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Initial commit to toolshed
author pieter.lukasse@wur.nl
date Thu, 16 Jan 2014 13:10:00 +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 $out_multi
5 </command>
6 <inputs>
7 <param format="tabular" name="caslookup_in" type="data" label="RIQC-Lookup RI for CAS output"
8 help="Select the output file from the CasLookup tool"/>
9 <param format="tabular" name="rankfilter_in" type="data" label="RIQC-RankFilter output"
10 help="Select the output file from the RankFilter tool"/>
11 </inputs>
12 <outputs>
13 <data format="tabular" label="${tool.name} (Single) on ${on_string}" name="out_single" />
14 <data format="tabular" label="${tool.name} (Multi) on ${on_string}" name="out_multi" />
15 </outputs>
16 <help>
17 Performs a combination of output files from the 'RankFilter' and 'Lookup RI for CAS' tools into two tab-separated files.
18
19 The files produced are contain either all hits for a compound on a single line (Single) or on separate lines
20 (Multi).
21
22 .. class:: infomark
23
24 **Notes**
25
26 The input data should be produced by the RankFilter and 'Lookup RI for CAS' tools provided on this Galaxy server with the
27 original headers kept intact. Processing steps include:
28
29 - Added columns showing the average Forward/Reverse values, RIexp - RIsvr and RI - RIexp values
30 - The ID column of the RankFilter tool output is split into 'Centrotype', 'cent.Factor', 'scan nr.', 'R.T. (umin)'
31 and 'nr. Peaks' fields.
32 - The formula is split off the 'Name' field in the RankFilter output
33
34 </help>
35 </tool>