<tool id="random_intervals1" name="Random Intervals">
<description>create a random set of intervals</description>
  <command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 ${input2.metadata.chromCol} ${input2.metadata.startCol} ${input2.metadata.endCol} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
  <inputs>
    <param name="input1" type="data" format="interval" label="File to Mimick">
      <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
    </param>
    <param name="input2" type="data" format="interval" label="Intervals to Mask"/>
    <param name="use_mask" type="select" label="Use mask">
      <option value="no_mask">No</option>
      <option value="use_mask">Yes</option>
    </param>
    <param name="strand_overlaps" type="select" label="Allow overlaps">
      <option value="all">Any</option>
      <option value="strand">Across Strands</option>
      <option value="none">None</option>
    </param>
    <param name="regions" type="select" label="Regions to use">
      <options from_file="regions.loc">
        <column name="name" index="2"/>
        <column name="value" index="1"/>
        <column name="dbkey" index="0"/>
        <filter type="data_meta" ref="input1" key="dbkey" column="0" />
        <validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/>
      </options>
    </param> 
  </inputs>
  <outputs>
    <data name="out_file1" format="input"/>
  </outputs>
  <help>

.. class:: warningmark

This tool currently only works with ENCODE data from genome builds hg16 or hg17.

-----

.. class:: infomark

**Note:** If you do not wish to mask a set of intervals, change the Use Mask option to No, this option will override any Mask files selected.

-----

**Syntax**

This tool will attempt to create a random set of intervals that mimic those found within your source file.  You may also specify a set of intervals to mask.

**Allow overlaps** options
  * **Across Strands** - random regions are allowed to overlap only if they are on different strands.
  * **Any** - all overlaps are allowed.
  * **None** - no overlapping regions are allowed.

**Regions to use** options
  * Bounding region of interest based on the dataset build.

  </help>
</tool>