Mercurial > repos > artbio > sambamba
changeset 3:de833cc76a8e draft default tip
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit 1b6bff4ab8aaac8a247f603648f63bbadb02e1fe"
| author | artbio |
|---|---|
| date | Thu, 30 Dec 2021 17:44:31 +0000 |
| parents | 7ad3484aa5db |
| children | |
| files | sambamba.xml test-data/regions.bed |
| diffstat | 2 files changed, 40 insertions(+), 12 deletions(-) [+] |
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--- a/sambamba.xml Thu Dec 30 02:06:08 2021 +0000 +++ b/sambamba.xml Thu Dec 30 17:44:31 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0"> +<tool id="sambamba_sample_or_filter" name="Sample, Slice or Filter BAM" version="0.7.1+galaxy1"> <description> on flags, fields, and tags using Sambamba </description> @@ -26,9 +26,14 @@ --subsampling-seed='$sambamba_options.seed' -s '$sambamba_options.fraction' -o '$outfile' input.bam + #end if - #else - sambamba slice -o '$outfile' input.bam $sambamba_options.region + #if $sambamba_options.selector == 'slice' + #if $sambamba_options.slice.slice_format == 'text' + sambamba slice -o '$outfile' input.bam $sambamba_options.slice.region + #else + sambamba slice --regions $sambamba_options.slice.bed_file -o '$outfile' input.bam + #end if #end if ]]></command> <inputs> @@ -64,15 +69,27 @@ </when> <when value="slice"> - <param name="region" type="text" size="40" label="Region in format chr:beg-end"> - <help> - Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' - (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' - (region between 1,000,000 and 2,000,000bp including the end points). - The coordinates are 1-based. NOTE that sambamba slice only outputs - BAM-format datasets. - </help> - </param> + <conditional name="slice"> + <param name="slice_format" type="select" label="specify in text field or a bed file"> + <option value="text">Specify in the region field</option> + <option value="bed" selected="true">BED file</option> + </param> + <when value="bed"> + <param name="bed_file" type="data" format="bed" label="BED file" + help="The coordinates are 0-based. NOTE that sambamba slice only outputs BAM-format datasets."/> + </when> + <when value="text"> + <param name="region" type="text" size="40" label="Region(s) in space-separated format chr:start-end"> + <help> + Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' + (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' + (region between 1,000,000 and 2,000,000bp including the end points). + The coordinates are 1-based. NOTE that sambamba slice only outputs + BAM-format datasets. + </help> + </param> + </when> + </conditional> </when> <when value="sample"> @@ -131,10 +148,19 @@ <test> <param name="input" value="c1215_fixmate.bam" ftype="bam" /> <param name="selector" value="slice" /> + <param name="slice_format" value="text" /> <param name="query" value='' /> <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" /> <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> </test> + <test> + <param name="input" value="c1215_fixmate.bam" ftype="bam" /> + <param name="selector" value="slice" /> + <param name="slice_format" value="bed" /> + <param name="query" value='' /> + <param name="bed_file" value="regions.bed" /> + <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> + </test> <test> <param name="input" value="ex1_header.sam" ftype="sam" /> <param name="selector" value="sample" />