Mercurial > repos > artbio > sambamba
diff sambamba.xml @ 2:7ad3484aa5db draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba commit ea1ce99d707fcf2d64f6f2cd96fdd1754f344df1"
author | artbio |
---|---|
date | Thu, 30 Dec 2021 02:06:08 +0000 |
parents | 6195f15d4541 |
children | de833cc76a8e |
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--- a/sambamba.xml Mon May 25 17:10:17 2020 -0400 +++ b/sambamba.xml Thu Dec 30 02:06:08 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.6"> +<tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0"> <description> on flags, fields, and tags using Sambamba </description> @@ -12,30 +12,38 @@ <command detect_errors="exit_code"><![CDATA[ ln -s $input input.bam && ln -s $input.metadata.bam_index input.bai && + #if $sambamba_options.selector == 'filter' sambamba view -h -t \${GALAXY_SLOTS:-4} #if $sambamba_options.query != '': --filter='$sambamba_options.query' #end if - -f '$format' -o $outfile input.bam $sambamba_options.region - #else - sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$format' - --subsampling-seed='$sambamba_options.seed' - -s '$sambamba_options.fraction' -o '$outfile' input.bam - #end if + -f '$sambamba_options.format' + -o $outfile input.bam $sambamba_options.region + + #else if $sambamba_options.selector == 'sample' + sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format' + --subsampling-seed='$sambamba_options.seed' + -s '$sambamba_options.fraction' + -o '$outfile' input.bam + + #else + sambamba slice -o '$outfile' input.bam $sambamba_options.region + #end if ]]></command> <inputs> - <param name="input" type="data" format="bam" label="BAM or SAM file to filter"/> - <param name="format" type="select" label="format of the tool output"> - <option value="bam">BAM</option> - <option value="sam">SAM</option> - </param> + <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/> <conditional name="sambamba_options"> - <param name="selector" type="select" label="Filter or Down-sample alignments"> + <param name="selector" type="select" label="Filter, Down-sample or slice alignments"> <option value="sample">Down-sample bam or sam alignments</option> <option value="filter" selected="true">Filter bam or sam alignements</option> + <option value="slice">Slice bam or sam alignements by chromosome or chromosome region</option> </param> <when value="filter"> + <param name="format" type="select" label="format of the tool output"> + <option value="bam">BAM</option> + <option value="sam">SAM</option> + </param> <param name="query" type="text" size="80"> <sanitizer invalid_char="X"> <valid initial="string.ascii_letters,string.digits, string.punctuation"> @@ -54,7 +62,24 @@ </help> </param> </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> + </when> + <when value="sample"> + <param name="format" type="select" label="format of the tool output"> + <option value="bam">BAM</option> + <option value="sam">SAM</option> + </param> <param name="seed" type="integer" value="123" size="10"> <label>Seed value for randomisation</label> <help> @@ -72,9 +97,9 @@ </conditional> </inputs> <outputs> - <data name="outfile" format="bam"> + <data name="outfile" format="bam" label="Filter, slice or sample on ${on_string}"> <change_format> - <when input="format" value="sam" format="sam" /> + <when input="sambamba_options['format']" value="sam" format="sam" /> </change_format> </data> </outputs> @@ -85,7 +110,7 @@ <param name="query" value="[H0] == 1 and read_name =~ /^EAS51_62/" /> <param name="format" value="bam" /> <param name="region" value="" /> - <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" /> + <output name="outfile" file="ex1_header_filtered.bam" ftype="bam" lines_diff="2"/> </test> <test> <param name="input" value="c1215_fixmate.bam" ftype="bam" /> @@ -103,13 +128,20 @@ <param name="region" value="AL096846:1000-5000" /> <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/> </test> + <test> + <param name="input" value="c1215_fixmate.bam" ftype="bam" /> + <param name="selector" value="slice" /> + <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="ex1_header.sam" ftype="sam" /> <param name="selector" value="sample" /> <param name="seed" value="123" /> <param name="fraction" value="0.1" /> <param name="format" value="bam" /> - <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" /> + <output name="outfile" file="ex1_header_sampled.bam" ftype="bam" lines_diff="2"/> </test> <test> <param name="input" value="c1215_fixmate.bam" ftype="bam" />