<?xml version='1.0' encoding='UTF-8'?>
<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="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 $param_struc_elem_unit:
  -struc_elem_unit
  #if " " in str($param_struc_elem_unit):
    "$param_struc_elem_unit"
  #else
    $param_struc_elem_unit
  #end if
#end if
#if $param_method:
  -method
  #if " " in str($param_method):
    "$param_method"
  #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 name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/>
    <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/>
    <param name="param_struc_elem_unit" type="select" optional="True" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) ">
      <option value="Thomson">Thomson</option>
      <option value="DataPoints">DataPoints</option>
    </param>
    <param name="param_method" type="select" optional="True" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default">
      <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 name="param_force" 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>**What it does**

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>
  <expand macro="references"/>
</tool>