<?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>