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annotate ERPairFinder.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="ERPairFinder" name="ERPairFinder" version="2.0.0">
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5 <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ERPairFinder</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>ERPairFinder
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_pair_in:
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19 -pair_in $param_pair_in
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_feature_out:
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25 -feature_out $param_feature_out
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26 #end if
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27 #if $param_precursor_mass_tolerance:
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28 -precursor_mass_tolerance $param_precursor_mass_tolerance
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $adv_opts.adv_opts_selector=='advanced':
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32 #if $adv_opts.param_RT_tolerance:
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33 -RT_tolerance $adv_opts.param_RT_tolerance
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34 #end if
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35 #if $adv_opts.param_max_charge:
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36 -max_charge $adv_opts.param_max_charge
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37 #end if
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38 #if $adv_opts.param_intensity_threshold:
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39 -intensity_threshold $adv_opts.param_intensity_threshold
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40 #end if
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41 #if $adv_opts.param_max_isotope:
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42 -max_isotope $adv_opts.param_max_isotope
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43 #end if
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44 #if $adv_opts.param_expansion_range:
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45 -expansion_range $adv_opts.param_expansion_range
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46 #end if
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47 #if $adv_opts.param_force:
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48 -force
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49 #end if
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50 #end if
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51 </command>
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52 <inputs>
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53 <param format="mzml" help="(-in) " label="Input mzML file containing the ER spectra" name="param_in" optional="False" type="data"/>
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54 <param format="txt" help="(-pair_in) " label="Pair-file in the format: m/z-light m/z-heavy charge rt" name="param_pair_in" optional="False" type="data"/>
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55 <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_precursor_mass_tolerance" optional="True" type="float" value="0.3"/>
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56 <expand macro="advanced_options">
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57 <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="1.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
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58 <param help="(-max_charge) " label="Maximal charge state features should be search fo" min="1" name="param_max_charge" optional="True" type="integer" value="3"/>
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59 <param help="(-intensity_threshold) " label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" min="-1.0" name="param_intensity_threshold" optional="True" type="float" value="-1.0"/>
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60 <param help="(-max_isotope) " label="Max isotope of the isotope distribution to be considered" min="2" name="param_max_isotope" optional="True" type="integer" value="3"/>
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61 <param help="(-expansion_range) " label="The range that is used to extend the isotope distribution with null intensity peaks in Th" min="0.0" name="param_expansion_range" optional="True" type="float" value="5.0"/>
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62 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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63 </expand>
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64 </inputs>
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65 <outputs>
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66 <data format="consensusxml" name="param_out"/>
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67 <data format="xml" name="param_feature_out"/>
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68 </outputs>
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69 <help>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
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71
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72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
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73 </tool>