comparison HighResPrecursorMassCorrector.xml @ 3:3419097ac19f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

2:9e26f5c770f8

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.1.0">
  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
  <macros>
    <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
    <import>macros.xml</import>
  </macros>

    "$param_nearest_peak_mz_tolerance_unit"
  #else
    $param_nearest_peak_mz_tolerance_unit
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_feature_max_trace:

    </param>
    <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/>
    <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) "/>
    <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) "/>
    <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)"/>
    <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"/>
    <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) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <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) "/>
    </expand>
  </inputs>

3:3419097ac19f

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.2.0">
  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
  <macros>
    <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
    <import>macros.xml</import>
  </macros>

    "$param_nearest_peak_mz_tolerance_unit"
  #else
    $param_nearest_peak_mz_tolerance_unit
  #end if
#end if
#if $param_highest_intensity_peak_mz_tolerance:
  -highest_intensity_peak:mz_tolerance $param_highest_intensity_peak_mz_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_feature_max_trace:

    </param>
    <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/>
    <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) "/>
    <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) "/>
    <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)"/>
    <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) (Disable method by setting value to 0.0)"/>
    <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) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <param name="param_highest_intensity_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak (Da)" help="(-mz_tolerance) Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <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) "/>
    </expand>
  </inputs>