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<tool id="vcf2maf" name="vcf2maf" version="1.0.0">
    <description>Converts VCF files into MAF format</description>

    <command>
         echo \$(which perl)
        echo \$VCF2MAF_SCRIPT_PATH;
        echo \$ENSEMBL_VEP_84_INSTALL_DIR;
        ln -s $input_vcf ./input.vcf;
        perl \$VCF2MAF_SCRIPT_PATH/vcf2maf.pl    
            --input-vcf ./input.vcf
            --output-maf $output_maf
	    --vep-forks 1
            #if $sampleid_source.sampleid_selector == "bamfile":
                --tumor-id `basename $sampleid_source.sampleid_tumour | sed 's/.bam$//g'`
                --normal-id `basename $sampleid_source.sampleid_normal | sed 's/.bam$//g'`
            #else:
                --tumor-id $sampleid_source.tumour_id
                --normal-id $sampleid_source.normal_id
            #end if
            
            --vep-path \$ENSEMBL_VEP_84_INSTALL_DIR
            --vep-data \${ENSEMBL_VEP_84_INSTALL_DIR}/cache
            --ref-fasta \${ENSEMBL_VEP_84_INSTALL_DIR}/cache/`echo $species_select.value | sed 's/-/\t/g' | cut -f1`/84_`echo $species_select.value | sed 's/-/\t/g' | cut -f2`/*.fa
            --species `echo $species_select.value | sed 's/-/\t/g' | cut -f1`
            --ncbi-build `echo $species_select.value | sed 's/-/\t/g' | cut -f2`;
	    mv $output_maf temp.maf;
	    grep -v version temp.maf > $output_maf;
    </command>

    <inputs>
        <conditional name="sampleid_source">
            <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
                <option value="bamfile">Bam File Name</option>
                <option value="manual">Manual</option>
            </param>
            <when value="bamfile">
                <param type="data" format="bam" name="sampleid_normal" label="Normal Bam"/>
                <param type="data" format="bam" name="sampleid_tumour" label="Tumour Bam"/>
            </when>
            <when value="manual">
                <param name="tumour_id" type="text" label="Tumour ID (Name)"/>
                <param name="normal_id" type="text" label="Normal ID (Name)"/>
            </when>
        </conditional>
        <expand macro="genome_list"/> 
        <param name="input_vcf" type="data" format="vcf" label="Input VCF File" />
    </inputs>

    <outputs>
        <data name="output_maf" format="maf" label="#echo os.path.splitext( str( $input_vcf.name ) )[ 0 ] #.${tool.name}.maf" />
    </outputs>

    <stdio>
        <exit_code range="1:" level="fatal" description="Failure" />
    </stdio>

    <requirements>

      <requirement type="package" version="5.18.1">perl</requirement>
      <requirement type="package" version="84">ensembl_vep</requirement>
        <requirement type="package" version="1.6.7">vcf2maf</requirement>
        <requirement type="package" version="84">ensembl_vep_perl_env</requirement>
    </requirements>

    <macros>
      <import>ensembl_vep_macros.xml</import>
    </macros>

    <help>

    </help>
</tool>