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comparison bamtools_split_mapped.xml @ 1:9dbf707bebb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
author iuc
date Wed, 11 Jan 2023 12:03:53 +0000
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0:09470ab960f1 1:9dbf707bebb0
1 <tool id="bamtools_split_mapped" name="Split BAM by Mapped" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 <![CDATA[
9 ln -s '${input_bam}' 'localbam.bam' &&
10 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
11 bamtools split -mapped
12 -in localbam.bam
13 -stub split_bam
14 ]]>
15 </command>
16 <inputs>
17 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/>
18 </inputs>
19 <outputs>
20 <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" />
21 <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
26 <output name="mapped" file="split_bam.MAPPED.bam" compare="sim_size" delta="200" />
27 <output name="unmapped" file="split_bam.UNMAPPED.bam" compare="sim_size" delta="200" />
28 </test>
29 </tests>
30 <help>
31 **What is does**
32
33 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).
34
35 -----
36
37 .. class:: warningmark
38
39
40 **How it works**
41
42 Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively.
43
44 -----
45
46 .. class:: infomark
47
48 **More information**
49
50 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
51
52 </help>
53 <citations>
54 <citation type="doi">10.1093/bioinformatics/btr174</citation>
55 </citations>
56 </tool>