comparison interproscan5/ips5.xml @ 3:74cf3f49f10c draft

Better HTML index.

2:d1d34608dba0

<tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.0mkh">
    <description>Interproscan functional predictions of ORFs.</description>
    <requirements>
        <!--
        <requirement type="package">signalp</requirement>
        <requirement type="package">phobius</requirement>

            $iprlookup
            $mode
            --output-file-base __base__
            2>&1;

        #if 'tsv' in str($output_types):
            mv __base__.tsv $tsv_file;
        #end if

        #if 'gff3' in str($output_types):
            mv __base__.gff3 $gff3_file;
        #end if

         #if 'html' in str($output_types):
            mkdir -p $html_file.files_path;
            #set temp_archive_file = '__base__.html.tar.gz'
            tar -C $html_file.files_path -xvmzf $temp_archive_file;
            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;
            rm $temp_archive_file;
        #end if

         #if 'svg' in str($output_types):
            mkdir -p $svg_file.files_path;
            #set temp_archive_file = '__base__.svg.tar.gz'
            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>

        <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>

        <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
               truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
               falsevalue=""/>

        <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
               label="Provide additional mappings"
               help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>

        <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats"
               help="Select the output formats to generate (at least one)">
            <option value="tsv" selected="true">Raw (TSV)</option>
            <option value="html" selected="true">HTML (Graphical)</option>
            <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
            <option value="gff3" selected="true">GFF3</option>
            <option value="xml" selected="false">XML</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}">
            <filter>'tsv' in output_types</filter>
        </data>
        <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
            <filter>'html' in output_types</filter>
        </data>
        <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
            <filter>'svg' in output_types</filter>

3:74cf3f49f10c

<tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.1mkh">
    <description>Interproscan functional predictions of ORFs.</description>
    <requirements>
        <!--
        <requirement type="package">signalp</requirement>
        <requirement type="package">phobius</requirement>

            $iprlookup
            $mode
            --output-file-base __base__
            2>&1;

        mv __base__.tsv $tsv_file;

        #if 'gff3' in str($output_types):
            mv __base__.gff3 $gff3_file;
        #end if

         #if 'html' in str($output_types):
            mkdir -p $html_file.files_path;
            #set temp_archive_file = '__base__.html.tar.gz'
            tar -C $html_file.files_path -xvmzf $temp_archive_file;
            #if str($seqtype) == 'p' and not str($getorfed):
                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
            #else
                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
            #end if
            rm $temp_archive_file;
        #end if

         #if 'svg' in str($output_types):
            mkdir -p $svg_file.files_path;
            #set temp_archive_file = '__base__.svg.tar.gz'
            tar -C $svg_file.files_path -xvmzf $temp_archive_file;
            #if str($seqtype) == 'p' and not str($getorfed):
                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
            #else
                python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
            #end if
            rm $temp_archive_file;
        #end if

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

        <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>

        <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
               truevalue="getorfed"
               falsevalue=""/>

        <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
               truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
               falsevalue=""/>

        <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
               label="Provide additional mappings"
               help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>

        <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
               help="Select the output formats to generate (at least one)">
            <option value="html" selected="true">HTML (Graphical)</option>
            <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
            <option value="gff3" selected="true">GFF3</option>
            <option value="xml" selected="false">XML</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
        <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
            <filter>'html' in output_types</filter>
        </data>
        <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
            <filter>'svg' in output_types</filter>