annotate MetaboliteSpectralMatcher.xml @ 6:399fae38a523 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="2.3.0">
  <description>Perform a spectral library search.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MetaboliteSpectralMatcher

#if $param_in:
  -in $param_in
#end if
#if $param_database:
  -database $param_database
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_prec_mass_error_value:
  -algorithm:prec_mass_error_value $param_algorithm_prec_mass_error_value
#end if
#if $param_algorithm_frag_mass_error_value:
  -algorithm:frag_mass_error_value $param_algorithm_frag_mass_error_value
#end if
#if $param_algorithm_mass_error_unit:
  -algorithm:mass_error_unit
  #if " " in str($param_algorithm_mass_error_unit):
    "$param_algorithm_mass_error_unit"
  #else
    $param_algorithm_mass_error_unit
  #end if
#end if
#if $param_algorithm_report_mode:
  -algorithm:report_mode
  #if " " in str($param_algorithm_report_mode):
    "$param_algorithm_report_mode"
  #else
    $param_algorithm_report_mode
  #end if
#end if
#if $param_algorithm_ionization_mode:
  -algorithm:ionization_mode
  #if " " in str($param_algorithm_ionization_mode):
    "$param_algorithm_ionization_mode"
  #else
    $param_algorithm_ionization_mode
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input spectra" help="(-in) "/>
    <param name="param_database" type="data" format="mzml" optional="True" value="CHEMISTRY/MetaboliteSpectralDB.mzML" label="Default spectral database" help="(-database) "/>
    <param name="param_algorithm_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass" help="(-prec_mass_error_value) "/>
    <param name="param_algorithm_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions" help="(-frag_mass_error_value) "/>
    <param name="param_algorithm_mass_error_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit) ">
      <option value="ppm" selected="true">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_algorithm_report_mode" display="radio" type="select" optional="False" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode) ">
      <option value="top3" selected="true">top3</option>
      <option value="best">best</option>
    </param>
    <param name="param_algorithm_ionization_mode" display="radio" type="select" optional="False" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode) ">
      <option value="positive" selected="true">positive</option>
      <option value="negative">negative</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) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
  </outputs>
  <help>Perform a spectral library search.


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