view pvac-seq.xml @ 5:e8072dc045fa draft default tip

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<tool id="pvac-seq" name="PVAC-seq" version="0.1.0">
    <command detect_errors="exit_code"><![CDATA[
        #if str( $epitope_length ) != "":
            #set $epitope_length = "-e " + str($epitope_length)
        #end if
        #set algs = ' '.join([str($alg) for $alg in $algorithms]) 
        pvacseq run 
        ${epitope_length} 
        --iedb-install-directory "\$IEDB_INSTALL_DIRECTORY"
        --tdna-vaf ${tdna_vaf} 
        --net-chop-method ${net_chop_method} 
        ${net_mhc_stab}
        --top-score-metric ${top_score_metric}
        --downstream-sequence-length ${downstream_sequence_length}
        ${input_vcf} 
        galaxy 
        ${allele} 
        ${algs} 
        `pwd` && 
        mv combined/galaxy.filtered.tsv ${output_filtered} && 
        mv combined/galaxy.all_epitopes.tsv ${output_all}

    ]]></command>
    <inputs>
        <param type="data" name="input_vcf" format="vcf" />
        <param type="text" name="allele" />
        <param name="algorithms" type="select" multiple="true" label="Epitope prediction algorithms">
            <option value="NNalign">NNalign</option>
            <option value="NetMHC">NetMHC</option>
            <option value="NetMHCIIpan">NetMHCIIpan</option>
            <option value="NetMHCcons">NetMHCcons</option>
            <option value="NetMHCpan">NetMHCpan</option>
            <option value="PickPocket">PickPocket</option>
            <option value="SMMPMBEC">SMMPMBEC</option>
            <option value="SMMalign">SMMalign</option>
        </param>

        <param type="text" name="epitope_length"/>
        <param type="text" name="downstream_sequence_length" value="1000" help="int or 'full'"/>
        <param type="text" name="tdna_vaf" value="40"/>
        <param name="net_chop_method" type="select" label="NetChop prediction method">
            <option value="cterm">cterm</option>
            <option value="20s">20S</option>
        </param>
        <param name="net_mhc_stab" type="select" label="Run NetMHCStabPan after all filtering?">
            <option value="--netmhc-stab">Yes</option>
            <option value="">No</option>
        </param>
        <param name="top_score_metric" type="select" label="The ic50 scoring metric to use">
            <option value="median">Median</option>
            <option value="lowest">Lowest</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_all" format="tabular"/>
        <data name="output_filtered" format="tabular"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>