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

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

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="ERPairFinder" name="ERPairFinder" version="1.12.0">
  <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="stdio"/>
  <expand macro="requirements"/>
  <command>ERPairFinder

-in ${param_in}
-pair_in ${param_pair_in}
-out ${param_out}
-feature_out ${param_feature_out}
-precursor_mass_tolerance ${param_precursor_mass_tolerance}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -RT_tolerance ${adv_opts.param_RT_tolerance}
    -max_charge ${adv_opts.param_max_charge}
    -intensity_threshold ${adv_opts.param_intensity_threshold}
    -max_isotope ${adv_opts.param_max_isotope}
    -expansion_range ${adv_opts.param_expansion_range}
#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 for." 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)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output consensusXML file were the pairs of the feature are written into." format="consensusXML"/>
    <data name="param_feature_out" label="Output featureXML file, only written if given, skipped otherwise." format="featureXML"/>
  </outputs>
  <help>**What it does**

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

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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>