Mercurial > repos > galaxyp > openms_maprttransformer

annotate MapRTTransformer.xml @ 2:b5b172f790c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:16:07 -0400
parents af8d0e751415
children 5b776e2133f1
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Map Alignment]-->
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4 <tool id="MapRTTransformer" name="MapRTTransformer" version="2.2.0">
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5 <description>Applies retention time transformations to maps.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MapRTTransformer</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>MapRTTransformer
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_trafo_in:
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22 -trafo_in $param_trafo_in
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23 #end if
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24 #if $param_trafo_out:
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25 -trafo_out $param_trafo_out
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26 #end if
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27 #if $param_invert:
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28 -invert
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29 #end if
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30 #if $param_store_original_rt:
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31 -store_original_rt
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32 #end if
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33 #if $param_model_type:
1
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34 -model:type
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35 #if " " in str($param_model_type):
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36 "$param_model_type"
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37 #else
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38 $param_model_type
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39 #end if
0
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40 #end if
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41 #if $param_model_linear_symmetric_regression:
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42 -model:linear:symmetric_regression
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43 #end if
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44 #if $param_model_b_spline_wavelength:
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45 -model:b_spline:wavelength $param_model_b_spline_wavelength
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46 #end if
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47 #if $param_model_b_spline_num_nodes:
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48 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
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49 #end if
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50 #if $param_model_b_spline_extrapolate:
1
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51 -model:b_spline:extrapolate
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52 #if " " in str($param_model_b_spline_extrapolate):
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53 "$param_model_b_spline_extrapolate"
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54 #else
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55 $param_model_b_spline_extrapolate
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56 #end if
0
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57 #end if
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58 #if $param_model_b_spline_boundary_condition:
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59 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
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60 #end if
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61 #if $param_model_lowess_span:
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62 -model:lowess:span $param_model_lowess_span
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63 #end if
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64 #if $param_model_lowess_num_iterations:
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65 -model:lowess:num_iterations $param_model_lowess_num_iterations
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66 #end if
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67 #if $param_model_lowess_delta:
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68 -model:lowess:delta $param_model_lowess_delta
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69 #end if
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70 #if $param_model_lowess_interpolation_type:
1
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71 -model:lowess:interpolation_type
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72 #if " " in str($param_model_lowess_interpolation_type):
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73 "$param_model_lowess_interpolation_type"
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74 #else
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75 $param_model_lowess_interpolation_type
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76 #end if
0
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77 #end if
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78 #if $param_model_lowess_extrapolation_type:
1
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79 -model:lowess:extrapolation_type
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80 #if " " in str($param_model_lowess_extrapolation_type):
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81 "$param_model_lowess_extrapolation_type"
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82 #else
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83 $param_model_lowess_extrapolation_type
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84 #end if
0
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85 #end if
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86 #if $param_model_interpolated_interpolation_type:
1
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87 -model:interpolated:interpolation_type
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88 #if " " in str($param_model_interpolated_interpolation_type):
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89 "$param_model_interpolated_interpolation_type"
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90 #else
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91 $param_model_interpolated_interpolation_type
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92 #end if
0
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93 #end if
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94 #if $param_model_interpolated_extrapolation_type:
1
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95 -model:interpolated:extrapolation_type
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96 #if " " in str($param_model_interpolated_extrapolation_type):
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97 "$param_model_interpolated_extrapolation_type"
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98 #else
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99 $param_model_interpolated_extrapolation_type
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100 #end if
0
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101 #end if
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102 #if $adv_opts.adv_opts_selector=='advanced':
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103 #if $adv_opts.param_force:
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104 -force
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105 #end if
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106 #end if
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107 </command>
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108 <inputs>
1
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109 <param name="param_in" type="data" format="mzml,featurexml,consensusxml,idxml" optional="True" label="Input file to transform (separated by blanks)" help="(-in) "/>
0
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110 <param name="param_trafo_in" type="data" format="trafoxml" optional="False" label="Transformation to apply" help="(-trafo_in) "/>
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111 <param name="param_invert" display="radio" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformation (approximatively) before applying it" help="(-invert) "/>
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112 <param name="param_store_original_rt" display="radio" type="boolean" truevalue="-store_original_rt" falsevalue="" checked="false" optional="True" label="Store the original retention times (before transformation) as meta data in the output file" help="(-store_original_rt) "/>
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113 <param name="param_model_type" type="select" optional="False" value="none" label="Type of model" help="(-type) ">
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114 <option value="none" selected="true">none</option>
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115 <option value="linear">linear</option>
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116 <option value="b_spline">b_spline</option>
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117 <option value="lowess">lowess</option>
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118 <option value="interpolated">interpolated</option>
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119 </param>
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120 <param name="param_model_linear_symmetric_regression" display="radio" 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'"/>
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121 <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"/>
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122 <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"/>
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123 <param name="param_model_b_spline_extrapolate" display="radio" type="select" optional="False" 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)">
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124 <option value="linear" selected="true">linear</option>
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125 <option value="b_spline">b_spline</option>
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126 <option value="constant">constant</option>
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127 <option value="global_linear">global_linear</option>
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128 </param>
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129 <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) "/>
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130 <param name="param_model_lowess_span" type="float" min="0.0" max="1.0" optional="True" value="0.666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="(-span) Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
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131 <param name="param_model_lowess_num_iterations" type="integer" min="0" optional="True" value="3" label="Number of robustifying iterations for lowess fitting" help="(-num_iterations) "/>
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132 <param name="param_model_lowess_delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input," help="(-delta) e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
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133 <param name="param_model_lowess_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Method to use for interpolation between datapoints computed by lowess" help="(-interpolation_type) 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
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134 <option value="linear">linear</option>
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135 <option value="cspline" selected="true">cspline</option>
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136 <option value="akima">akima</option>
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137 </param>
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138 <param name="param_model_lowess_extrapolation_type" display="radio" type="select" optional="False" value="four-point-linear" label="Method to use for extrapolation outside the data range" help="(-extrapolation_type) 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
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139 <option value="two-point-linear">two-point-linear</option>
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140 <option value="four-point-linear" selected="true">four-point-linear</option>
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141 <option value="global-linear">global-linear</option>
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142 </param>
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143 <param name="param_model_interpolated_interpolation_type" display="radio" type="select" optional="False" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
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144 <option value="linear">linear</option>
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145 <option value="cspline" selected="true">cspline</option>
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146 <option value="akima">akima</option>
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147 </param>
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148 <param name="param_model_interpolated_extrapolation_type" display="radio" type="select" optional="False" value="two-point-linear" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="(-extrapolation_type) Note that global-linear may not be continuous at the border">
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149 <option value="two-point-linear" selected="true">two-point-linear</option>
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150 <option value="four-point-linear">four-point-linear</option>
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151 <option value="global-linear">global-linear</option>
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152 </param>
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153 <expand macro="advanced_options">
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154 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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155 </expand>
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156 </inputs>
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157 <outputs>
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158 <data name="param_out" metadata_source="param_in" format="input"/>
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159 <data name="param_trafo_out" format="trafoxml"/>
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160 </outputs>
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161 <help>Applies retention time transformations to maps.
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162
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164 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
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165 </tool>