<?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

#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 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</help>
  </tool>