|
0
|
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>
|
