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comparison sambamba_filter.xml @ 5:123168c85390

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updated to 0.4.7; use precompiled binaries
author lomereiter <lomereiter@gmail.com>
date Tue, 04 Nov 2014 18:34:37 +0300
parents a03e95059256
children
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4:6d875183e6f7 5:123168c85390
1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="1.0"> 1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="1.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.3.3">sambamba</requirement> 3 <requirement type="package" version="0.4.7">sambamba</requirement>
4 </requirements> 4 </requirements>
5 <description> 5 <description>
6 on flags, fields, and tags using Sambamba 6 on flags, fields, and tags using Sambamba
7 </description> 7 </description>
8 <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command> 8 <version_command>sambamba 2>&amp;1 | grep "sambamba v" | sed 's/^sambamba v\(.*\)/\1/'</version_command>
18 #set $query = $query.replace('__lt__', chr(60)) 18 #set $query = $query.replace('__lt__', chr(60))
19 #end if 19 #end if
20 #set $input1 = 'input.bam' 20 #set $input1 = 'input.bam'
21 ln -s $input $input1 &amp;&amp; 21 ln -s $input $input1 &amp;&amp;
22 ln -s $input.metadata.bam_index input.bai &amp;&amp; 22 ln -s $input.metadata.bam_index input.bai &amp;&amp;
23 sambamba view 23 sambamba view -t \${GALAXY_SLOTS:-8}
24 #if $query != "": 24 #if $query != "":
25 --filter="$query" 25 --filter="$query"
26 #end if 26 #end if
27 -f bam -o $outfile $input1 $region 27 -f bam -o $outfile $input1 $region
28 </command> 28 </command>
68 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file. 68 This tool uses the sambamba_ ``view`` command to filter BAM/SAM on flags, fields, tags, and region. Input is SAM or BAM file.
69 69
70 70
71 Filter Syntax 71 Filter Syntax
72 ============= 72 =============
73
74 Complete documentation of filter syntax is available at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax.
75 73
76 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed. 74 A *filter expression* is a number of *basic conditions* linked by ``and``, ``or``, ``not`` logical operators, and enclosed in parentheses where needed.
77 75
78 *Basic condition* is a one for a single record field, tag, or flag. 76 *Basic condition* is a one for a single record field, tag, or flag.
79 77
155 [RG] != null and [AM] == 37 153 [RG] != null and [AM] == 37
156 154
157 ----- 155 -----
158 156
159 .. _sambamba: http://github.com/lomereiter/sambamba 157 .. _sambamba: http://github.com/lomereiter/sambamba
160 .. _filter-syntax: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
161 158
162 </help> 159 </help>
163 </tool> 160 </tool>