annotate MRMPairFinder.xml @ 2:00e1e071ecf4 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: [Utilities]-->
<tool id="MRMPairFinder" name="MRMPairFinder" version="2.2.0">
  <description>Util which can be used to evaluate labeled pair ratios on MRM features.</description>
  <macros>
    <token name="@EXECUTABLE@">MRMPairFinder</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMPairFinder

#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 $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_mass_tolerance:
  -mass_tolerance $adv_opts.param_mass_tolerance
#end if
    #if $adv_opts.param_RT_tolerance:
  -RT_tolerance $adv_opts.param_RT_tolerance
#end if
    #if $adv_opts.param_RT_pair_tolerance:
  -RT_pair_tolerance $adv_opts.param_RT_pair_tolerance
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featurexml" optional="False" label="Input featureXML file containing the features of the MRM experiment spectra" help="(-in) "/>
    <param name="param_pair_in" type="data" format="tabular" optional="False" label="Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt" help="(-pair_in) "/>
    <expand macro="advanced_options">
      <param name="param_mass_tolerance" type="float" min="0.0" optional="True" value="0.01" 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="(-mass_tolerance) "/>
      <param name="param_RT_tolerance" type="float" min="0.0" 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_RT_pair_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have" help="(-RT_pair_tolerance) "/>
      <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 labeled pair ratios on MRM features.


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