view annotate.xml @ 1:9d4894e61812 draft

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<tool id="annotate" name="Annotate" version="1.0.0">
    <description>
        Annotate VCF files using Ensemble VEP
    </description>
    <command>
        perl \$ENSEMBL_VEP_84_INSTALL_DIR/variant_effect_predictor.pl
            --fork 4
            --offline 
            --species \$( echo $species_select.value | sed 's/#/\t/g' | cut -f1) 
	    --dir \$ENSEMBL_VEP_76_CACHE_DIR 
            --no_stats 
            --force_overwrite 
            --everything 
            --check_existing 
            --total_length 
            --allele_number 
            --no_escape 
            --gencode_basic 
            --xref_refseq 
	    #if "#" in $species_select.value
            --assembly \$( echo $species_select.value | sed 's/#/\t/g' | cut -f2)
            #end if
            --vcf 
            --input_file $input_vcf 
            --output_file $output_vcf
    </command>
    <inputs>
        <param name="input_vcf" type="data" format="vcf" label="Input VCF File" />
        <expand macro="genome_list"/>
    </inputs>

    <outputs>
        <data format="vcf" name="output_vcf" label="${input.name}_vep-annotated" />
    </outputs>

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

    <requirements>
        <requirement type="package" version="84">ensembl_vep</requirement>
	<requirement type="package" version="5.18.1">perl</requirement>
    </requirements>
    <macros>
      <import>ensembl_vep_macros.xml</import>
    </macros>

</tool>