<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 given 'RankFilter' and 'Lookup RI for CAS' files into two tab-separated files.

This combination is a merge of the given files based on the Centrotype field.
In the 'RIQC-RankFilter output' the centrotype is found in the 'ID' field (first part before the "-"). In the 'RIQC-Lookup RI for CAS output'
the centrotype is found in the 'Centrotype' field. 

The files produced 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>