annotate HighResPrecursorMassCorrector.xml @ 4:a0ea30030f55 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

<?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>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>HighResPrecursorMassCorrector

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_csv:
  -out_csv $param_out_csv
#end if
#if $param_feature_in:
  -feature:in $param_feature_in
#end if
#if $param_feature_mz_tolerance:
  -feature:mz_tolerance $param_feature_mz_tolerance
#end if
#if $param_feature_mz_tolerance_unit:
  -feature:mz_tolerance_unit
  #if " " in str($param_feature_mz_tolerance_unit):
    "$param_feature_mz_tolerance_unit"
  #else
    $param_feature_mz_tolerance_unit
  #end if
#end if
#if $param_feature_rt_tolerance:
  -feature:rt_tolerance $param_feature_rt_tolerance
#end if
#if $param_feature_believe_charge:
  -feature:believe_charge
#end if
#if $param_feature_keep_original:
  -feature:keep_original
#end if
#if $param_feature_assign_all_matching:
  -feature:assign_all_matching
#end if
#if $param_nearest_peak_mz_tolerance:
  -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
#end if
#if $param_nearest_peak_mz_tolerance_unit:
  -nearest_peak:mz_tolerance_unit
  #if " " in str($param_nearest_peak_mz_tolerance_unit):
    "$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:
  -feature:max_trace $adv_opts.param_feature_max_trace
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file (centroided data)" help="(-in) "/>
    <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Features used to correct precursor masses" help="(-in) "/>
    <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"/>
    <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) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </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>
  <outputs>
    <data name="param_out" format="mzml"/>
    <data name="param_out_csv" format="tabular"/>
  </outputs>
  <help>Corrects the precursor mass and charge determined by the instrument software.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help>
</tool>