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<?xml version="1.0"?>
<tool id="shear_sv" name="SHEAR-SV" version="0.0.1">
  <description>find SVs and estimate the heterogeneity levels from a BAM</description>
  <requirements>
    <requirement type="package" version="0.1.2">shear</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="0.6.2">bwa</requirement>
    <requirement type="package" version="1.0.1">crest</requirement>
    <requirement type="package" version="latest">kent</requirement>
  </requirements>
  <!--
  <version_command></version_command>
  -->
  <command>java -jar  \$SHEAR_JAR_PATH/SHEAR.jar sv -r $prefix 
     -b $bamfile 
     #if $genomeSource.refGenomeSource == 'indexed':
       -f $genomeSource.ref_fastas.fields.path 
       -i $genomeSource.bwa_indices.fields.path 
       -t $genomeSource.twobit_indice.fields.paths
     #else:
       -f $genomeSource.ref_fasta
       -i $genomeSource.bwa_index
       -t $genomeSource.twobit
     #end if
  </command>
  <inputs>
    <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> 
    <!-- reference data -->
    <conditional name="genomeSource">
      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
        <option value="indexed" selected="true">Use a cached reference genome</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="ref_fastas" type="select" label="Select a reference genome">
          <options from_data_table="all_fasta">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No reference fasta files are available" />
          </options>
        </param>
        <param name="twobit_indices" type="select" label="Select a reference genome">
          <options from_data_table="twobit">
            <filter type="sort_by" column="0" />
            <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
        <param name="bwa_indices" type="select" label="Select a reference genome">
          <options from_data_table="bwa_indexes">
            <filter type="sort_by" column="2" />
            <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
        <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" />
        <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>
    <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
  </inputs>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error" />
  </stdio>
  <outputs>
    <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: shear_sv.sdi" from_work_dir="shear_sv.sdi" />
    <data format="txt" name="report" label="${tool.name} on ${on_string}: shear_sv.report" from_work_dir="shear_sv.report"/>
  </outputs>
  <tests>
    <test>
      <param name="bamfile" ftype="bam" value="simulated-data.bam"/>
      <param name="refGenomeSource" value="history"/>
      <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
      <param name="bwa_index" ftype="" value="syn.fa"/>
      <param name="twobit" ftype="twobit" value="syn.2bit"/>
      <output name="shear.sdi"  file="shear_sv.sdi"/>
      <output name="report"  file="shear_sv.report"/>
    </test>
  </tests>
  <help>
SHEAR-SV will process a BAM alignment file to find SVs and estimate the
heterogeneity level of those SVs. It will output a *.report file reporing the
SVs and their heterogeneity levels, and it will output a *.sdi file that can be
used for SHEAR-Assemble to reconstruct the new genome.
  </help>
</tool>