<?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: [Targeted Experiments]-->
<tool id="MRMMapper" name="MRMMapper" version="2.3.0">
  <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
  <macros>
    <token name="@EXECUTABLE@">MRMMapper</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MRMMapper

#if $param_in:
  -in $param_in
#end if
#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_precursor_tolerance:
  -precursor_tolerance $param_precursor_tolerance
#end if
#if $param_product_tolerance:
  -product_tolerance $param_product_tolerance
#end if
#if $param_no_strict:
  -no-strict
#end if
#if $param_allow_multiple_mappings:
  -allow_multiple_mappings
#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 file containing chromatograms (converted mzXML file)" help="(-in) "/>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>
    <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
    <param name="param_allow_multiple_mappings" display="radio" type="boolean" truevalue="-allow_multiple_mappings" falsevalue="" checked="false" optional="True" label="Allow multiple mappings (will take the last matching from the TraML)" help="(-allow_multiple_mappings) "/>
    <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="mzml"/>
  </outputs>
  <help>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)


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