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annotate GCMS/combine_output.xml @ 14:346ff9ad8c7a

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fix for rankfilter, removed pfd read functional
author linda.bakker@wur.nl <linda.bakker@wur.nl>
date Fri, 20 Mar 2015 17:10:04 +0100
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1 <tool id="combine_output" name="RIQC-Combine RankFilter and CasLookup output" version="1.0.2">
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2 <description>Perform a combination of output data from the RankFilter and CasLookup tools</description>
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3 <command interpreter="python">
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4 combine_output.py $rankfilter_in $caslookup_in $out_single $out_multi
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5 </command>
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6 <inputs>
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7 <param format="tabular" name="rankfilter_in" type="data" label="RIQC-RankFilter output (Estimated RI)"
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8 help="Select the output file from the RankFilter tool"/>
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9 <param format="tabular" name="caslookup_in" type="data" label="RIQC-Lookup RI for CAS output ('Known' RI)"
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10 help="Select the output file from the CasLookup tool"/>
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11 <!-- <param TODO : could add "tolerance for ERI-KRI"(Estimated RI-Known RI)-->
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12 </inputs>
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13 <outputs>
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14 <data format="tabular" label="${tool.name} (Single) on ${on_string}" name="out_single" />
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15 <data format="tabular" label="${tool.name} (Multi) on ${on_string}" name="out_multi" />
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16 </outputs>
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17 <help>
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18 Performs a combination of output files from the 'RankFilter' and 'Lookup RI for CAS' tools into two tab-separated files.
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20 Merges data from both input dictionaries based on the Centrotype field.
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21 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'
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22 the centrotype is found in the 'Centrotype' field.
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24 The files produced are contain either all hits for a compound on a single line (Single) or on separate lines
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25 (Multi).
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26
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27 .. class:: infomark
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28
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29 **Notes**
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30
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31 The input data should be produced by the RankFilter and 'Lookup RI for CAS' tools provided on this Galaxy server with the
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32 original headers kept intact. Processing steps include:
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33
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34 - Added columns showing the average Forward/Reverse values, RIexp - RIsvr and RI - RIexp values
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35 - The ID column of the RankFilter tool output is split into 'Centrotype', 'cent.Factor', 'scan nr.', 'R.T. (umin)'
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36 and 'nr. Peaks' fields.
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37 - The formula is split off the 'Name' field in the RankFilter output
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38
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39 </help>
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40 </tool>