Mercurial > repos > jbrayet > samtools_1_2_docker
changeset 3:695b40cab89b draft
Uploaded
author | jbrayet |
---|---|
date | Wed, 25 Nov 2015 03:21:58 -0500 |
parents | fb7fc6b2e74c |
children | 8be7fb96589d |
files | samtools_bedcov.xml |
diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_bedcov.xml Wed Nov 25 03:21:58 2015 -0500 @@ -0,0 +1,57 @@ +<tool id="samtools_bedcov" name="BedCov" version="2.0"> + <description>calculate read depth for a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command><![CDATA[ + for bamfile in + #for dataset in $input_bams: + "${dataset}" + #end for + ; do + if [ ! -f \$bamfile.bai ] ; then + ln -s \$bamfile && samtools index `basename \$bamfile` ; + else + ln -s \$bamfile && ln -s \$bamfile.bai ; + fi ; + done ; + samtools bedcov "${input_bed}" + #for dataset in $input_bams: + `basename "${dataset}"` + #end for + > "${output}" + ]]> + </command> + <inputs> + <param name="input_bed" type="data" format="bed" label="BED file" /> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out1.tab" /> + </test> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out2.tab" /> + </test> + </tests> + <help> +**What it does** + +Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command:: + + samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT] + + </help> + <expand macro="citations"></expand> +</tool> +