--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MapRTTransformer.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,142 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<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="stdio"/>
+  <expand macro="requirements"/>
+  <command>MapRTTransformer
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+
+#if $rep_param_out:
+-out
+  #for token in $rep_param_out:
+    #if " " in str(token):
+      "$token.param_out"
+    #else
+      $token.param_out
+    #end if
+  #end for
+#end if
+-trafo_in
+  #for token in $param_trafo_in:
+    $token
+  #end for
+
+#if $rep_param_trafo_out:
+-trafo_out
+  #for token in $rep_param_trafo_out:
+    #if " " in str(token):
+      "$token.param_trafo_out"
+    #else
+      $token.param_trafo_out
+    #end if
+  #end for
+#end if
+#if $param_invert:
+  -invert
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_model_type:
+  -model:type
+  #if " " in str($param_model_type):
+    "$param_model_type"
+  #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 $param_model_b_spline_extrapolate:
+  -model:b_spline:extrapolate
+  #if " " in str($param_model_b_spline_extrapolate):
+    "$param_model_b_spline_extrapolate"
+  #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 $param_model_interpolated_interpolation_type:
+  -model:interpolated:interpolation_type
+  #if " " in str($param_model_interpolated_interpolation_type):
+    "$param_model_interpolated_interpolation_type"
+  #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="featurexml,consensusxml,mzml,idxml" multiple="true" optional="True" size="30" label="Input files to transform (separated by blanks)" help="(-in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_trafo_in" type="data" format="trafoxml" multiple="true" optional="False" size="30" label="Transformations to apply (files separated by blanks)" help="(-trafo_in) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_invert" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert) "/>
+    <param name="param_model_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_model_linear_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
+    <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" 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"/>
+    <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
+    <param name="param_model_b_spline_extrapolate" type="select" optional="True" value="linear" label="Method to use for extrapolation beyond the original data range" 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)">
+      <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 name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/>
+    <param name="param_model_interpolated_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>
+    <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" metadata_source="param_in" format="input"/>
+    <data name="param_trafo_out" format="trafoxml"/>
+  </outputs>
+  <help>**What it does**
+
+Applies retention time transformations to maps.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
+  <expand macro="references"/>
+</tool>