Mercurial > repos > galaxyp > openms_highresprecursormasscorrector

annotate HighResPrecursorMassCorrector.xml @ 0:e37289d08990 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:55:06 -0500
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e37289d08990 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="2.1.0">
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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 #if $param_feature_in:
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25 -feature:in $param_feature_in
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26 #end if
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27 #if $param_feature_mz_tolerance:
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28 -feature:mz_tolerance $param_feature_mz_tolerance
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29 #end if
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30 #if $param_feature_mz_tolerance_unit:
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31 -feature:mz_tolerance_unit $param_feature_mz_tolerance_unit
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32 #end if
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33 #if $param_feature_rt_tolerance:
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34 -feature:rt_tolerance $param_feature_rt_tolerance
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35 #end if
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36 #if $param_feature_believe_charge:
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37 -feature:believe_charge
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38 #end if
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39 #if $param_feature_keep_original:
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40 -feature:keep_original
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41 #end if
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42 #if $param_feature_assign_all_matching:
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43 -feature:assign_all_matching
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44 #end if
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45 #if $param_nearest_peak_mz_tolerance:
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46 -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
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47 #end if
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48 #if $param_nearest_peak_mz_tolerance_unit:
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49 -nearest_peak:mz_tolerance_unit $param_nearest_peak_mz_tolerance_unit
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50 #end if
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51 #if $adv_opts.adv_opts_selector=='advanced':
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52 #if $adv_opts.param_force:
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53 -force
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54 #end if
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55 #if $adv_opts.param_feature_max_trace:
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56 -feature:max_trace $adv_opts.param_feature_max_trace
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57 #end if
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58 #end if
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59 </command>
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60 <inputs>
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61 <param name="param_in" type="data" format="mzml" optional="False" label="Input file (centroided data)" help="(-in) "/>
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62 <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Features used to correct precursor masses" help="(-in) "/>
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63 <param name="param_feature_mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="(-mz_tolerance) Used to determine matching to feature mass traces"/>
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64 <param name="param_feature_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
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65 <option value="Da">Da</option>
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66 <option value="ppm" selected="true">ppm</option>
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67 </param>
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68 <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/>
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69 <param name="param_feature_believe_charge" display="radio" type="boolean" truevalue="-feature:believe_charge" falsevalue="" checked="false" optional="True" label="Assume precursor charge to be correct" help="(-believe_charge) "/>
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70 <param name="param_feature_keep_original" display="radio" type="boolean" truevalue="-feature:keep_original" falsevalue="" checked="false" optional="True" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help="(-keep_original) "/>
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71 <param name="param_feature_assign_all_matching" display="radio" type="boolean" truevalue="-feature:assign_all_matching" falsevalue="" checked="false" optional="True" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)"/>
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72 <param name="param_nearest_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(-mz_tolerance) Set to 0.0 to disable"/>
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73 <param name="param_nearest_peak_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
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74 <option value="Da">Da</option>
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75 <option value="ppm" selected="true">ppm</option>
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76 </param>
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77 <expand macro="advanced_options">
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78 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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79 <param name="param_feature_max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help="(-max_trace) "/>
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80 </expand>
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81 </inputs>
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82 <outputs>
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83 <data name="param_out" format="mzml"/>
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84 <data name="param_out_csv" format="tabular"/>
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85 </outputs>
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86 <help>Corrects the precursor mass and charge determined by the instrument software.
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87
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88
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89 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help>
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90 </tool>