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<tool id="strelka" name="Strelka" version="1.0.14">
    <description>
        detects somatic SNVs and small indels in tumour/normal pairs
    </description>
    <macros>
        <import>citations.xml</import>
    </macros>    
    <requirements>
<requirement type="package" version="1.0.14">strelka</requirement>
    </requirements>
    <command detect_errors="aggressive">

    ln -s $normal normal.bam;
    ln -s $normal.metadata.bam_index normal.bam.bai;
    ln -s $tumour tumour.bam;
    ln -s $tumour.metadata.bam_index tumour.bam.bai;
    
    touch config.ini;
    echo "[user]" > config.ini;
    #if $depthfilters.seqType == "genome":
       echo "isSkipDepthFilters = 0" >> config.ini;
       echo "maxInputDepth = 10000" >> config.ini;
       echo "depthFilterMultiple = 3.0" >> config.ini;
    #elif $depthfilters.seqType == "exome":
       echo "isSkipDepthFilters = 1" >> config.ini;
       echo "maxInputDepth = 10000" >> config.ini;
       echo "depthFilterMultiple = 3.0" >> config.ini;
    #elif $depthfilters.seqType == "targeted":
       echo "isSkipDepthFilters = 1" >> config.ini;
       echo "maxInputDepth = 10000" >> config.ini;
       echo "depthFilterMultiple = 3.0" >> config.ini;
    #else:
       echo "isSkipDepthFilters = " $depthfilters.isSkipDepthFilters >> config.ini;
       echo "maxInputDepth = " $depthfilters.maxInputDepth >> config.ini;
       echo "depthFilterMultiple = " $depthfilters.depthFilterMultiple >> config.ini;
    #end if

    echo "snvMaxFilteredBasecallFrac = " $advancedsettings.snvMaxFilteredBasecallFrac >> config.ini;
    echo "snvMaxSpanningDeletionFrac = " $advancedsettings.snvMaxSpanningDeletionFrac >> config.ini;
    echo "indelMaxRefRepeat = " $advancedsettings.indelMaxRefRepeat >> config.ini;
    echo "indelMaxWindowFilteredBasecallFrac = " $advancedsettings.indelMaxWindowFilteredBasecallFrac >> config.ini;
    echo "indelMaxIntHpolLength = " $advancedsettings.indelMaxIntHpolLength >> config.ini;
    echo "ssnvPrior = " $advancedsettings.ssnvPrior >> config.ini;
    echo "sindelPrior = " $advancedsettings.sindelPrior >> config.ini;
    echo "ssnvNoise = " $advancedsettings.ssnvNoise >> config.ini;
    echo "sindelNoise = " $advancedsettings.sindelNoise >> config.ini;
    echo "ssnvNoiseStrandBiasFrac = " $advancedsettings.ssnvNoiseStrandBiasFrac >> config.ini;
    echo "minTier1Mapq = " $advancedsettings.minTier1Mapq >> config.ini;
    echo "minTier2Mapq = " $advancedsettings.minTier2Mapq >> config.ini;
    echo "ssnvQuality_LowerBound = " $advancedsettings.ssnvQuality_LowerBound >> config.ini;
    echo "sindelQuality_LowerBound = " $advancedsettings.sindelQuality_LowerBound >> config.ini;
    echo "isWriteRealignedBam = 0" >> config.ini;
    echo "binSize = 25000000" >> config.ini;
    echo "extraStrelkaArguments = " >> config.ini;

    cat config.ini > $config;

    #if $reference_source.reference_source_selector == "history":
        ln -s $reference_source.ref_file ref.fa;
        samtools faidx ref.fa;
    #end if

    \${STRELKA_INSTALL_DIR}/bin/configureStrelkaWorkflow.pl
    --normal \$(pwd)/normal.bam
    --tumor \$(pwd)/tumour.bam
    
    #if $reference_source.reference_source_selector == "history":
        --ref \$(pwd)/ref.fa
    #else:
        --ref ${reference_source.ref_file.fields.path}
    #end if
    
    --config \$(pwd)/config.ini;

    #if $interval_file
      
      cp ./strelkaAnalysis/Makefile ./;
   
      for int in \$( cat $interval_file ); do
        
        python $__tool_directory__/parse_strelka_makefile.py 
        --makefile Makefile
        --chrom \$int
        --output ./strelkaAnalysis/Makefile;

    #end if

    cd strelkaAnalysis;
    make -j \${GALAXY_SLOTS:-1};
    cd ../;

    #if $interval_file

        cat ./strelkaAnalysis/chromosomes/\$int/somatic.snvs.vcf | grep -v "^#.*" >> $snvs;
        cat ./strelkaAnalysis/chromosomes/\$int/somatic.indels.vcf | grep -v "^#.*" >> $indels;
        
        done;
        
    #else

        cat ./strelkaAnalysis/results/passed.somatic.snvs.vcf > $snvs;
        cat ./strelkaAnalysis/results/padded.somatic.indels.vcf > $indels; 

    #end if

    </command>
    <inputs>
<conditional name="reference_source">
            <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <param label="Genome" name="ref_file" type="select">
                    <options from_data_table="fasta_indexes"/>
                </param>
            </when>
            <when value="history">
                <param label="Genome" name="ref_file" type="data" format="fasta"/>
            </when>
        </conditional>
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
        <param type="data" format="txt" optional="true" name="interval_file" label="Inteval file" help="Created by make parallel, only use when parallelism is turned on"/>
        <conditional name="depthfilters">
            <param type="select" name="seqType" label="What Type of Sequencing?">
                <option value="genome" selected="true">Whole Genome</option>
                <option value="exome">Exome</option>
                <option value="targeted">Targeted</option>
                <option value="other">What are you hiding from me?</option>
            </param>
            <when value="other">
                <param name="isSkipDepthFilters" type="boolean" label="Skip Reads Above Depth Threshold?" help="Should we skip reads if they exist above the chromosome average depth multiplied by the Depth Filter Multiple? Should only be true for Whole Genome Sequencing." checked="true" truevalue="0" falsevalue="1"/>
                <param name="depthFilterMultiple" type="float" label="Depth Filter Multiple" value="3.0"/>
                <param name="maxInputDepth" type="integer" label="Max Input Depth" value="10000" help="The upper bound on input depth to load into memory. This filter should not occur with Deep Targeted Sequencing but should occur with Exome or Whole Genome Sequencing. Set to 0 to turn off" min="0"/>
            </when>
        </conditional>
        <section name="advancedsettings" title="Advanced Settings" expanded="false">
            <param type="float"   name="snvMaxFilteredBasecallFrac"         value="0.4"       label="SNV Max Filtered Basecall Fraction" help="Filter SNV calls when greater than this fraction of basecalls have been removed by a mismatch density filter in either sample."/> 
            <param type="float"   name="snvMaxSpanningDeletionFrac"         value="0.75"      label="SNV Max Spanning Deletion Fraction" help="Filter SNV calls at sites where greater than this fraction of overlapping reads contain deletions which span the SNV call site."/>
            <param type="integer" name="indelMaxRefRepeat"                  value="8"         label="Indel Max Reference Homopolymer Length" help="Filter Indel calls if they represent an expansion or contraction of a repeated pattern with a repeat count greater than this value in the reference."/>
            <param type="float"   name="indelMaxWindowFilteredBasecallFrac" value="0.3"       label="Indel Max Window Filtered Basecall Fraction" help="Filter Indel calls if greater than this fraction of basecalls in a window extending 50 bases to each side of the indel's call positions have been removed by the mismatch density filter."/>
            <param type="integer" name="indelMaxIntHpolLength"              value="14"        label="Indel Max Interrupted Homopolymers Length" help="Filter Indel calls if the longest homopolymer which can be found intersecting or adjacent to the called indel when a single non-homopolymer base is allowed is greater than this length."/>
            <param type="float"   name="ssnvPrior"                          value="0.000001"  label="SNV Prior Probability"/>
            <param type="float"   name="sindelPrior"                        value="0.000001"  label="Indel Prior Probability"/>
            <param type="float"   name="ssnvNoise"                          value="0.0000005" label="SNV Noise Probability"/>
            <param type="float"   name="sindelNoise"                        value="0.000001"  label="Indel Noise Probability"/>
            <param type="float"   name="ssnvNoiseStrandBiasFrac"            value="0.5"       label="SNV Noise Fraction Attributed to Strand Bias"/>
            <param type="integer" name="minTier1Mapq"                       value="20"        label="Min Tier1 Mapping Quality"/>
            <param type="integer" name="minTier2Mapq"                       value="5"         label="Min Tier2 Mapping Quality"/>
            <param type="integer" name="ssnvQuality_LowerBound"             value="15"        label="SNV Quality Score Lower Bound"/>
            <param type="integer" name="sindelQuality_LowerBound"           value="30"        label="Indel Quality Score Lower Bound"/>
        </section>
    </inputs>
    <outputs>
        <data format="vcf" name="snvs"/>
        <data format="vcf" name="indels"/>
        <data format="txt" name="config" />
    </outputs>
    <tests>
        <test>
            <param name="normal" value="test.normal.bam"/>
            <param name="normal.metadata.bam_index" value="test.normal.bam.bai"/>
          <param name="tumour" value="test.tumour.bam"/>
          <param name="tumour.metadata.bam_index" value="test.tumour.bam.bai"/>
            <param name="reference_source.reference_source_selector" value="history"/>
            <param name="reference_source.ref_file" value="test.fa"/>
            <output name="snvs" ftype="vcf" file="all.somatic.snvs.vcf" lines_diff="2"/>
        </test>
    </tests>
    <help>

This tool generates VCF files by calling Strelka, a Somatic Nucleotide Variant Caller, on Tumour Normal Pairs.

    </help>    
    <citations>
        <expand macro="morinlab_citation"/>
        <expand macro="galaxy_citation"/>
        <expand macro="strelka_citation"/>
    </citations>
</tool>