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

    #for $sf in $file:

    #if $sf == "CLUSTER_TABLE.csv"
    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${cluster_table}
    ;
    #end if

    #if $sf == "COMPARATIVE_ANALYSIS_COUNTS.csv"
    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${comparative_analysis_count}
    ;
    #end if

    #if $sf == "SUPERCLUSTER_TABLE.csv"
    unzip -p -j ${RepeatExplorer_archive} ${sf}  &gt; ${supercluster_table}
    ;
    #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>