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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_feature_in:
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19 -feature_in $param_feature_in
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20 #end if
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21 #if $param_precursor_mass_tolerance:
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22 -precursor_mass_tolerance $param_precursor_mass_tolerance
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23 #end if
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24 -threads \${GALAXY_SLOTS:-24}
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25 #if $adv_opts.adv_opts_selector=='advanced':
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26 #if $adv_opts.param_max_charge:
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27 -max_charge $adv_opts.param_max_charge
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28 #end if
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29 #if $adv_opts.param_intensity_threshold:
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30 -intensity_threshold $adv_opts.param_intensity_threshold
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31 #end if
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32 #if $adv_opts.param_force:
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33 -force
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34 #end if
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35 #end if
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36 </command>
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37 <inputs>
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38 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/>
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39 <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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40 <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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41 <expand macro="advanced_options">
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42 <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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43 <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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44 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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45 </expand>
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46 </inputs>
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47 <outputs>
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48 <data name="param_out" format="mzml"/>
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49 </outputs>
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50 <help>**What it does**
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51
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52 Corrects the precursor entries of MS/MS spectra, by using MS1 information.
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html</help>
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56 <expand macro="references"/>
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57 </tool>
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