comparison interproscan5/ips5.xml @ 1:e2d4343d73ad draft

Minor fixes.

0:fe8e43a26870

        <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
    </requirements>

    <command>
        #import os

        \$IPS_HOME/interproscan.sh
            ## disables the precalculated lookup service, all calculation will be run locally
            -dp
            --input $infile
            --seqtype $seqtype
            -f $output_types
            --applications $appl
            --tempdir \$TEMP

            $pathways
            $goterms
            $iprlookup
            $mode

            tar -C $svg_file.files_path -xvmzf $temp_archive_file;
            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
            rm $temp_archive_file;
        #end if

        echo "End of ipsfaux"
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>

        <param name="seqtype" type="select" label="Type of the input sequences" help="">
            <option value="p" selected="true">Protein</option>
            <option value="n">DNA / RNA</option>
        </param>

1:e2d4343d73ad

        <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
    </requirements>

    <command>
        #import os
        echo "Start timestamp: $(date)";
        \$IPS_HOME/interproscan.sh
            ## disables the precalculated lookup service, all calculation will be run locally
            -dp
            --input $infile
            --seqtype $seqtype
            -f $output_types
            --applications $appl

            $pathways
            $goterms
            $iprlookup
            $mode

            tar -C $svg_file.files_path -xvmzf $temp_archive_file;
            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
            rm $temp_archive_file;
        #end if

        echo "End timestamp: $(date)"
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Sequence Fasta File"/>

        <param name="seqtype" type="select" label="Type of the input sequences" help="">
            <option value="p" selected="true">Protein</option>
            <option value="n">DNA / RNA</option>
        </param>