Mercurial > repos > galaxyp > mzmatch
comparison extract_background_ions.xml @ 0:201a15633354 draft default tip
Initial commit.
| author | galaxyp |
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| date | Fri, 10 May 2013 17:28:02 -0400 |
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| -1:000000000000 | 0:201a15633354 |
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| 1 <tool id="mzmatch_extract_background_ions" version="0.1.0" name="Extract Background Ions"> | |
| 2 <description> | |
| 3 </description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="stdio" /> | |
| 8 <expand macro="requires" /> | |
| 9 <command interpreter="python"> | |
| 10 mzmatch_wrapper.py | |
| 11 --executable '__SHELL__' --config $setup | |
| 12 --executable 'ExtractBackgroundIons' --config $config | |
| 13 </command> | |
| 14 <configfiles> | |
| 15 <configfile name="setup">ln -s $input1 input.${input1.ext}</configfile> | |
| 16 <configfile name="config">-ppm $ppm -i input.${input1.ext} -o $output -threshold $threshold</configfile> | |
| 17 </configfiles> | |
| 18 <inputs> | |
| 19 <param name="input1" label="Input" type="data" format="mzml,mzxml" /> | |
| 20 <param name="ppm" label="ppm" value="3" type="float" help="The accuracy of the measurement in parts-per-milion. This value is used for the collection of the data-points belonging to a background ion and needs to be reasonable for the equipment used to make the measurement (the LTQ-Orbitrap manages approximatetly 3 ppm)." /> | |
| 21 <param name="threshold" type="float" value="0.02" label="Treshold" help="The percentage (a value between 0 and 1) of scans that minimally need to contain a measurement." /> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="peakml" name="output" /> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 29 Extracts background ions (x-axis: RT; y-axis: Intensity) from 2D mass spectrometry data (LC/MS or GC/MS). The raw data is loaded from the open standard file formats (mzML, mzXML or mzData) and all of the individidual mass traces (M/Z +/- ppm over the whole scan range) are retrieved. A mass trace is retained when it is present in more than the given percentage of scans (option 'threshold'). | |
| 30 | |
| 31 The resulting output file is in PeakML-format, containing a list of all the extracted background ions. | |
| 32 | |
| 33 **Citation** | |
| 34 | |
| 35 For the underlying tool, please cite ``PeakML/mzMatch: A File Format, Java Library, R Library, and Tool-Chain for Mass Spectrometry Data Analysis. Richard A. Scheltema, Andris Jankevics, Ritsert C. Jansen, Morris A. Swertz, and Rainer Breitling. Analytical Chemistry 2011 83 (7), pp 2786-2793`` | |
| 36 | |
| 37 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-mzmatch | |
| 38 </help> | |
| 39 </tool> |