--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/region_motif_compare.xml	Tue Aug 05 13:56:22 2014 -0400
@@ -0,0 +1,29 @@
+<tool id="region_motif_compare" name="Region Motif Count Compare">
+  <description>for comparing the motif counts in different region sets</description>
+  <command interpreter="bash">
+    /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/tools/my_tools/region_motif_compare.r --args $GALAXY_ROOT_DIR $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots
+  </command>
+  <inputs>
+    <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/>
+    <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/>
+    <param name="db_type" type="select" label="Select Motif Database" >
+      <option value="t">Test Pouya Subset (hg19)</option>
+      <option value="p">Pouya Encode Motifs (hg19)</option>
+      <option value="j">Jaspar and Jolma Motifs (hg19)</option>
+      <option value="m">Mouse Motifs (mm9)</option>
+      <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_enriched" format="tabular" label="Enriched Motifs"/>
+    <data name="out_depleted" format="tabular" label="Depleted Motifs"/>
+    <data name="out_plots" format="png" label="Motif Count Comparison Plots"/>
+  </outputs>
+
+  <help>
+    This tools reads in two counts file and determines enriched and depleted
+    motifs in two different region sets based on poisson calculation with
+    gc correction.
+  </help>
+ 
+</tool>
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