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comparison bamtools-split-mapped.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="bamSplitMapped" name="Split BAM by Mapped" version="2.4.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="2.4.0">bamtools</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 ln -s '${input_bam}' 'localbam.bam' &&
9 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
10 bamtools split -mapped
11 -in localbam.bam
12 -stub split_bam
13 ]]>
14 </command>
15 <inputs>
16 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/>
17 </inputs>
18 <outputs>
19 <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" />
20 <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
25 <output name="mapped" file="split_bam.MAPPED.bam" compare="sim_size" delta="200" />
26 <output name="unmapped" file="split_bam.UNMAPPED.bam" compare="sim_size" delta="200" />
27 </test>
28 </tests>
29 <help>
30 **What is does**
31
32 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).
33
34 -----
35
36 .. class:: warningmark
37
38
39 **How it works**
40
41 Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively.
42
43 -----
44
45 .. class:: infomark
46
47 **More information**
48
49 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
50
51 </help>
52 <citations>
53 <citation type="doi">10.1093/bioinformatics/btr174</citation>
54 </citations>
55 </tool>