Mercurial > repos > artbio > sambamba
comparison sambamba.xml @ 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 |
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| 2:7ad3484aa5db | 3:de833cc76a8e |
|---|---|
| 1 <tool id="sambamba_sample_or_filter" name="Sample or Filter BAM" version="0.7.1+galaxy0"> | 1 <tool id="sambamba_sample_or_filter" name="Sample, Slice or Filter BAM" version="0.7.1+galaxy1"> |
| 2 <description> | 2 <description> |
| 3 on flags, fields, and tags using Sambamba | 3 on flags, fields, and tags using Sambamba |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="0.7.1">sambamba</requirement> | 6 <requirement type="package" version="0.7.1">sambamba</requirement> |
| 24 #else if $sambamba_options.selector == 'sample' | 24 #else if $sambamba_options.selector == 'sample' |
| 25 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format' | 25 sambamba view -h -t \${GALAXY_SLOTS:-4} -f '$sambamba_options.format' |
| 26 --subsampling-seed='$sambamba_options.seed' | 26 --subsampling-seed='$sambamba_options.seed' |
| 27 -s '$sambamba_options.fraction' | 27 -s '$sambamba_options.fraction' |
| 28 -o '$outfile' input.bam | 28 -o '$outfile' input.bam |
| 29 | 29 #end if |
| 30 #else | 30 |
| 31 sambamba slice -o '$outfile' input.bam $sambamba_options.region | 31 #if $sambamba_options.selector == 'slice' |
| 32 #if $sambamba_options.slice.slice_format == 'text' | |
| 33 sambamba slice -o '$outfile' input.bam $sambamba_options.slice.region | |
| 34 #else | |
| 35 sambamba slice --regions $sambamba_options.slice.bed_file -o '$outfile' input.bam | |
| 36 #end if | |
| 32 #end if | 37 #end if |
| 33 ]]></command> | 38 ]]></command> |
| 34 <inputs> | 39 <inputs> |
| 35 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/> | 40 <param name="input" type="data" format="bam" label="BAM or SAM input file(s)"/> |
| 36 <conditional name="sambamba_options"> | 41 <conditional name="sambamba_options"> |
| 62 </help> | 67 </help> |
| 63 </param> | 68 </param> |
| 64 </when> | 69 </when> |
| 65 | 70 |
| 66 <when value="slice"> | 71 <when value="slice"> |
| 67 <param name="region" type="text" size="40" label="Region in format chr:beg-end"> | 72 <conditional name="slice"> |
| 68 <help> | 73 <param name="slice_format" type="select" label="specify in text field or a bed file"> |
| 69 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' | 74 <option value="text">Specify in the region field</option> |
| 70 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' | 75 <option value="bed" selected="true">BED file</option> |
| 71 (region between 1,000,000 and 2,000,000bp including the end points). | 76 </param> |
| 72 The coordinates are 1-based. NOTE that sambamba slice only outputs | 77 <when value="bed"> |
| 73 BAM-format datasets. | 78 <param name="bed_file" type="data" format="bed" label="BED file" |
| 74 </help> | 79 help="The coordinates are 0-based. NOTE that sambamba slice only outputs BAM-format datasets."/> |
| 75 </param> | 80 </when> |
| 81 <when value="text"> | |
| 82 <param name="region" type="text" size="40" label="Region(s) in space-separated format chr:start-end"> | |
| 83 <help> | |
| 84 Regions can be specified as 'chr2' (the whole chr2), 'chr2:1000000' | |
| 85 (region starting from 1,000,000bp) or 'chr2:1,000,000-2,000,000' | |
| 86 (region between 1,000,000 and 2,000,000bp including the end points). | |
| 87 The coordinates are 1-based. NOTE that sambamba slice only outputs | |
| 88 BAM-format datasets. | |
| 89 </help> | |
| 90 </param> | |
| 91 </when> | |
| 92 </conditional> | |
| 76 </when> | 93 </when> |
| 77 | 94 |
| 78 <when value="sample"> | 95 <when value="sample"> |
| 79 <param name="format" type="select" label="format of the tool output"> | 96 <param name="format" type="select" label="format of the tool output"> |
| 80 <option value="bam">BAM</option> | 97 <option value="bam">BAM</option> |
| 129 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/> | 146 <output name="outfile" file="c1215_fixmate_region-filtered.sam" ftype="sam" lines_diff="2"/> |
| 130 </test> | 147 </test> |
| 131 <test> | 148 <test> |
| 132 <param name="input" value="c1215_fixmate.bam" ftype="bam" /> | 149 <param name="input" value="c1215_fixmate.bam" ftype="bam" /> |
| 133 <param name="selector" value="slice" /> | 150 <param name="selector" value="slice" /> |
| 151 <param name="slice_format" value="text" /> | |
| 134 <param name="query" value='' /> | 152 <param name="query" value='' /> |
| 135 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" /> | 153 <param name="region" value="AL096846:1000-2000 AL096846:4000-5000" /> |
| 154 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> | |
| 155 </test> | |
| 156 <test> | |
| 157 <param name="input" value="c1215_fixmate.bam" ftype="bam" /> | |
| 158 <param name="selector" value="slice" /> | |
| 159 <param name="slice_format" value="bed" /> | |
| 160 <param name="query" value='' /> | |
| 161 <param name="bed_file" value="regions.bed" /> | |
| 136 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> | 162 <output name="outfile" file="c1215_fixmate_region-sliced.bam" ftype="bam"/> |
| 137 </test> | 163 </test> |
| 138 <test> | 164 <test> |
| 139 <param name="input" value="ex1_header.sam" ftype="sam" /> | 165 <param name="input" value="ex1_header.sam" ftype="sam" /> |
| 140 <param name="selector" value="sample" /> | 166 <param name="selector" value="sample" /> |