view maf2maf.xml @ 3:15dc9358f476 draft default tip

Uploaded

<tool id="maf2maf" name="maf2maf" version="1.0.0">
    <description>Reannotates MAF file creating a new MAF file</description>

    <command>
        echo \$VCF2MAF_SCRIPT_PATH;
        echo \$ENSEMBL_VEP_84_INSTALL_DIR;
        cat $input_maf | perl -ne '@a=split /\t/;if(\$a[4] == 23){\$a[4] = "X";}print join "\t", @a;' > ./input.maf;
        perl \$VCF2MAF_SCRIPT_PATH/maf2maf.pl
            --input-maf ./input.maf
            --output-maf $output_maf
            --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`;
    </command>

    <inputs>
        <expand macro="genome_list" />
        <param name="input_maf" type="data" format="maf" label="Input MAF file" />
    </inputs>

    <outputs>
        <data name="output_maf" format="maf" label="#echo os.path.splitext( str( $input_maf.name ) )[ 0 ] #.${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="1.6.7">vcf2maf</requirement>
        <requirement type="package" version="84">ensembl_vep_perl_env</requirement>
        <requirement type="package" version="84">ensembl_vep</requirement>
        <requirement type="package" version="1.6.7">vcf2maf</requirement>
        <requirement type="paclage" version="84">ensembl_vep_perl_environment</requirement>
    </requirements>

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

    <help>

    </help>

</tool>