<?xml version="1.0"?>

<tool id="call_miseq_vars" name="Call miSeq variants">
  <description>using a BAM file</description>
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">call_miseq_variants $__tool_data_path__ geno . $inputBAM ${targetBED}.bed ${ref_genome}.bed ${ref_genome}.fa 12</command>
  <inputs>
    <param format="bam" name="inputBAM" type="data" label="Source BAM (mapped and realigned reads) file"/>
    <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were aligned"/>
    <param name="targetBED" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
  </inputs>
  <outputs>
    <data format="achri_snp_table" label="Confident genotypes" name="confident_genotypes" from_work_dir="geno.combined.collapsed.confident.hgvs.txt"/>
    <data format="achri_snp_table" label="Marginal genotypes" name="marginal_genotypes" from_work_dir="geno.combined.collapsed.marginal.hgvs.txt"/>
    <data format="text" label="Genotyping log" name="genotyping log" from_work_dir="geno.call_variants.log.txt"/>
  </outputs>

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

  <help>
This tool runs a BAM file against multiple genotypers (FreeBayes 0.8.7, GATKHaplotypeCaller 3.1) and generates a consensus (confident) table of variant calls, 
including caveats about haplotype phase inconsistencies and other potential false positive indicators.
 </help>

</tool>