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comparison bamtools-split-tag.xml @ 0:8c17ddca0eee draft

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author jjohnson
date Mon, 15 May 2017 16:27:18 -0400
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1 <tool id="bamSplitTag" name="Split BAM by Tag" version="2.4.0">
2 <description>into dataset list collection</description>
3 <requirements>
4 <requirement type="package" version="2.4.0">bamtools</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 #import re
9 #set $name = 'split_bam' + $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name))
10 ln -s '${input_bam}' 'localbam.bam' &&
11 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
12 bamtools split -tag $tag_name
13 -in 'localbam.bam'
14 -stub '$name'
15 ]]>
16 </command>
17 <inputs>
18 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by tag value"/>
19 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
20 </inputs>
21 <outputs>
22 <collection name="output_bams" type="list" label="${input_bam.name} Split List">
23 <discover_datasets pattern="split_bam(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="false"/>
24 </collection>
25 </outputs>
26 <tests>
27 <test>
28 <param name="input_bam" ftype="bam" value="bamtools-input-tags.bam"/>
29 <param name="tag_name" value="XG"/>
30 <output_collection name="output_bams" type="list">
31 <element name="bamtools_input_tags.TAG_XG_V.bam" file="bamtools_input_tags.TAG_XG_V.bam" compare="sim_size" delta="500" />
32 </output_collection>
33 </test>
34
35 </tests>
36 <help>
37 **What is does**
38
39 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
40
41 -----
42
43 .. class:: warningmark
44
45 **DANGER: Multiple Outputs**
46
47 As described below, splitting a BAM dataset(s) on tag value can produce very large numbers of outputs. Read below and know what you are doing.
48
49 -----
50
51 **How it works**
52
53 Split alignments by tag name into a dataset list collection.
54
55 This can generate a huge number of output datasets depending on the number of distinct values of the TAG.
56
57
58 -----
59
60 .. class:: infomark
61
62 **More information**
63
64 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
65
66 </help>
67 <citations>
68 <citation type="doi">10.1093/bioinformatics/btr174</citation>
69 </citations>
70 </tool>