Mercurial > repos > yusuf > poor_gene_coverage
comparison PoorGeneCoverage.xml @ 0:7cdd13ff182a default tip
initial commit
| author | Yusuf Ali <ali@yusuf.email> |
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| date | Wed, 25 Mar 2015 15:49:28 -0600 |
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| -1:000000000000 | 0:7cdd13ff182a |
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| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id="poor_gene_coverage" name="Report Poor Coverage"> | |
| 4 <description>regions for a set of genes</description> | |
| 5 <version_string>echo 1.0.0</version_string> | |
| 6 <command interpreter="perl">annotate_low_coverage $__tool_data_path__ ${captureKitRegions} $poorCaptureRegions $outputTable | |
| 7 #if $targetGenes.dataset and str($targetGenes) > '': | |
| 8 $targetGenes | |
| 9 #else: | |
| 10 /dev/null | |
| 11 #end if | |
| 12 NM_ | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="sampleName" type="text" label="Biological sample name" help="Will be used to name the output files"/> | |
| 16 <param name="captureKitRegions" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/> | |
| 17 <param format="bed" name="poorCaptureRegions" type="data" label="BED file of low coverage regions"/> | |
| 18 <param format="text" name="targetGenes" type="data" optional="true" label="List of genes to report, one per line"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="tabular" name="outputTable"/> | |
| 22 </outputs> | |
| 23 | |
| 24 <!-- the following code populates the selection from the public capture kit BED datasets available in the local Galaxy installation --> | |
| 25 <code file="capture_kits.py"/> | |
| 26 <tests/> | |
| 27 | |
| 28 <help>This tools summarized low coverage regions on a per gene basis, including information on clinically relevant variants (according to ClinVar) that might have been missed</help> | |
| 29 | |
| 30 </tool> |