<?xml version="1.0"?>

<tool id="poor_gene_coverage" name="Report Poor Coverage">
  <description>regions for a set of genes</description>
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">annotate_low_coverage $__tool_data_path__  ${captureKitRegions} $poorCaptureRegions $outputTable 
     #if $targetGenes.dataset and str($targetGenes) > '':
       $targetGenes 
     #else:
       /dev/null
     #end if
     NM_
  </command>
  <inputs>
    <param name="sampleName" type="text" label="Biological sample name" help="Will be used to name the output files"/>
    <param name="captureKitRegions" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
    <param format="bed" name="poorCaptureRegions" type="data" label="BED file of low coverage regions"/>
    <param format="text" name="targetGenes" type="data" optional="true" label="List of genes to report, one per line"/>
  </inputs>
  <outputs>
    <data format="tabular" name="outputTable"/>
  </outputs>

  <!-- the following code populates the  selection from the public capture kit BED datasets available in the local Galaxy installation -->
  <code file="capture_kits.py"/>
  <tests/>

  <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>

</tool>