--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/C and D finder/CandD.xml	Fri May 25 10:56:10 2018 -0400
@@ -0,0 +1,44 @@
+<tool id="commonality_r" name="commonality_finder" version="1.0.0">
+    <description>finds commonality</description>
+    <requirements>
+       <requirement type="package">R</requirement>
+    </requirements>
+    <command><![CDATA[
+		ln -s '$input1' input1.csv &&
+		ln -s '$input2' input2.csv &&
+		ln -s '$input3' input3.csv &&
+		ln -s '$input4' input4.csv &&
+		ln -s '$input5' input5.csv &&
+		ln -s '$input6' input6.csv &&
+		
+		Rscript '$__tool_directory__/CandD.R' NO NO YES
+    ]]></command>
+    <inputs>
+		<param format="csv" name="input1" type="data" label="First Substrate Set"/>
+        <param format="csv" name="input2" type="data" label="First Substrate Background Frequency"/>
+		<param format="csv" name="input3" type="data" label="Second Substrate Set"/>
+		<param format="csv" name="input4" type="data" label="Second Substrate Background Frequency"/>
+		<param format="csv" name="input5" type="data" label="Third Substrate Set"/>
+		<param format="csv" name="input6" type="data" label="Third Substrate Background Frequency"/>
+		<param name="outGroup" type="text" value="kinase" label="Kinase Name"/>
+    </inputs>      
+    <outputs>
+        <data format="csv" name="substrates" from_work_dir="sharedmotifs.csv" label="${outGroup}_shared Substrates.csv"/>
+		<data format="csv" name="SBF" from_work_dir="sharedSBF.csv" label="${outGroup}_shared SBF.csv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1.csv" ftype="csv" value="input1.csv"/>
+            <param name="positives" ftype="csv" value="substrates.csv"/>
+            <param name="SBF" ftype="csv" value="SBF.csv"/>
+			<output name="Negatives" file="negatives.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+	This tool uses the output from 3 Kinamine runs to determine what motifs are shared between the three runs
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1021/ja507164a</citation>
+    </citations>
+</tool>
+