view MRMMapper.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: [Targeted Experiments]-->
  <tool id="MRMMapper" name="MRMMapper" version="2.0.0">
    <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
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="Input file containing chromatograms (converted mzXML file)" name="param_in" optional="False" type="data"/>
      <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/>
      <param help="(-precursor_tolerance) " label="Precursor tolerance when mapping (in Th)" name="param_precursor_tolerance" type="float" value="0.1"/>
      <param help="(-product_tolerance) " label="Product tolerance when mapping (in Th)" name="param_product_tolerance" type="float" value="0.1"/>
      <param checked="false" falsevalue="" help="(-no-strict) " label="run in non-strict mode and allow some chromatograms to not be mapped" name="param_no_strict" optional="True" truevalue="-no-strict" type="boolean"/>
      <expand macro="advanced_options">
        <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="mzml" name="param_out"/>
    </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>