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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="1.12.0">
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3 <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">PrecursorMassCorrector</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>PrecursorMassCorrector
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -feature_in ${param_feature_in}
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15 -precursor_mass_tolerance ${param_precursor_mass_tolerance}
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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 -max_charge ${adv_opts.param_max_charge}
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19 -intensity_threshold ${adv_opts.param_intensity_threshold}
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20 #end if
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21 </command>
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22 <inputs>
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23 <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the spectra." help="(-in)"/>
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24 <param name="param_feature_in" type="data" format="featureXML" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries #br#will be matched to the feature m/z values if possible." help="(-feature_in)"/>
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25 <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;#br#this value should be set to the instruments selection window." help="(-precursor_mass_tolerance)"/>
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26 <expand macro="advanced_options">
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27 <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge)"/>
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28 <param name="param_intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details." help="(-intensity_threshold)"/>
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29 </expand>
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30 </inputs>
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31 <outputs>
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32 <data name="param_out" label="Output mzML file." format="mzML"/>
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33 </outputs>
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34 <help>**What it does**
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35
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36 Corrects the precursor entries of MS/MS spectra, by using MS1 information.
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37
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38
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39 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html
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40
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41 @REFERENCES@
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42 </help>
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43 </tool>
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