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comparison sambamba_filter.xml @ 0:668e187566d5

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uploaded xml wrapper
author lomereiter
date Mon, 13 Aug 2012 02:13:09 -0400
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children 806b3253c996
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1 <tool id="sambamba_filter" name="Filter BAM or SAM" version="0.2.3">
2 <requirements>
3 <requirement type="binary">sambamba</requirement>
4 </requirements>
5 <description>
6 on flags, fields, and tags
7 </description>
8 <command>
9 #if $query != None:
10 #set $query = $query.replace('__sq__', '\'')
11 #set $query = $query.replace('__ob__', '[')
12 #set $query = $query.replace('__cb__', ']')
13 #set $query = $query.replace('__dq__', '"')
14 #set $query = $query.replace('__oc__', '{')
15 #set $query = $query.replace('__cc__', '}')
16 #set $query = $query.replace('__gt__', chr(62))
17 #set $query = $query.replace('__lt__', chr(60))
18 #end if
19 #if $outputformat.format == 'bam':
20 #set $header = ''
21 #else
22 #set $header = $outputformat.header
23 #end if
24 #if isinstance($input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__):
25 #set $input1 = 'input.bam'
26 ln -s $input $input1 &amp;&amp;
27 ln -s $input.metadata.bam_index input.bai &amp;&amp;
28 sambamba view --filter="$query" -f $outputformat.format -o $outfile $input1 $header $region
29 #else
30 sambamba view -S --filter="$query" -f $outputformat.format -o $outfile $input $header
31 #end if
32 </command>
33 <inputs>
34 <param name="input" type="data" format="bam,sam" label="BAM or SAM file to filter"/>
35 <param name="query" type="text" size="80">
36 <label>Filter expression</label>
37 <help>
38 The syntax is described at sambamba wiki: https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax
39 </help>
40 </param>
41
42 <conditional name="outputformat">
43 <param name="format" type="select">
44 <label>Output format</label>
45 <option value="sam">SAM</option>
46 <option value="bam">BAM</option>
47 </param>
48 <when value="sam">
49 <param name="header" type="select">
50 <label>Include SAM header in output</label>
51 <option value="-h">Yes</option>
52 <option value="">No</option>
53 </param>
54 </when>
55 <when value="bam"/>
56 </conditional>
57 <param name="region" type="text" size="40" label="Region in format chr:beg-end, works for BAM input only">
58 <help>
59 The syntax is the same as in samtools, start and end coordinates are 1-based.
60 </help>
61 </param>
62 </inputs>
63 <outputs>
64 <data name="outfile" format="bam">
65 <change_format>
66 <when input="outputformat.format" value="sam" format="sam"/>
67 </change_format>
68 </data>
69 </outputs>
70 <help>
71 **What it does**
72
73 This tool uses sambamba view to filter BAM/SAM on flags, fields, tags, and region.
74 In order to install sambamba, visit its website_ and either download
75 a Debian package for your architecture, or build the tool from source.
76
77 Input is SAM or BAM file, output is chosen by user.
78
79 **Note**
80
81 Filtering by region works only for coordinate-sorted BAM files. For SAM files this parameter is just ignored.
82
83 -----
84
85 .. _website: http://github.com/lomereiter/sambamba
86
87
88 </help>
89 <!-- TODO: tests -->
90 </tool>