output">
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	73 <option value="-h">Include Header</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	74 <option value="">Exclude Header</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	75 <option value="-H">Only the Header</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	76 </param>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	77 <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score" help="(-q)">
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	78 <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	79 </param>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	80 <conditional name="flag">
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	81 <param name="filter" type="select" label="Filter on bitwise flag">
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	82 <option value="no">no</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	83 <option value="yes">yes</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	84 </param>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	85 <when value="no"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	86 <when value="yes">
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	87 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)">
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	88 <option value="0x0001">Read is paired</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	89 <option value="0x0002">Read is mapped in a proper pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	90 <option value="0x0004">The read is unmapped</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	91 <option value="0x0008">The mate is unmapped</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	92 <option value="0x0010">Read strand</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	93 <option value="0x0020">Mate strand</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	94 <option value="0x0040">Read is the first in a pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	95 <option value="0x0080">Read is the second in a pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	96 <option value="0x0100">The alignment or this read is not primary</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	97 <option value="0x0200">The read fails platform/vendor quality checks</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	98 <option value="0x0400">The read is a PCR or optical duplicate</option>
4 d3292b4a0c78 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 47865f133813c9e61ffc63d70aad1ff782c645ac devteam parents: 3 diff changeset	99 <option value="0x0800">Supplementary alignment</option>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	100 </param>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	101 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)">
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	102 <option value="0x0001">Read is paired</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	103 <option value="0x0002">Read is mapped in a proper pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	104 <option value="0x0004">The read is unmapped</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	105 <option value="0x0008">The mate is unmapped</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	106 <option value="0x0010">Read strand</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	107 <option value="0x0020">Mate strand</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	108 <option value="0x0040">Read is the first in a pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	109 <option value="0x0080">Read is the second in a pair</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	110 <option value="0x0100">The alignment or this read is not primary</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	111 <option value="0x0200">The read fails platform/vendor quality checks</option>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	112 <option value="0x0400">The read is a PCR or optical duplicate</option>
4 d3292b4a0c78 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 47865f133813c9e61ffc63d70aad1ff782c645ac devteam parents: 3 diff changeset	113 <option value="0x0800">Supplementary alignment</option>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	114 </param>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	115 </when>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	116 </conditional>
2 886b73f04847 planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1 devteam parents: 1 diff changeset	117 <param name="library" type="text" value="" label="Select alignments from Library"
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	118 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
2 886b73f04847 planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1 devteam parents: 1 diff changeset	119 <param name="read_group" type="text" value="" label="Select alignments from Read Group"
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	120 help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	121 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
3 c31a37f6d48a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828 devteam parents: 2 diff changeset	122 <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
2 886b73f04847 planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1 devteam parents: 1 diff changeset	123 <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	124 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	125 <param name="outputtype" type="select" label="Select the output format">
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	126 <option value="bam">BAM (-b)</option>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	127 <option value="sam">SAM</option>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	128 </param>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	129 </inputs>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	130 <outputs>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	131 <data name="output1" format="sam" label="${tool.name} on ${on_string}: ${outputtype}">
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	132 <change_format>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	133 <when input="outputtype" value="bam" format="bam" />
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	134 </change_format>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	135 </data>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	136 </outputs>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	137 <tests>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	138 <test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	139 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	140 <param name="header" value=""/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	141 <param name="filter" value="yes"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	142 <param name="reqBits" value="0x0080"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	143 <param name="outputtype" value="sam"/>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	144 <output name="output1">
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	145 <assert_contents>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	146 <has_text text="141" />
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	147 <not_has_text text="77" />
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	148 </assert_contents>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	149 </output>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	150 </test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	151 <test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	152 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	153 <param name="header" value=""/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	154 <param name="filter" value="no"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	155 <param name="read_group" value="rg1"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	156 <param name="outputtype" value="sam"/>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	157 <output name="output1">
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	158 <assert_contents>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	159 <has_text text="rg1" />
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	160 <not_has_text text="rg2" />
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	161 </assert_contents>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	162 </output>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	163 </test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	164 <test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	165 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	166 <param name="header" value=""/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	167 <param name="filter" value="yes"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	168 <param name="skipBits" value="0x0008"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	169 <param name="mapq" value="250"/>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	170 <param name="outputtype" value="sam"/>
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	171 <output name="output1">
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	172 <assert_contents>
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	173 <has_text text="both_reads_align_clip_marked" />
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	174 <not_has_text text="both_reads_present_only_first_aligns" />
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	175 </assert_contents>
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	176 </output>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	177 </test>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	178 </tests>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	179 <help>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	180 What it does
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	181
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	182 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	183
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	184 Input
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	185
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	186 Input is either a SAM or BAM file.
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	187
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	188 Output
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	189
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	190 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	191
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	192 Options
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	193
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	194 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	195
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	196 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	197 A region can be presented, for example, in the following format::
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	198
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	199 chr2 (the whole chr2)
1 94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	200 chr2:1000000 (region starting from 1,000,000bp)
94d5786febc4 planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062 devteam parents: 0 diff changeset	201 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	202
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	203 Note: The coordinate is 1-based.
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	204
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	205 Multiple regions may be specified, separated by a space character::
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	206
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	207 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	208
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	209
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	210
5 b7aa423007bf planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1 devteam parents: 4 diff changeset	211 .. _SAMtools: http://www.htslib.org/
0 2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	212
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	213 </help>
2d4ae2f8231e Imported from capsule None devteam parents: diff changeset	214 </tool>

Mercurial > repos > devteam > samtool_filter2

annotate samtool_filter2.xml @ 6:dc6ff68ea5e8 draft