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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MRMPairFinder" name="MRMPairFinder" version="2.0.0">
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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 #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_pair_in:
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16 -pair_in $param_pair_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_feature_out:
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22 -feature_out $param_feature_out
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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_mass_tolerance:
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27 -mass_tolerance $adv_opts.param_mass_tolerance
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28 #end if
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29 #if $adv_opts.param_RT_tolerance:
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30 -RT_tolerance $adv_opts.param_RT_tolerance
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31 #end if
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32 #if $adv_opts.param_RT_pair_tolerance:
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33 -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
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34 #end if
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35 #if $adv_opts.param_force:
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36 -force
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37 #end if
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38 #end if
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39 </command>
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40 <inputs>
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41 <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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42 <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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43 <expand macro="advanced_options">
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44 <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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45 <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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46 <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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47 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data name="param_out" format="consensusxml"/>
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52 <data name="param_feature_out" format="featurexml"/>
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53 </outputs>
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54 <help>**What it does**
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55
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56 Util which can be used to evaluate labeled pair ratios on MRM features.
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57
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58
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59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMPairFinder.html</help>
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60 <expand macro="references"/>
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61 </tool>
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