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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MRMPairFinder" name="MRMPairFinder" version="1.12.0">
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3 <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MRMPairFinder</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>MRMPairFinder
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11
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12 -in ${param_in}
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13 -pair_in ${param_pair_in}
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14 -out ${param_out}
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15 -feature_out ${param_feature_out}
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16 -threads \${GALAXY_SLOTS:-24}
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17 #if $adv_opts.adv_opts_selector=='advanced':
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18 -mass_tolerance ${adv_opts.param_mass_tolerance}
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19 -RT_tolerance ${adv_opts.param_RT_tolerance}
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20 -RT_pair_tolerance ${adv_opts.param_RT_pair_tolerance}
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21 #end if
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22 </command>
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23 <inputs>
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24 <param name="param_in" type="data" format="featureXML" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra." help="(-in)"/>
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25 <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in)"/>
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26 <expand macro="advanced_options">
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27 <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features." help="(-mass_tolerance)"/>
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28 <param name="param_RT_tolerance" type="float" min="0.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file." help="(-RT_tolerance)"/>
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29 <param name="param_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have." help="(-RT_pair_tolerance)"/>
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30 </expand>
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31 </inputs>
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32 <outputs>
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33 <data name="param_out" label="Output consensusXML file were the pairs of the features will be written to." format="consensusXML"/>
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34 <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
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35 </outputs>
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36 <help>**What it does**
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37
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38 Util which can be used to evaluate labeled pair ratios on MRM features.
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39
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40
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41 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html
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42
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43 @REFERENCES@
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44 </help>
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45 </tool>
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