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comparison combine_output.xml @ 0:dffc38727496

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author pieter.lukasse@wur.nl
date Sat, 07 Feb 2015 22:02:00 +0100
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1 <tool id="combine_output" name="RIQC-Combine RankFilter and CasLookup output" version="1.0.2">
2 <description>Perform a combination of output data from the RankFilter and CasLookup tools</description>
3 <command interpreter="python">
4 combine_output.py $rankfilter_in $caslookup_in $out_single $out_multi
5 </command>
6 <inputs>
7 <param format="tabular" name="rankfilter_in" type="data" label="RIQC-RankFilter output (Estimated RI)"
8 help="Select the output file from the RankFilter tool"/>
9 <param format="tabular" name="caslookup_in" type="data" label="RIQC-Lookup RI for CAS output ('Known' RI)"
10 help="Select the output file from the CasLookup tool"/>
11 <!-- <param TODO : could add "tolerance for ERI-KRI"(Estimated RI-Known RI)-->
12 </inputs>
13 <outputs>
14 <data format="tabular" label="${tool.name} (Single) on ${on_string}" name="out_single" />
15 <data format="tabular" label="${tool.name} (Multi) on ${on_string}" name="out_multi" />
16 </outputs>
17 <help>
18 Performs a combination of output files from the 'RankFilter' and 'Lookup RI for CAS' tools into two tab-separated files.
19
20 The files produced are contain either all hits for a compound on a single line (Single) or on separate lines
21 (Multi).
22
23 .. class:: infomark
24
25 **Notes**
26
27 The input data should be produced by the RankFilter and 'Lookup RI for CAS' tools provided on this Galaxy server with the
28 original headers kept intact. Processing steps include:
29
30 - Added columns showing the average Forward/Reverse values, RIexp - RIsvr and RI - RIexp values
31 - The ID column of the RankFilter tool output is split into 'Centrotype', 'cent.Factor', 'scan nr.', 'R.T. (umin)'
32 and 'nr. Peaks' fields.
33 - The formula is split off the 'Name' field in the RankFilter output
34
35 </help>
36 </tool>