annotate ERPairFinder.xml @ 6:e301986c34e2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab

<?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: [Utilities]-->
<tool id="ERPairFinder" name="ERPairFinder" version="2.2.0">
  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
  <macros>
    <token name="@EXECUTABLE@">ERPairFinder</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ERPairFinder

#if $param_in:
  -in $param_in
#end if
#if $param_pair_in:
  -pair_in $param_pair_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_feature_out:
  -feature_out $param_feature_out
#end if
#if $param_precursor_mass_tolerance:
  -precursor_mass_tolerance $param_precursor_mass_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_RT_tolerance:
  -RT_tolerance $adv_opts.param_RT_tolerance
#end if
    #if $adv_opts.param_max_charge:
  -max_charge $adv_opts.param_max_charge
#end if
    #if $adv_opts.param_intensity_threshold:
  -intensity_threshold $adv_opts.param_intensity_threshold
#end if
    #if $adv_opts.param_max_isotope:
  -max_isotope $adv_opts.param_max_isotope
#end if
    #if $adv_opts.param_expansion_range:
  -expansion_range $adv_opts.param_expansion_range
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/>
    <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in) "/>
    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help="(-precursor_mass_tolerance) "/>
    <expand macro="advanced_options">
      <param name="param_RT_tolerance" type="float" min="1.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance) "/>
      <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search fo" help="(-max_charge) "/>
      <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help="(-intensity_threshold) "/>
      <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope) "/>
      <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help="(-expansion_range) "/>
      <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="consensusxml"/>
    <data name="param_feature_out" format="featurexml"/>
  </outputs>
  <help>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.


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