Mercurial > repos > kyost > atac_primer_tool
view filter_bam.xml @ 5:3cd53127a838 draft default tip
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
author | kyost |
---|---|
date | Fri, 04 May 2018 02:24:47 -0400 |
parents | fd3ea97a96bc |
children |
line wrap: on
line source
<tool id="filter_bam" name="Filter bam files" version="0.1.0"> <description> Filters bam files for reads in regions of interest.</description> <requirements> <requirement type="package" version="1.3">samtools</requirement> <requirement type="package" version="2.27.0.0">bedtools</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ #set input_name = str( $input1.name ) $__tool_directory__/./filter_bam.bash "$input1" "$input2" "$input3" "$output1" "$output2" "$output3" "$input_name" ]]></command> <inputs> <param type="data" name="input1" format="bam" label="Bam File"/> <param type="data" name="input2" format="bed" label="Peak Bed File"/> <param type="data" name="input3" format="tabular" label="chrom.sizes"/> </inputs> <outputs> <data name="output1" format="bed" label="Extended Peak File"/> <data name="output2" format="bam" label="Filtered Bam File"/> <data name="output3" format="tabular" label="Read Counts" /> </outputs> <tests> <test> <param name="input1" value="test.bam"/> <param name="input2" value="test.bed"/> <param name="input3" value="mm9.chrom.sizes.txt"/> <output name="output1" file="ext_peak"/> <output name="output2" file="test.filter.bam"/> <output name="output3" file="test.readcounts.txt"/> </test> </tests> <help><![CDATA[ This tools takes a bam file and filters to reads mapping to regions specified by input bed file. Outputs include filtered bam file and count of total numbers of reads in original bam file. ]]></help> <citations> <citation type="doi">doi:10.1038/nmeth.4663</citation> </citations> </tool>