<tool id="extract_var_files_from_re"
      name="Extract various files from RepeatExplorer2 archive" version="1.0.0.3">
    <command detect_errors="exit_code">
        <![CDATA[



    #for $sf in $file:
    #if $sf == "CLUSTER_TABLE.csv"
    mkdir -p tempdir
    &&
    unzip ${RepeatExplorer_archive} ${sf} -d tempdir
    &&
    find tempdir -type f -name "${sf}" -exec cat {} + > ${cluster_table}
    &&
    rm -r tempdir
    ;
    #end if

    #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
    mkdir -p tempdir
    &&
    unzip ${RepeatExplorer_archive} ${sf} -d tempdir
    &&
    find tempdir -type f -name "${sf}" -exec cat {} + > ${comparative_analysis_count}
    &&
    rm -r tempdir
    ;
    #end if

    #if $sf == "SUPERCLUSTER_TABLE.csv"
    mkdir -p tempdir
    &&
    unzip ${RepeatExplorer_archive} ${sf} -d tempdir
    &&
    find tempdir -type f -name "${sf}" -exec cat {} + > ${supercluster_table}
    &&
    rm -r tempdir
    #end if

    #end for

]]>


    </command>

    <inputs>
        <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results"
               type="data" format="zip"/>

        <param name="file" type="select" label="select files you want to extract"
               multiple="true" optional="false">
            <option value="CLUSTER_TABLE.csv">CLUSTER_TABLE.csv</option>
            <option value="COMPARATIVE_ANALYSIS_COUNTS.csv">
                COMPARATIVE_ANALYSIS_COUNTS.csv
            </option>
            <option value="SUPERCLUSTER_TABLE.csv">SUPERCLUSTER_TABLE.csv</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="cluster_table"
              label="CLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
            <filter>"CLUSTER_TABLE.csv" in file</filter>
        </data>
        <data format="tabular" name="supercluster_table"
              label="SUPERCLUSTER_TABLE.csv from ${RepeatExplorer_archive.hid}">
            <filter>"SUPERCLUSTER_TABLE.csv" in file</filter>
        </data>
        <data format="tabular" name="comparative_analysis_count"
              label="COMPARATIVE_ANALYSIS_COUNTS.csv from ${RepeatExplorer_archive.hid}">
            <filter>"COMPARATIVE_ANALYSIS_COUNTS.csv" in file</filter>
        </data>
    </outputs>
</tool>