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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ERPairFinder" name="ERPairFinder" version="2.0.0">
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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 #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 #if $param_precursor_mass_tolerance:
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25 -precursor_mass_tolerance $param_precursor_mass_tolerance
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $adv_opts.adv_opts_selector=='advanced':
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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_max_charge:
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33 -max_charge $adv_opts.param_max_charge
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34 #end if
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35 #if $adv_opts.param_intensity_threshold:
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36 -intensity_threshold $adv_opts.param_intensity_threshold
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37 #end if
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38 #if $adv_opts.param_max_isotope:
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39 -max_isotope $adv_opts.param_max_isotope
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40 #end if
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41 #if $adv_opts.param_expansion_range:
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42 -expansion_range $adv_opts.param_expansion_range
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43 #end if
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44 #if $adv_opts.param_force:
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45 -force
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46 #end if
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47 #end if
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48 </command>
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49 <inputs>
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50 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/>
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51 <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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52 <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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53 <expand macro="advanced_options">
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54 <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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55 <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search fo" help="(-max_charge) "/>
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56 <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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57 <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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58 <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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59 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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60 </expand>
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61 </inputs>
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62 <outputs>
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63 <data name="param_out" format="consensusxml"/>
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64 <data name="param_feature_out" format="featurexml"/>
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65 </outputs>
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66 <help>**What it does**
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67
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68 Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
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69
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70
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71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
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72 <expand macro="references"/>
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73 </tool>
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