--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/encode/random_intervals.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,58 @@
+<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>
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