--- a/BaselineFilter.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/BaselineFilter.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,51 +1,77 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="BaselineFilter" name="BaselineFilter" version="1.12.0">
-  <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
+<?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
 
--in ${param_in}
--out ${param_out}
--struc_elem_length ${param_struc_elem_length}
--struc_elem_unit ${param_struc_elem_unit}
--method ${param_method}
--threads \${GALAXY_SLOTS:-24} 
+#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 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' parameter." 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. If you are unsure, use the default." help="(-method)">
-      <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>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output raw data file " format="mzML"/>
-  </outputs>
-  <help>**What it does**
-
-Removes the baseline from profile spectra using a top-hat filter.
+    <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
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_BaselineFilter.html</help>
+  </tool>