<?xml version="1.0"?>

<tool id="depth_reports_1" name="Compute depth of sequencing coverage">
  <description>over targeted regions in a genome</description>
  <version_string>depth_reports -v</version_string>
  <command interpreter="perl">depth_reports $__tool_data_path__ -q $input_bam ${target_bed}.bed $out_summary_table $out_poor_coverage_bed $out_depth_graph $out_depth_table $out_mapped_percentile_table $dud_bed</command>
  <inputs>
    <param format="bam" name="input_bam" type="data" label="Mapped alignment file"/>
    <param name="target_bed" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
    <param format="bed" name="dud_bed" type="data" label="Targeted regions to ignore (known duds)" optional="true" default="/dev/null"/>
  </inputs>
  <outputs>
    <data name="out_summary_table" format="achri_depth_summary_table" label="Depth of coverage summary (mean, median, etc.)"/>
    <data name="out_poor_coverage_bed" format="bed" label="Low coverage targeted regions"/>
    <data name="out_depth_graph" format="png" label="Cumulative depth of coverage graph"/>
    <data name="out_depth_table" format="tabular" label="Number of bases at each depth of coverage"/>
    <data name="out_mapped_percentile_table" format="tabular" label="Mapped read depth percentiles"/>
  </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>
    <test>
     <param name="input_bam" value="depth_test.bam" ftype="bam"/>
     <param name="target_bed" value="brcas.bed" ftype="bed"/>
     <output name="out_summary_table">
       <assert_contents>
         <has_text text="targeted nucleotide bases: 155091"/>
         <has_text text="bases mapped to targeted regions: 11473773"/>
         <has_text text="bases with less than 20-fold coverage: 19046"/>
       </assert_contents>
     </output>
     <output name="out_depth_graph" ftype="png"/>
    </test>
  </tests>

  <help>
This tool reports several statistics describing the depth of coverage of a next-gen sequencing run over its targeted reference genome. 
These results can be used to assess the quality of the sequencing for SNP calls, etc.
  </help>

</tool>