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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="vardictjava" name="VarDictJava" version="1.4.6">
    <description>
        calls SNVs and indels for tumour-normal pairs.
    </description>

    <requirements>
        <requirement type="package" version="5.18.1">perl</requirement>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="1.4.6">vardictjava</requirement>
        <requirement type="set_environment">VARDICTJAVA_ROOT_DIR</requirement>
    </requirements>

    <command detect_errors="aggressive"><![CDATA[
        ## LINK BAM INDEX
        ln -s $normal ./normal.bam;
        ln -s $normal.metadata.bam_index ./normal.bam.bai;
        ln -s $tumour tumor.bam;
        ln -s $tumour.metadata.bam_index ./tumor.bam.bai;

        ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
        #if $reference_source.reference_source_selector == "history":
            ln -s $reference_source.ref_file ref.fa;
            samtools faidx ref.fa;
        #else if $reference_source.reference_source_selector == "cached"
            ln -s $reference_source.ref_file.fields.path ref.fa; 
            ln -s ${reference_source.ref_file.fields.path}.fai ref.fa.fai; 
        #end if

        ## BUILD BED FILE FROM CHROMOSOME LIST
        #if $interval_file:
            grep -w -f $interval_file ref.fa.fai > chromosomes.fa.fai; 
        #else
            ln -s ref.fa.fai chromosomes.fa.fai; 
        #end if
        awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' chromosomes.fa.fai > regions.bed; 

        ## BUILD VARDICT COMMAND
        \$VARDICTJAVA_ROOT_DIR/build/install/VarDict/bin/VarDict
        -b "./tumor.bam|./normal.bam"
        -G ref.fa
        -z
        -th \${GALAXY_SLOTS:-1}

        ## ADVANCED OPTIONS
        -f $advancedsettings.f
        -k $advancedsettings.k
        -r $advancedsettings.r
        -B $advancedsettings.B
        -Q $advancedsettings.Q
        -q $advancedsettings.q
        -m $advancedsettings.m
        -T $advancedsettings.T
        -X $advancedsettings.X
        -P $advancedsettings.P
        -o $advancedsettings.o
        -O $advancedsettings.O
        -V $advancedsettings.V

        ## CONSTRUCT VCF TABLE
        -c 1 -S 2 -E 3 -g 4

        ## REGION SPECIFICATION (ENTIRE CHROMOSOMES)
        regions.bed

        ## POSTPROCESSING
        | \$VARDICTJAVA_ROOT_DIR/VarDict/testsomatic.R 
        | \$VARDICTJAVA_ROOT_DIR/VarDict/var2vcf_somatic.pl 
        -f $advancedsettings.f 

        > $all_variants;

        ## Filter for PASS variants
        awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' $all_variants > $passed_variants
    ]]></command>

    <inputs>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file">
                <option value="cached" selected="True">Use a built-in genome</option>
                <option value="history">Use a genome from the history</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Reference Genome File">
                    <options from_data_table="fasta_indexes"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" format="fasta" type="data" label="Reference Genome File" />
            </when>
        </conditional>

        <param name="normal" type="data" format="bam" label="Normal Alignment File" />
        <param name="tumour" type="data" format="bam" label="Tumour Alignment File" />
        <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />

        <section name="advancedsettings" title="Advanced Settings" expanded="False">
            <param name="f" type="float" value="0.01" label="Minimum variant allele fraction" />
            <param name="k" type="integer" value="1" label="Set to 0 to disable local realignment" />
            <param name="r" type="integer" value="2" label="Minimum number of reads supporting the variant" />
            <param name="B" type="integer" value="2" label="Minimum number of reads for determining strand bias" />
            <param name="Q" type="integer" value="1" label="Minimum mapping quality for reads to be considered" />
            <param name="m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" />
            <param name="T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" />
            <param name="X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />
            <param name="P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />
            <param name="q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />
            <param name="o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />
            <param name="O" type="float" value="0" label="Minimum average mapping quality" />
            <param name="V" type="float" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />
        </section>
    </inputs>

    <outputs>
        <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />
        <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />
    </outputs>

    <help>
        <![CDATA[
        https://github.com/AstraZeneca-NGS/VarDictJava
        ]]>
    </help>

    <citations>
        <expand macro="morinlab_citation" />
        <expand macro="galaxy_citation" />
        <expand macro="vardict_citation" />
    </citations>
</tool>