Mercurial > repos > devteam > samtool_filter2

comparison samtool_filter2.xml @ 5:b7aa423007bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit 94a7407227beb0139c49d92c7f922499dc7f0cd1
author devteam
date Fri, 20 Jan 2017 04:51:36 -0500
parents d3292b4a0c78
children dc6ff68ea5e8
comparison
equal deleted inserted replaced
4:d3292b4a0c78 5:b7aa423007bf
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 ##set up input files, regions requires input.bam and input.bai 11 ##set up input files, regions requires input.bam and input.bai
12 #if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__): 12 #if $input1.is_of_type('bam')
13 #set $input = 'input.bam' 13 #set $input = 'input.bam'
14 ln -s "$input1" $input && 14 ln -s '$input1' $input &&
15 ln -s "$input1.metadata.bam_index" input.bai && 15 ln -s '$input1.metadata.bam_index' input.bai &&
16 #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__): 16 #elif $input1.is_of_type('sam')
17 #set $input = 'input.sam' 17 #set $input = 'input.sam'
18 ln -s "$input1" $input && 18 ln -s '$input1' $input &&
19 #end if 19 #end if
20 samtools view $possibly_select_inverse "$output1" $header 20 samtools view $possibly_select_inverse '$output1' $header
21 21
22 #if $input1.datatype.file_ext == 'sam': 22 #if $input1.is_of_type('sam')
23 -S 23 -S
24 #end if 24 #end if
25 25
26 #if $outputtype.__str__ == "bam": 26 #if str($outputtype) == 'bam'
27 -b 27 -b
28 #end if 28 #end if
29 29
30 #if $mapq.__str__ != '': 30 #if str($mapq)
31 -q $mapq 31 -q $mapq
32 #end if 32 #end if
33 #if $flag.filter.__str__ == 'yes': 33 #if $flag.filter == 'yes'
34 #if $flag.reqBits.__str__ != 'None': 34 #if str($flag.reqBits) != 'None'
35 #set $reqs = $flag.reqBits.__str__.split(',') 35 #set $reqs = str($flag.reqBits).split(',')
36 #set $reqFlag = 0 36 #set $reqFlag = 0
37 #for $xn in $reqs: 37 #for $xn in $reqs:
38 #set $reqFlag += int(xn,16) 38 #set $reqFlag += int($xn, 16)
39 #end for 39 #end for
40 -f $hex($reqFlag) 40 -f $hex($reqFlag)
41 #end if 41 #end if
42 #if $flag.skipBits.__str__ != 'None': 42 #if str($flag.skipBits) != 'None'
43 #set $skips = $flag.skipBits.__str__.split(',') 43 #set $skips = str($flag.skipBits).split(',')
44 #set $skipFlag = 0 44 #set $skipFlag = 0
45 #for $xn in $skips: 45 #for $xn in $skips:
46 #set $skipFlag += int(xn,16) 46 #set $skipFlag += int(xn,16)
47 #end for 47 #end for
48 -F $hex($skipFlag) 48 -F $hex($skipFlag)
49 #end if 49 #end if
50 #end if 50 #end if
51 #if $read_group.__str__.strip() != '': 51 #if str($read_group).strip()
52 -r $read_group 52 -r '$read_group'
53 #end if 53 #end if
54 #if $library.__str__.strip() != '': 54 #if str($library).strip()
55 -l $library 55 -l '$library'
56 #end if 56 #end if
57 #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0: 57 #if $bed_file
58 -L "$bed_file" 58 -L '$bed_file'
59 #end if 59 #end if
60 $input 60 $input
61 #if $regions.__str__.strip() != '' and $input1.datatype.file_ext == 'bam': 61 #if str($regions).strip() and $input1.is_of_type('bam')
62 $regions.__str__.strip() 62 '$regions'
63 #end if 63 #end if
64 ## need to redirect stderr message so galaxy does not think this failed 64 ## need to redirect stderr message so galaxy does not think this failed
65 2>&1 65 2>&1
66 ]]> 66 ]]>
67 </command> 67 </command>
204 204
205 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX 205 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
206 206
207 207
208 208
209 .. _SAMtools: http://samtools.sourceforge.net/ 209 .. _SAMtools: http://www.htslib.org/
210 210
211 </help> 211 </help>
212 </tool> 212 </tool>