Mercurial > repos > iuc > bamtools_split_mapped
comparison bamtools_split_mapped.xml @ 0:2ed961caae0a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 10:03:10 +0000 |
| parents | |
| children | 6dbef7ea2253 |
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| -1:000000000000 | 0:2ed961caae0a |
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| 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> |