Mercurial > repos > iuc > bamtools_split_mapped
changeset 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 | f2c21525a960 |
| files | bamtools_split_mapped.xml macros.xml test-data/bamtools-input-paired.bam test-data/bamtools-input-tags.bam test-data/bamtools-input1.bam test-data/bamtools-input2.bam test-data/bamtools-split-test1.bam test-data/bamtools_input2.chr1 test-data/bamtools_input_tags.TAG_XG_N.bam test-data/bamtools_input_tags.TAG_XG_V.bam test-data/split_bam.MAPPED.bam test-data/split_bam.PAIRED_END.bam test-data/split_bam.SINGLE_END.bam test-data/split_bam.UNMAPPED.bam |
| diffstat | 14 files changed, 72 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools_split_mapped.xml Sat Nov 27 10:03:10 2021 +0000 @@ -0,0 +1,56 @@ +<tool id="bamtools_split_mapped" name="Split BAM by Mapped" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + <![CDATA[ + ln -s '${input_bam}' 'localbam.bam' && + ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' && + bamtools split -mapped + -in localbam.bam + -stub split_bam + ]]> + </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/> + </inputs> + <outputs> + <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" /> + <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" /> + </outputs> + <tests> + <test> + <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <output name="mapped" file="split_bam.MAPPED.bam" compare="sim_size" delta="200" /> + <output name="unmapped" file="split_bam.UNMAPPED.bam" compare="sim_size" delta="200" /> + </test> + </tests> + <help> +**What is does** + +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). + +----- + +.. class:: warningmark + + +**How it works** + +Splits the input BAM file into 2 output files named (MAPPED) and (UNMAPPED) containing mapped and unmapped reads, respectively. + +----- + +.. class:: infomark + +**More information** + +Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Nov 27 10:03:10 2021 +0000 @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.5.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement> + <requirement type="package" version="1.4.1">samtools</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> + </xml> +</macros> \ No newline at end of file