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1 <?xml version="1.0"?>
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2
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3 <tool id="poor_gene_coverage" name="Report Poor Coverage">
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4 <description>regions for a set of genes</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">annotate_low_coverage $__tool_data_path__ ${captureKitRegions} $poorCaptureRegions $outputTable
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7 #if $targetGenes.dataset and str($targetGenes) > '':
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8 $targetGenes
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9 #else:
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10 /dev/null
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11 #end if
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12 NM_
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13 </command>
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14 <inputs>
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15 <param name="sampleName" type="text" label="Biological sample name" help="Will be used to name the output files"/>
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16 <param name="captureKitRegions" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
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17 <param format="bed" name="poorCaptureRegions" type="data" label="BED file of low coverage regions"/>
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18 <param format="text" name="targetGenes" type="data" optional="true" label="List of genes to report, one per line"/>
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" name="outputTable"/>
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22 </outputs>
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23
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24 <!-- the following code populates the selection from the public capture kit BED datasets available in the local Galaxy installation -->
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25 <code file="capture_kits.py"/>
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26 <tests/>
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27
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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>
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29
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30 </tool>
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