--- a/MapRTTransformer.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MapRTTransformer.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,58 +1,114 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MapRTTransformer" name="MapRTTransformer" version="1.12.0">
-  <description>Applies retention time transformations to maps.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MapRTTransformer</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MapRTTransformer
+<?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: [Map Alignment]-->
+  <tool id="MapRTTransformer" name="MapRTTransformer" version="2.0.0">
+    <description>Applies retention time transformations to maps.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MapRTTransformer</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MapRTTransformer
 
--in ${param_in}
--out ${param_out}
--trafo_in ${param_trafo_in}
--trafo_out ${param_trafo_out}
-${param_invert}
--threads \${GALAXY_SLOTS:-24} 
--model:type ${param_type}
-${param_symmetric_regression}
--model:interpolated:interpolation_type ${param_interpolation_type}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_trafo_in:
+  -trafo_in $param_trafo_in
+#end if
+#if $param_trafo_out:
+  -trafo_out $param_trafo_out
+#end if
+#if $param_invert:
+  -invert
+#end if
+#if $param_store_original_rt:
+  -store_original_rt
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_model_type:
+  -model:type
+  #if &quot; &quot; in str($param_model_type):
+    &quot;$param_model_type&quot;
+  #else
+    $param_model_type
+  #end if
+#end if
+#if $param_model_linear_symmetric_regression:
+  -model:linear:symmetric_regression
+#end if
+#if $param_model_b_spline_wavelength:
+  -model:b_spline:wavelength $param_model_b_spline_wavelength
+#end if
+#if $param_model_b_spline_num_nodes:
+  -model:b_spline:num_nodes $param_model_b_spline_num_nodes
+#end if
+#if $param_model_b_spline_extrapolate:
+  -model:b_spline:extrapolate
+  #if &quot; &quot; in str($param_model_b_spline_extrapolate):
+    &quot;$param_model_b_spline_extrapolate&quot;
+  #else
+    $param_model_b_spline_extrapolate
+  #end if
+#end if
+#if $param_model_b_spline_boundary_condition:
+  -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
+#end if
+#if $param_model_interpolated_interpolation_type:
+  -model:interpolated:interpolation_type
+  #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
+    &quot;$param_model_interpolated_interpolation_type&quot;
+  #else
+    $param_model_interpolated_interpolation_type
+  #end if
+#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,featureXML,consensusXML,idXML" optional="True" size="20" label="Input files to transform (separated by blanks)" help="(-in)"/>
-    <param name="param_trafo_in" type="data" format="" optional="False" size="20" label="Transformations to apply (files separated by blanks)" help="(-trafo_in)"/>
-    <param name="param_invert" type="boolean" truevalue="-invert true" falsevalue="-invert false" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert)"/>
-    <param name="param_type" type="select" optional="True" value="none" label="Type of model" help="(-type)">
-      <option value="none">none</option>
-      <option value="linear">linear</option>
-      <option value="b_spline">b_spline</option>
-      <option value="interpolated">interpolated</option>
-    </param>
-    <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
-    <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
-      <option value="linear">linear</option>
-      <option value="cspline">cspline</option>
-      <option value="akima">akima</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together." format="idXML">
-      <change_format>
-        <when input="param_out_type" value="mzML" format="mzML"/>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
-      </change_format>
-    </data>
-    <data name="param_trafo_out" label="Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together." format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Applies retention time transformations to maps.
+    <inputs>
+      <param format="xml,consensusxml,mzml" help="(-in) " label="Input file to transform (separated by blanks)" name="param_in" optional="True" type="data"/>
+      <param format="trafoxml" help="(-trafo_in) " label="Transformation to apply" name="param_trafo_in" optional="False" type="data"/>
+      <param checked="false" falsevalue="" help="(-invert) " label="Invert transformation (approximatively) before applying it" name="param_invert" optional="True" truevalue="-invert" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-store_original_rt) " label="Store the original retention times (before transformation) as meta data in the output file" name="param_store_original_rt" optional="True" truevalue="-store_original_rt" type="boolean"/>
+      <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="none">
+        <option value="none">none</option>
+        <option value="linear">linear</option>
+        <option value="b_spline">b_spline</option>
+        <option value="interpolated">interpolated</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Perform linear regression on 'y - x' vs" name="param_model_linear_symmetric_regression" optional="True" truevalue="-model:linear:symmetric_regression" type="boolean"/>
+      <param help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" min="0.0" name="param_model_b_spline_wavelength" optional="True" type="float" value="0.0"/>
+      <param help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing" label="Number of nodes for B-spline fitting" min="0" name="param_model_b_spline_num_nodes" optional="True" type="integer" value="5"/>
+      <param help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)" label="Method to use for extrapolation beyond the original data range" name="param_model_b_spline_extrapolate" optional="True" type="select" value="linear">
+        <option value="linear">linear</option>
+        <option value="b_spline">b_spline</option>
+        <option value="constant">constant</option>
+        <option value="global_linear">global_linear</option>
+      </param>
+      <param help="(-boundary_condition) " label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" max="2" min="0" name="param_model_b_spline_boundary_condition" optional="True" type="integer" value="2"/>
+      <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline">
+        <option value="linear">linear</option>
+        <option value="cspline">cspline</option>
+        <option value="akima">akima</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="input" metadata_source="param_in" name="param_out"/>
+      <data format="trafoxml" name="param_trafo_out"/>
+    </outputs>
+    <help>Applies retention time transformations to maps.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
+  </tool>