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annotate HighResPrecursorMassCorrector.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: [Signal processing and preprocessing]-->
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4 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.0.0">
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5 <description>Corrects the precursor mass and charge determined by the instrument software.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</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>HighResPrecursorMassCorrector
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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_out:
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19 -out $param_out
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20 #end if
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21 #if $param_out_csv:
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22 -out_csv $param_out_csv
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23 #end if
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24 -threads \${GALAXY_SLOTS:-24}
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25 #if $param_feature_in:
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26 -feature:in $param_feature_in
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27 #end if
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28 #if $param_feature_mz_tolerance:
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29 -feature:mz_tolerance $param_feature_mz_tolerance
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30 #end if
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31 #if $param_feature_mz_tolerance_unit:
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32 -feature:mz_tolerance_unit
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33 #if &quot; &quot; in str($param_feature_mz_tolerance_unit):
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34 &quot;$param_feature_mz_tolerance_unit&quot;
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35 #else
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36 $param_feature_mz_tolerance_unit
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37 #end if
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38 #end if
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39 #if $param_feature_rt_tolerance:
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40 -feature:rt_tolerance $param_feature_rt_tolerance
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41 #end if
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42 #if $param_feature_believe_charge:
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43 -feature:believe_charge
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44 #end if
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45 #if $param_feature_keep_original:
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46 -feature:keep_original
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47 #end if
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48 #if $param_feature_assign_all_matching:
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49 -feature:assign_all_matching
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50 #end if
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51 #if $param_nearest_peak_mz_tolerance:
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52 -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
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53 #end if
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54 #if $param_nearest_peak_mz_tolerance_unit:
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55 -nearest_peak:mz_tolerance_unit
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56 #if &quot; &quot; in str($param_nearest_peak_mz_tolerance_unit):
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57 &quot;$param_nearest_peak_mz_tolerance_unit&quot;
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58 #else
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59 $param_nearest_peak_mz_tolerance_unit
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60 #end if
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61 #end if
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62 #if $adv_opts.adv_opts_selector=='advanced':
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63 #if $adv_opts.param_force:
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64 -force
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65 #end if
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66 #if $adv_opts.param_feature_max_trace:
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67 -feature:max_trace $adv_opts.param_feature_max_trace
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68 #end if
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69 #end if
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70 </command>
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71 <inputs>
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72 <param format="mzml" help="(-in) " label="input file (centroided data)" name="param_in" optional="False" type="data"/>
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73 <param format="xml" help="(-in) " label="features used to correct precursor masses" name="param_feature_in" optional="True" type="data"/>
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74 <param help="(-mz_tolerance) Used to determine matching to feature mass traces" label="The precursor mass tolerance" name="param_feature_mz_tolerance" type="float" value="5.0"/>
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75 <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_feature_mz_tolerance_unit" optional="True" type="select" value="ppm">
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76 <option value="Da">Da</option>
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77 <option value="ppm">ppm</option>
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78 </param>
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79 <param help="(-rt_tolerance) " label="Additional retention time tolerance added to feature boundaries" name="param_feature_rt_tolerance" type="float" value="0.0"/>
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80 <param checked="false" falsevalue="" help="(-believe_charge) " label="Whether precursor charge is assumed correct" name="param_feature_believe_charge" optional="True" truevalue="-feature:believe_charge" type="boolean"/>
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81 <param checked="false" falsevalue="" help="(-keep_original) " label="Whether a copy of the precusor and MS2 should be made (true) or if the original should be discarded (false)" name="param_feature_keep_original" optional="True" truevalue="-feature:keep_original" type="boolean"/>
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82 <param checked="false" falsevalue="" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)" label="Whether a precursor should be corrected to all matching features (true) or only the nearest (false)" name="param_feature_assign_all_matching" optional="True" truevalue="-feature:assign_all_matching" type="boolean"/>
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83 <param help="(-mz_tolerance) Used to determine matching to next MS1 peak" label="The precursor mass tolerance" name="param_nearest_peak_mz_tolerance" type="float" value="0.0"/>
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84 <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_nearest_peak_mz_tolerance_unit" optional="True" type="select" value="ppm">
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85 <option value="Da">Da</option>
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86 <option value="ppm">ppm</option>
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87 </param>
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88 <expand macro="advanced_options">
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89 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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90 <param help="(-max_trace) " label="Maximum isotopic trace considered in matching a precursor to a feature" name="param_feature_max_trace" type="integer" value="2"/>
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91 </expand>
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92 </inputs>
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93 <outputs>
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94 <data format="mzml" name="param_out"/>
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95 <data format="tabular" name="param_out_csv"/>
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96 </outputs>
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97 <help>Corrects the precursor mass and charge determined by the instrument software.
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98
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99
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100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help>
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101 </tool>