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1 <tool id="mzmatch_extract_background_ions" version="0.1.0" name="Extract Background Ions">
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2 <description>
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="stdio" />
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8 <expand macro="requires" />
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9 <command interpreter="python">
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10 mzmatch_wrapper.py
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11 --executable '__SHELL__' --config $setup
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12 --executable 'ExtractBackgroundIons' --config $config
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13 </command>
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14 <configfiles>
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15 <configfile name="setup">ln -s $input1 input.${input1.ext}</configfile>
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16 <configfile name="config">-ppm $ppm -i input.${input1.ext} -o $output -threshold $threshold</configfile>
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17 </configfiles>
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18 <inputs>
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19 <param name="input1" label="Input" type="data" format="mzml,mzxml" />
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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)." />
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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." />
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22 </inputs>
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23 <outputs>
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24 <data format="peakml" name="output" />
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25 </outputs>
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26 <help>
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27 **What it does**
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28
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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').
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30
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31 The resulting output file is in PeakML-format, containing a list of all the extracted background ions.
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32
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33 **Citation**
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34
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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``
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36
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37 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-mzmatch
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38 </help>
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39 </tool>
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