--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GALAXY_FILES/tools/EMBER/Compare_Targets.xml	Wed Feb 29 15:03:33 2012 -0500
@@ -0,0 +1,50 @@
+<tool id="compare_targets" name="Compare Targets" version="1.3">
+  <description>Compares the target genes from two EMBER runs</description>
+  <command interpreter="perl">Compare_Targets.pl -t1 $set1 -t2 $set2 -o $output -of $outtype -n $comptype</command>
+  <inputs>
+    <param format="txt" name="set1" type="data" label="Targets file 1"/>
+    <param format="txt" name="set2" type="data" label="Targets file 2"/>
+    <param name="outtype" type="select" label="Output type">
+        <option value="0" selected="true">All shared targets</option>
+        <option value="1">Targets unique to file 1</option>
+        <option value="2">Targets unique to file 2</option>
+        <option value="3">Union of targets from files 1 and 2</option>
+    </param>
+    <param name="comptype" type="select" label="Value to compare">
+        <option value="1" selected="true">Gene names</option>
+        <option value="0">Probe set IDs</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="set1" value="EMBER/patterns-1.targets"/>
+      <param name="set2" value="EMBER/patterns-1.targets"/>
+      <param name="outtype" value="0"/>
+      <param name="comptype" value="1"/>
+      <output name="output" file="EMBER/targets_1-1.txt"/>
+    </test>
+  </tests>
+
+
+  <help>
+
+This tool compares the list of gene targets from different EMBER runs.
+
+-----
+
+Description of inputs:
+
+*Targets files 1 and 2*: the .targets outputs of EMBER.
+
+*Output type*: This tool compares the gene sets, and you can choose which comparison to print, either the intersection, difference, or union.
+
+*Value to compare*: Choose gene name or probe set ID; some genes have multiple probe sets.
+
+  </help>
+
+</tool>
+