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author galaxyp
date Fri, 10 May 2013 17:28:02 -0400
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1 <tool id="mzmatch_export" version="0.1.0" name="Peakml Export">
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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 --executable 'convert.ConvertToText' --config $config
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11 </command>
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12 <configfiles>
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13 <configfile name="config">-i $input1 -o $output</configfile>
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14 </configfiles>
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15 <inputs>
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16 <param name="input1" label="Input" type="data" format="peakml" />
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="output" />
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20 </outputs>
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21 <help>
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22 **What it does**
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23
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24 Converts the contents of a PeakML file to a tab-separated text file. In order to make the file useable in a spreadsheet environment, only the top-level data for each measurement is given in the file.
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25
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26 **Citation**
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27
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28 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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29
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30 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-mzmatch
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31 </help>
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32 </tool>