Mercurial > repos > kyost > atac_primer_tool
diff filter_bam.xml @ 0:fd3ea97a96bc draft
planemo upload commit 103cb51ec368438642504c3f98b76c363db478bb
| author | kyost |
|---|---|
| date | Sat, 28 Apr 2018 15:07:26 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_bam.xml Sat Apr 28 15:07:26 2018 -0400 @@ -0,0 +1,40 @@ +<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>