Mercurial > repos > pieterlukasse > prims_metabolomics2
annotate GCMS/combine_output.xml @ 16:fe4682eb938c
small improvement
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 23 Mar 2015 08:40:42 +0100 |
| parents | 346ff9ad8c7a |
| children |
| rev | line source |
|---|---|
| 6 | 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> | |
| 16 | 18 Performs a combination of given 'RankFilter' and 'Lookup RI for CAS' files into two tab-separated files. |
| 6 | 19 |
| 16 | 20 This combination is a merge of the given files based on the Centrotype field. |
|
14
346ff9ad8c7a
fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents:
6
diff
changeset
|
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' |
|
346ff9ad8c7a
fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents:
6
diff
changeset
|
22 the centrotype is found in the 'Centrotype' field. |
|
346ff9ad8c7a
fix for rankfilter, removed pfd read functional
linda.bakker@wur.nl <linda.bakker@wur.nl>
parents:
6
diff
changeset
|
23 |
| 16 | 24 The files produced contain either all hits for a compound on a single line (Single) or on separate lines |
| 6 | 25 (Multi). |
| 26 | |
| 27 .. class:: infomark | |
| 28 | |
| 29 **Notes** | |
| 30 | |
| 31 The input data should be produced by the RankFilter and 'Lookup RI for CAS' tools provided on this Galaxy server with the | |
| 32 original headers kept intact. Processing steps include: | |
| 33 | |
| 34 - Added columns showing the average Forward/Reverse values, RIexp - RIsvr and RI - RIexp values | |
| 35 - The ID column of the RankFilter tool output is split into 'Centrotype', 'cent.Factor', 'scan nr.', 'R.T. (umin)' | |
| 36 and 'nr. Peaks' fields. | |
| 37 - The formula is split off the 'Name' field in the RankFilter output | |
| 38 | |
| 39 </help> | |
| 40 </tool> |