view ERPairFinder.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="2.0.0">
    <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
-threads \${GALAXY_SLOTS:-24}
#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 format="mzml" help="(-in) " label="Input mzML file containing the ER spectra" name="param_in" optional="False" type="data"/>
      <param format="txt" help="(-pair_in) " label="Pair-file in the format: m/z-light m/z-heavy charge rt" name="param_pair_in" optional="False" type="data"/>
      <param help="(-precursor_mass_tolerance) " label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" min="0.0" name="param_precursor_mass_tolerance" optional="True" type="float" value="0.3"/>
      <expand macro="advanced_options">
        <param help="(-RT_tolerance) " label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" min="1.0" name="param_RT_tolerance" optional="True" type="float" value="200.0"/>
        <param help="(-max_charge) " label="Maximal charge state features should be search fo" min="1" name="param_max_charge" optional="True" type="integer" value="3"/>
        <param help="(-intensity_threshold) " label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" min="-1.0" name="param_intensity_threshold" optional="True" type="float" value="-1.0"/>
        <param help="(-max_isotope) " label="Max isotope of the isotope distribution to be considered" min="2" name="param_max_isotope" optional="True" type="integer" value="3"/>
        <param help="(-expansion_range) " label="The range that is used to extend the isotope distribution with null intensity peaks in Th" min="0.0" name="param_expansion_range" optional="True" type="float" value="5.0"/>
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out"/>
      <data format="xml" name="param_feature_out"/>
    </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>