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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ERPairFinder" name="ERPairFinder" version="1.12.0">
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3 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ERPairFinder</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>ERPairFinder
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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 -precursor_mass_tolerance ${param_precursor_mass_tolerance}
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17 -threads \${GALAXY_SLOTS:-24}
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18 #if $adv_opts.adv_opts_selector=='advanced':
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19 -RT_tolerance ${adv_opts.param_RT_tolerance}
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20 -max_charge ${adv_opts.param_max_charge}
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21 -intensity_threshold ${adv_opts.param_intensity_threshold}
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22 -max_isotope ${adv_opts.param_max_isotope}
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23 -expansion_range ${adv_opts.param_expansion_range}
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the ER spectra." help="(-in)"/>
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28 <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in)"/>
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29 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" 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="(-precursor_mass_tolerance)"/>
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30 <expand macro="advanced_options">
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31 <param name="param_RT_tolerance" type="float" min="1.0" 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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32 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search for." help="(-max_charge)"/>
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33 <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation." help="(-intensity_threshold)"/>
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34 <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope)"/>
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35 <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th." help="(-expansion_range)"/>
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36 </expand>
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37 </inputs>
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38 <outputs>
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39 <data name="param_out" label="Output consensusXML file were the pairs of the feature are written into." format="consensusXML"/>
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40 <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
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41 </outputs>
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42 <help>**What it does**
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43
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44 Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
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45
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46
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47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html
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48
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49 @REFERENCES@
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50 </help>
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51 </tool>
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