Mercurial > repos > galaxyp > openms_maprttransformer

annotate MapRTTransformer.xml @ 13:aec26bf377fb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:37 +0000
parents 88ac532206c7
children 317a5cb79894
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652ee76d7113 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Map Alignment]-->
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4 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 #if $in:
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18 mkdir in &&
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19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 #end if
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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22 mkdir out &&
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23 #end if
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24 mkdir trafo_in &&
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25 ln -s '$trafo_in' 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)' &&
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26 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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27 mkdir trafo_out &&
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28 #end if
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30 ## Main program call
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32 set -o pipefail &&
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33 @EXECUTABLE@ -write_ctd ./ &&
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34 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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35 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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36 #if $in:
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37 -in
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38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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39 #end if
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40 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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41 -out
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42 'out/output.${in.ext}'
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43 #end if
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44 -trafo_in
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45 'trafo_in/${re.sub("[^\w\-_]", "_", $trafo_in.element_identifier)}.$gxy2omsext($trafo_in.ext)'
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46 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 -trafo_out
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48 'trafo_out/output.${gxy2omsext("trafoxml")}'
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49 #end if
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50 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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51 | tee '$stdout'
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52 #end if
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53
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54 ## Postprocessing
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55 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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56 && mv 'out/output.${in.ext}' '$out'
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57 #end if
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58 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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59 && mv 'trafo_out/output.${gxy2omsext("trafoxml")}' '$trafo_out'
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60 #end if
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61 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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62 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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63 #end if]]></command>
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64 <configfiles>
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65 <inputs name="args_json" data_style="paths"/>
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66 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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67 </configfiles>
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68 <inputs>
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69 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" optional="true" label="Input file to transform (separated by blanks)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
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70 <param argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
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71 <param argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/>
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72 <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output file" help=""/>
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73 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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74 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
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75 <option value="none" selected="true">none</option>
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76 <option value="linear">linear</option>
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77 <option value="b_spline">b_spline</option>
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78 <option value="lowess">lowess</option>
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79 <option value="interpolated">interpolated</option>
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80 <expand macro="list_string_san" name="type"/>
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81 </param>
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82 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
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83 <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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84 <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
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85 <option value="1/x">1/x</option>
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86 <option value="1/x2">1/x2</option>
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87 <option value="ln(x)">ln(x)</option>
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88 <option value=""></option>
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89 <expand macro="list_string_san" name="x_weight"/>
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90 </param>
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91 <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
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92 <option value="1/y">1/y</option>
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93 <option value="1/y2">1/y2</option>
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94 <option value="ln(y)">ln(y)</option>
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95 <option value=""></option>
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96 <expand macro="list_string_san" name="y_weight"/>
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97 </param>
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98 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
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99 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
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100 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
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101 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
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102 </section>
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103 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
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104 <param name="wavelength" argument="-model:b_spline:wavelength" type="float" optional="true" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="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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105 <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
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106 <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" optional="true" label="Method to use for extrapolation beyond the original data range" help="'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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107 <option value="linear" selected="true">linear</option>
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108 <option value="b_spline">b_spline</option>
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109 <option value="constant">constant</option>
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110 <option value="global_linear">global_linear</option>
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111 <expand macro="list_string_san" name="extrapolate"/>
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112 </param>
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113 <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" optional="true" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
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114 </section>
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115 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
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116 <param name="span" argument="-model:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
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117 <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" optional="true" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
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118 <param name="delta" argument="-model:lowess:delta" type="float" optional="true" 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="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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119 <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" optional="true" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
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120 <option value="linear">linear</option>
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121 <option value="cspline" selected="true">cspline</option>
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122 <option value="akima">akima</option>
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123 <expand macro="list_string_san" name="interpolation_type"/>
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124 </param>
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125 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" optional="true" label="Method to use for extrapolation outside the data range" help="'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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126 <option value="two-point-linear">two-point-linear</option>
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127 <option value="four-point-linear" selected="true">four-point-linear</option>
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128 <option value="global-linear">global-linear</option>
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129 <expand macro="list_string_san" name="extrapolation_type"/>
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130 </param>
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131 </section>
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132 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
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133 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
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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 <expand macro="list_string_san" name="interpolation_type"/>
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138 </param>
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139 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" optional="true" 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="Note that global-linear may not be continuous at the border">
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140 <option value="two-point-linear" selected="true">two-point-linear</option>
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141 <option value="four-point-linear">four-point-linear</option>
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142 <option value="global-linear">global-linear</option>
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143 <expand macro="list_string_san" name="extrapolation_type"/>
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144 </param>
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145 </section>
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146 </section>
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147 <expand macro="adv_opts_macro">
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148 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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149 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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150 <expand macro="list_string_san" name="test"/>
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151 </param>
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152 </expand>
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153 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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154 <option value="out_FLAG">out (Output file (same file type as 'in'))</option>
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155 <option value="trafo_out_FLAG">trafo_out (Transformation output file)</option>
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156 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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157 </param>
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158 </inputs>
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159 <outputs>
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160 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in">
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161 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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162 </data>
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163 <data name="trafo_out" label="${tool.name} on ${on_string}: trafo_out" format="trafoxml">
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164 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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165 </data>
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166 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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167 <filter>OPTIONAL_OUTPUTS is None</filter>
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168 </data>
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169 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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170 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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171 </data>
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172 </outputs>
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173 <tests><!-- TOPP_MapRTTransformer_1 -->
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174 <test expect_num_outputs="2">
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175 <section name="adv_opts">
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176 <param name="force" value="false"/>
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177 <param name="test" value="true"/>
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178 </section>
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179 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
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180 <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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181 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
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182 <param name="invert" value="false"/>
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183 <param name="store_original_rt" value="false"/>
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184 <section name="model">
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185 <param name="type" value="none"/>
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186 <section name="linear">
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187 <param name="symmetric_regression" value="false"/>
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188 <param name="x_weight"/>
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189 <param name="y_weight"/>
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190 <param name="x_datum_min" value="1e-15"/>
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191 <param name="x_datum_max" value="1000000000000000.0"/>
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192 <param name="y_datum_min" value="1e-15"/>
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193 <param name="y_datum_max" value="1000000000000000.0"/>
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194 </section>
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195 <section name="b_spline">
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196 <param name="wavelength" value="0.0"/>
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197 <param name="num_nodes" value="5"/>
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198 <param name="extrapolate" value="linear"/>
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199 <param name="boundary_condition" value="2"/>
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200 </section>
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201 <section name="lowess">
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202 <param name="span" value="0.666666666666667"/>
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203 <param name="num_iterations" value="3"/>
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204 <param name="delta" value="-1.0"/>
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205 <param name="interpolation_type" value="cspline"/>
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206 <param name="extrapolation_type" value="four-point-linear"/>
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207 </section>
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208 <section name="interpolated">
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209 <param name="interpolation_type" value="cspline"/>
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210 <param name="extrapolation_type" value="two-point-linear"/>
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211 </section>
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212 </section>
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213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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214 <output name="ctd_out" ftype="xml">
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215 <assert_contents>
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216 <is_valid_xml/>
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217 </assert_contents>
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218 </output>
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219 </test>
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220 <!-- TOPP_MapRTTransformer_2 -->
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221 <test expect_num_outputs="2">
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222 <section name="adv_opts">
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223 <param name="force" value="false"/>
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224 <param name="test" value="true"/>
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225 </section>
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226 <param name="in" value="MapRTTransformer_2_input.mzML"/>
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227 <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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228 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
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229 <param name="invert" value="false"/>
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230 <param name="store_original_rt" value="false"/>
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231 <section name="model">
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232 <param name="type" value="none"/>
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233 <section name="linear">
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234 <param name="symmetric_regression" value="false"/>
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235 <param name="x_weight"/>
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236 <param name="y_weight"/>
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237 <param name="x_datum_min" value="1e-15"/>
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238 <param name="x_datum_max" value="1000000000000000.0"/>
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239 <param name="y_datum_min" value="1e-15"/>
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240 <param name="y_datum_max" value="1000000000000000.0"/>
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241 </section>
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242 <section name="b_spline">
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243 <param name="wavelength" value="0.0"/>
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244 <param name="num_nodes" value="5"/>
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245 <param name="extrapolate" value="linear"/>
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246 <param name="boundary_condition" value="2"/>
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247 </section>
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248 <section name="lowess">
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249 <param name="span" value="0.666666666666667"/>
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250 <param name="num_iterations" value="3"/>
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251 <param name="delta" value="-1.0"/>
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252 <param name="interpolation_type" value="cspline"/>
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253 <param name="extrapolation_type" value="four-point-linear"/>
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254 </section>
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255 <section name="interpolated">
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256 <param name="interpolation_type" value="cspline"/>
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257 <param name="extrapolation_type" value="two-point-linear"/>
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258 </section>
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259 </section>
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260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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261 <output name="ctd_out" ftype="xml">
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262 <assert_contents>
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263 <is_valid_xml/>
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264 </assert_contents>
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265 </output>
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266 </test>
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267 <!-- TOPP_MapRTTransformer_3 -->
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268 <test expect_num_outputs="2">
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269 <section name="adv_opts">
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270 <param name="force" value="false"/>
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271 <param name="test" value="true"/>
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272 </section>
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273 <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
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274 <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
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275 <param name="invert" value="true"/>
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276 <param name="store_original_rt" value="false"/>
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277 <section name="model">
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278 <param name="type" value="none"/>
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279 <section name="linear">
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280 <param name="symmetric_regression" value="false"/>
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281 <param name="x_weight"/>
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282 <param name="y_weight"/>
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283 <param name="x_datum_min" value="1e-15"/>
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284 <param name="x_datum_max" value="1000000000000000.0"/>
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285 <param name="y_datum_min" value="1e-15"/>
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286 <param name="y_datum_max" value="1000000000000000.0"/>
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287 </section>
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288 <section name="b_spline">
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289 <param name="wavelength" value="0.0"/>
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290 <param name="num_nodes" value="5"/>
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291 <param name="extrapolate" value="linear"/>
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292 <param name="boundary_condition" value="2"/>
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293 </section>
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294 <section name="lowess">
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295 <param name="span" value="0.666666666666667"/>
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296 <param name="num_iterations" value="3"/>
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297 <param name="delta" value="-1.0"/>
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298 <param name="interpolation_type" value="cspline"/>
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299 <param name="extrapolation_type" value="four-point-linear"/>
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300 </section>
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301 <section name="interpolated">
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302 <param name="interpolation_type" value="cspline"/>
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303 <param name="extrapolation_type" value="two-point-linear"/>
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304 </section>
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305 </section>
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306 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
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307 <output name="ctd_out" ftype="xml">
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308 <assert_contents>
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309 <is_valid_xml/>
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310 </assert_contents>
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311 </output>
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312 </test>
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313 <!-- TOPP_MapRTTransformer_4 -->
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314 <test expect_num_outputs="2">
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315 <section name="adv_opts">
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316 <param name="force" value="false"/>
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317 <param name="test" value="true"/>
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318 </section>
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319 <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
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320 <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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321 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
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322 <param name="invert" value="false"/>
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323 <param name="store_original_rt" value="false"/>
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324 <section name="model">
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325 <param name="type" value="none"/>
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326 <section name="linear">
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327 <param name="symmetric_regression" value="false"/>
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328 <param name="x_weight"/>
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329 <param name="y_weight"/>
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330 <param name="x_datum_min" value="1e-15"/>
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331 <param name="x_datum_max" value="1000000000000000.0"/>
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332 <param name="y_datum_min" value="1e-15"/>
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333 <param name="y_datum_max" value="1000000000000000.0"/>
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334 </section>
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335 <section name="b_spline">
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336 <param name="wavelength" value="0.0"/>
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337 <param name="num_nodes" value="5"/>
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338 <param name="extrapolate" value="linear"/>
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339 <param name="boundary_condition" value="2"/>
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340 </section>
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341 <section name="lowess">
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342 <param name="span" value="0.666666666666667"/>
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343 <param name="num_iterations" value="3"/>
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344 <param name="delta" value="-1.0"/>
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345 <param name="interpolation_type" value="cspline"/>
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346 <param name="extrapolation_type" value="four-point-linear"/>
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347 </section>
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348 <section name="interpolated">
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349 <param name="interpolation_type" value="cspline"/>
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350 <param name="extrapolation_type" value="two-point-linear"/>
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351 </section>
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352 </section>
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353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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354 <output name="ctd_out" ftype="xml">
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355 <assert_contents>
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356 <is_valid_xml/>
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357 </assert_contents>
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358 </output>
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359 </test>
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360 <!-- TOPP_MapRTTransformer_5 -->
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361 <test expect_num_outputs="2">
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362 <section name="adv_opts">
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363 <param name="force" value="false"/>
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364 <param name="test" value="true"/>
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365 </section>
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366 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
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367 <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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368 <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
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369 <param name="invert" value="false"/>
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370 <param name="store_original_rt" value="false"/>
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371 <section name="model">
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372 <param name="type" value="none"/>
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373 <section name="linear">
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374 <param name="symmetric_regression" value="false"/>
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375 <param name="x_weight"/>
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376 <param name="y_weight"/>
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377 <param name="x_datum_min" value="1e-15"/>
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378 <param name="x_datum_max" value="1000000000000000.0"/>
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379 <param name="y_datum_min" value="1e-15"/>
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380 <param name="y_datum_max" value="1000000000000000.0"/>
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381 </section>
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382 <section name="b_spline">
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383 <param name="wavelength" value="0.0"/>
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384 <param name="num_nodes" value="5"/>
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385 <param name="extrapolate" value="linear"/>
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386 <param name="boundary_condition" value="2"/>
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387 </section>
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388 <section name="lowess">
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389 <param name="span" value="0.666666666666667"/>
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390 <param name="num_iterations" value="3"/>
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391 <param name="delta" value="-1.0"/>
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392 <param name="interpolation_type" value="cspline"/>
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393 <param name="extrapolation_type" value="four-point-linear"/>
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394 </section>
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395 <section name="interpolated">
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396 <param name="interpolation_type" value="cspline"/>
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397 <param name="extrapolation_type" value="two-point-linear"/>
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398 </section>
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399 </section>
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400 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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401 <output name="ctd_out" ftype="xml">
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402 <assert_contents>
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403 <is_valid_xml/>
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404 </assert_contents>
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405 </output>
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406 </test>
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407 <!-- TOPP_MapRTTransformer_6 -->
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408 <test expect_num_outputs="2">
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409 <section name="adv_opts">
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410 <param name="force" value="false"/>
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411 <param name="test" value="true"/>
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412 </section>
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413 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
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414 <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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415 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
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416 <param name="invert" value="false"/>
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417 <param name="store_original_rt" value="true"/>
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418 <section name="model">
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419 <param name="type" value="none"/>
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420 <section name="linear">
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421 <param name="symmetric_regression" value="false"/>
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422 <param name="x_weight"/>
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423 <param name="y_weight"/>
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424 <param name="x_datum_min" value="1e-15"/>
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425 <param name="x_datum_max" value="1000000000000000.0"/>
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426 <param name="y_datum_min" value="1e-15"/>
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427 <param name="y_datum_max" value="1000000000000000.0"/>
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428 </section>
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429 <section name="b_spline">
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430 <param name="wavelength" value="0.0"/>
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431 <param name="num_nodes" value="5"/>
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432 <param name="extrapolate" value="linear"/>
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433 <param name="boundary_condition" value="2"/>
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434 </section>
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435 <section name="lowess">
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436 <param name="span" value="0.666666666666667"/>
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437 <param name="num_iterations" value="3"/>
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438 <param name="delta" value="-1.0"/>
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439 <param name="interpolation_type" value="cspline"/>
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440 <param name="extrapolation_type" value="four-point-linear"/>
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441 </section>
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442 <section name="interpolated">
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443 <param name="interpolation_type" value="cspline"/>
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444 <param name="extrapolation_type" value="two-point-linear"/>
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445 </section>
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446 </section>
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447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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448 <output name="ctd_out" ftype="xml">
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449 <assert_contents>
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450 <is_valid_xml/>
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451 </assert_contents>
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452 </output>
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453 </test>
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454 </tests>
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455 <help><![CDATA[Applies retention time transformations to maps.
0
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456
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457
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458 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapRTTransformer.html]]></help>
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459 <expand macro="references"/>
0
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460 </tool>