view fetch_interval.xml @ 2:9422cd200be0 draft default tip

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<tool id="fetch_interval" name="Fetch Interval" version="1.0.0">
  <description> Creates Interval files used to parallelize certain Galaxy Tools </description>
  <requirements>
    <requirement type="package" version="1.0.0">fetch_interval</requirement>
    <requirement type="set_environment">FETCH_REPOSITORY_DIR</requirement>
  </requirements>
  <command>
  <![CDATA[	
  
      mkdir outputs;
      #if $output_option.output_option_selector == "collection":
          python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --order $order --output output.txt --chromosome --group_according_to_largest_chromosome --prefixes_to_ignore GL NC MT;
  
      #else:
          python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --output $order --chromosome --prefixes_to_ignore GL NC MT;
          cat $order > ./outputs/samp1.bed;

      #end if
  
  ]]>
  </command>
  <inputs>
    <conditional name="output_option">
      <param type="select" name="output_option_selector" label="How to Output?">
        <option value="collection">Collection</option>
        <option value="file">Single File</option>
      </param>
    </conditional>
    <param type="data" format="bam" name="input" label="BAM Alignment File" help="Information is pulled from the header, ensure consistent across BAMs"/>
  </inputs>
  <outputs>
    <collection name="list_output" type="list" description="Interval Files">
      <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
    </collection>
    <data format="txt" name="order"/>
  </outputs>
</tool>