--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/region_motif_compare.xml	Sat May 16 22:35:26 2015 -0400
@@ -0,0 +1,44 @@
+<tool id="region_motif_compare" name="Region Motif Count Compare">
+  <description>for comparing the motif counts in different region sets</description>
+  <requirements>
+    <requirement type="set_environment">RMOTIF_PATH</requirement>
+  </requirements>
+  <command interpreter="Rscript">
+    region_motif_compare.r --args \$RMOTIF_PATH $pwm_file.fields.path $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="pwm_file" type="select" label="Using motif database PWM file">
+      <options from_data_table="motif_databases"/>
+    </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>
+
+  <tests>
+    <test>
+      <param name="in_tab_1" value="XXX.tab" />
+      <param name="in_tab_2" value="XXX.tab" />
+      <param name="pwm_file" value="XXX.meme.txt" />
+      <output name="out_enriched" file="XXX.tab" />
+      <output name="out_depleted" file="XXX.tab" />     
+      <output name="out_plots" file="XXX.png" />          
+    </test>
+  </tests>
+
+  <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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