<?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: [Signal processing and preprocessing]-->
  <tool id="BaselineFilter" name="BaselineFilter" version="2.0.0">
    <description>Removes the baseline from profile spectra using a top-hat filter.</description>
    <macros>
      <token name="@EXECUTABLE@">BaselineFilter</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>BaselineFilter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_struc_elem_length:
  -struc_elem_length $param_struc_elem_length
#end if
#if $param_struc_elem_unit:
  -struc_elem_unit
  #if &quot; &quot; in str($param_struc_elem_unit):
    &quot;$param_struc_elem_unit&quot;
  #else
    $param_struc_elem_unit
  #end if
#end if
#if $param_method:
  -method
  #if &quot; &quot; in str($param_method):
    &quot;$param_method&quot;
  #else
    $param_method
  #end if
#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 raw data file" name="param_in" optional="False" type="data"/>
      <param help="(-struc_elem_length) " label="Length of the structuring element (should be wider than maximal peak width - see documentation)" name="param_struc_elem_length" type="float" value="3.0"/>
      <param help="(-struc_elem_unit) " label="Unit of 'struc_elem_length' paramete" name="param_struc_elem_unit" optional="True" type="select" value="Thomson">
        <option value="Thomson">Thomson</option>
        <option value="DataPoints">DataPoints</option>
      </param>
      <param help="(-method) If you are unsure, use the default" label="The name of the morphological filter to be applied" name="param_method" optional="True" type="select" value="tophat">
        <option value="identity">identity</option>
        <option value="erosion">erosion</option>
        <option value="dilation">dilation</option>
        <option value="opening">opening</option>
        <option value="closing">closing</option>
        <option value="gradient">gradient</option>
        <option value="tophat">tophat</option>
        <option value="bothat">bothat</option>
        <option value="erosion_simple">erosion_simple</option>
        <option value="dilation_simple">dilation_simple</option>
      </param>
      <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>Removes the baseline from profile spectra using a top-hat filter.


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