--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GCMS/combine_output.xml	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,36 @@
+<tool id="combine_output" name="RIQC-Combine RankFilter and CasLookup output" version="1.0.2">
+  <description>Perform a combination of output data from the RankFilter and CasLookup tools</description>
+  <command interpreter="python">
+    combine_output.py $rankfilter_in $caslookup_in $out_single $out_multi
+  </command>
+  <inputs>
+    <param format="tabular" name="rankfilter_in" type="data" label="RIQC-RankFilter output (Estimated RI)" 
+    	help="Select the output file from the RankFilter tool"/>
+    <param format="tabular" name="caslookup_in" type="data" label="RIQC-Lookup RI for CAS output ('Known' RI)"
+    	help="Select the output file from the CasLookup tool"/>
+    <!--   <param TODO : could add "tolerance for ERI-KRI"(Estimated RI-Known RI)--> 
+  </inputs>
+  <outputs>
+    <data format="tabular" label="${tool.name} (Single) on ${on_string}" name="out_single" />
+    <data format="tabular" label="${tool.name} (Multi) on ${on_string}" name="out_multi" />
+  </outputs>
+  <help>
+Performs a combination of output files from the 'RankFilter' and 'Lookup RI for CAS' tools into two tab-separated files.
+
+The files produced are contain either all hits for a compound on a single line (Single) or on separate lines 
+(Multi). 
+
+.. class:: infomark
+
+**Notes**
+   
+The input data should be produced by the RankFilter and 'Lookup RI for CAS' tools provided on this Galaxy server with the 
+original headers kept intact. Processing steps include:
+   
+   - Added columns showing the average Forward/Reverse values, RIexp - RIsvr and RI - RIexp values
+   - The ID column of the RankFilter tool output is split into 'Centrotype', 'cent.Factor', 'scan nr.', 'R.T. (umin)'
+     and 'nr. Peaks' fields.
+   - The formula is split off the 'Name' field in the RankFilter output    
+    
+  </help>
+</tool>