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comparison 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
comparison
equal deleted inserted replaced
12:04883c24494e 13:aec26bf377fb
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Map Alignment]--> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MapRTTransformer" name="MapRTTransformer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies retention time transformations to maps.</description> 5 <description>Applies retention time transformations to maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapRTTransformer</token> 7 <token name="@EXECUTABLE@">MapRTTransformer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
66 <configfiles> 64 <configfiles>
67 <inputs name="args_json" data_style="paths"/> 65 <inputs name="args_json" data_style="paths"/>
68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 66 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
69 </configfiles> 67 </configfiles>
70 <inputs> 68 <inputs>
71 <param name="in" 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)"/> 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)"/>
72 <param name="trafo_in" argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/> 70 <param argument="-trafo_in" type="data" format="trafoxml" optional="false" label="Transformation to apply" help=" select trafoxml data sets(s)"/>
73 <param name="invert" argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/> 71 <param argument="-invert" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Invert transformation (approximatively) before applying it" help=""/>
74 <param name="store_original_rt" 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=""/> 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=""/>
75 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false"> 73 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
76 <param name="type" argument="-model:type" type="select" optional="false" label="Type of model" help=""> 74 <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
77 <option value="none" selected="true">none</option> 75 <option value="none" selected="true">none</option>
78 <option value="linear">linear</option> 76 <option value="linear">linear</option>
79 <option value="b_spline">b_spline</option> 77 <option value="b_spline">b_spline</option>
80 <option value="lowess">lowess</option> 78 <option value="lowess">lowess</option>
81 <option value="interpolated">interpolated</option> 79 <option value="interpolated">interpolated</option>
82 <expand macro="list_string_san"/> 80 <expand macro="list_string_san" name="type"/>
83 </param> 81 </param>
84 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false"> 82 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
85 <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'"/> 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'"/>
86 <param name="x_weight" argument="-model:linear:x_weight" display="radio" type="select" optional="true" label="Weight x values" help=""> 84 <param name="x_weight" argument="-model:linear:x_weight" type="select" optional="true" label="Weight x values" help="">
87 <option value="">default (nothing chosen)</option>
88 <option value="1/x">1/x</option> 85 <option value="1/x">1/x</option>
89 <option value="1/x2">1/x2</option> 86 <option value="1/x2">1/x2</option>
90 <option value="ln(x)">ln(x)</option> 87 <option value="ln(x)">ln(x)</option>
91 <option value=""></option> 88 <option value=""></option>
92 <expand macro="list_string_san"/> 89 <expand macro="list_string_san" name="x_weight"/>
93 </param> 90 </param>
94 <param name="y_weight" argument="-model:linear:y_weight" display="radio" type="select" optional="true" label="Weight y values" help=""> 91 <param name="y_weight" argument="-model:linear:y_weight" type="select" optional="true" label="Weight y values" help="">
95 <option value="">default (nothing chosen)</option>
96 <option value="1/y">1/y</option> 92 <option value="1/y">1/y</option>
97 <option value="1/y2">1/y2</option> 93 <option value="1/y2">1/y2</option>
98 <option value="ln(y)">ln(y)</option> 94 <option value="ln(y)">ln(y)</option>
99 <option value=""></option> 95 <option value=""></option>
100 <expand macro="list_string_san"/> 96 <expand macro="list_string_san" name="y_weight"/>
101 </param> 97 </param>
102 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/> 98 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" optional="true" value="1e-15" label="Minimum x value" help=""/>
103 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/> 99 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum x value" help=""/>
104 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/> 100 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" optional="true" value="1e-15" label="Minimum y value" help=""/>
105 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/> 101 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" optional="true" value="1000000000000000.0" label="Maximum y value" help=""/>
106 </section> 102 </section>
107 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false"> 103 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
108 <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"/> 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"/>
109 <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"/> 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"/>
110 <param name="extrapolate" argument="-model:b_spline:extrapolate" display="radio" type="select" optional="false" 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)"> 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)">
111 <option value="linear" selected="true">linear</option> 107 <option value="linear" selected="true">linear</option>
112 <option value="b_spline">b_spline</option> 108 <option value="b_spline">b_spline</option>
113 <option value="constant">constant</option> 109 <option value="constant">constant</option>
114 <option value="global_linear">global_linear</option> 110 <option value="global_linear">global_linear</option>
115 <expand macro="list_string_san"/> 111 <expand macro="list_string_san" name="extrapolate"/>
116 </param> 112 </param>
117 <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=""/> 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=""/>
118 </section> 114 </section>
119 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false"> 115 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
120 <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"/> 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"/>
121 <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=""/> 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=""/>
122 <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"/> 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"/>
123 <param name="interpolation_type" argument="-model:lowess:interpolation_type" display="radio" type="select" optional="false" 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"> 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">
124 <option value="linear">linear</option> 120 <option value="linear">linear</option>
125 <option value="cspline" selected="true">cspline</option> 121 <option value="cspline" selected="true">cspline</option>
126 <option value="akima">akima</option> 122 <option value="akima">akima</option>
127 <expand macro="list_string_san"/> 123 <expand macro="list_string_san" name="interpolation_type"/>
128 </param> 124 </param>
129 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" display="radio" type="select" optional="false" 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"> 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">
130 <option value="two-point-linear">two-point-linear</option> 126 <option value="two-point-linear">two-point-linear</option>
131 <option value="four-point-linear" selected="true">four-point-linear</option> 127 <option value="four-point-linear" selected="true">four-point-linear</option>
132 <option value="global-linear">global-linear</option> 128 <option value="global-linear">global-linear</option>
133 <expand macro="list_string_san"/> 129 <expand macro="list_string_san" name="extrapolation_type"/>
134 </param> 130 </param>
135 </section> 131 </section>
136 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false"> 132 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
137 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" display="radio" type="select" optional="false" label="Type of interpolation to apply" help=""> 133 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" optional="true" label="Type of interpolation to apply" help="">
138 <option value="linear">linear</option> 134 <option value="linear">linear</option>
139 <option value="cspline" selected="true">cspline</option> 135 <option value="cspline" selected="true">cspline</option>
140 <option value="akima">akima</option> 136 <option value="akima">akima</option>
141 <expand macro="list_string_san"/> 137 <expand macro="list_string_san" name="interpolation_type"/>
142 </param> 138 </param>
143 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" display="radio" type="select" optional="false" 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"> 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">
144 <option value="two-point-linear" selected="true">two-point-linear</option> 140 <option value="two-point-linear" selected="true">two-point-linear</option>
145 <option value="four-point-linear">four-point-linear</option> 141 <option value="four-point-linear">four-point-linear</option>
146 <option value="global-linear">global-linear</option> 142 <option value="global-linear">global-linear</option>
147 <expand macro="list_string_san"/> 143 <expand macro="list_string_san" name="extrapolation_type"/>
148 </param> 144 </param>
149 </section> 145 </section>
150 </section> 146 </section>
151 <expand macro="adv_opts_macro"> 147 <expand macro="adv_opts_macro">
152 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 148 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
153 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 149 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
154 <expand macro="list_string_san"/> 150 <expand macro="list_string_san" name="test"/>
155 </param> 151 </param>
156 </expand> 152 </expand>
157 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 153 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
158 <option value="out_FLAG">out (Output file (same file type as 'in'))</option> 154 <option value="out_FLAG">out (Output file (same file type as 'in'))</option>
159 <option value="trafo_out_FLAG">trafo_out (Transformation output file)</option> 155 <option value="trafo_out_FLAG">trafo_out (Transformation output file)</option>
172 </data> 168 </data>
173 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 169 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
174 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 170 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
175 </data> 171 </data>
176 </outputs> 172 </outputs>
177 <tests> 173 <tests><!-- TOPP_MapRTTransformer_1 -->
178 <expand macro="autotest_MapRTTransformer"/> 174 <test expect_num_outputs="2">
179 <expand macro="manutest_MapRTTransformer"/> 175 <section name="adv_opts">
176 <param name="force" value="false"/>
177 <param name="test" value="true"/>
178 </section>
179 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
180 <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
181 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
182 <param name="invert" value="false"/>
183 <param name="store_original_rt" value="false"/>
184 <section name="model">
185 <param name="type" value="none"/>
186 <section name="linear">
187 <param name="symmetric_regression" value="false"/>
188 <param name="x_weight"/>
189 <param name="y_weight"/>
190 <param name="x_datum_min" value="1e-15"/>
191 <param name="x_datum_max" value="1000000000000000.0"/>
192 <param name="y_datum_min" value="1e-15"/>
193 <param name="y_datum_max" value="1000000000000000.0"/>
194 </section>
195 <section name="b_spline">
196 <param name="wavelength" value="0.0"/>
197 <param name="num_nodes" value="5"/>
198 <param name="extrapolate" value="linear"/>
199 <param name="boundary_condition" value="2"/>
200 </section>
201 <section name="lowess">
202 <param name="span" value="0.666666666666667"/>
203 <param name="num_iterations" value="3"/>
204 <param name="delta" value="-1.0"/>
205 <param name="interpolation_type" value="cspline"/>
206 <param name="extrapolation_type" value="four-point-linear"/>
207 </section>
208 <section name="interpolated">
209 <param name="interpolation_type" value="cspline"/>
210 <param name="extrapolation_type" value="two-point-linear"/>
211 </section>
212 </section>
213 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
214 <output name="ctd_out" ftype="xml">
215 <assert_contents>
216 <is_valid_xml/>
217 </assert_contents>
218 </output>
219 </test>
220 <!-- TOPP_MapRTTransformer_2 -->
221 <test expect_num_outputs="2">
222 <section name="adv_opts">
223 <param name="force" value="false"/>
224 <param name="test" value="true"/>
225 </section>
226 <param name="in" value="MapRTTransformer_2_input.mzML"/>
227 <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
228 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
229 <param name="invert" value="false"/>
230 <param name="store_original_rt" value="false"/>
231 <section name="model">
232 <param name="type" value="none"/>
233 <section name="linear">
234 <param name="symmetric_regression" value="false"/>
235 <param name="x_weight"/>
236 <param name="y_weight"/>
237 <param name="x_datum_min" value="1e-15"/>
238 <param name="x_datum_max" value="1000000000000000.0"/>
239 <param name="y_datum_min" value="1e-15"/>
240 <param name="y_datum_max" value="1000000000000000.0"/>
241 </section>
242 <section name="b_spline">
243 <param name="wavelength" value="0.0"/>
244 <param name="num_nodes" value="5"/>
245 <param name="extrapolate" value="linear"/>
246 <param name="boundary_condition" value="2"/>
247 </section>
248 <section name="lowess">
249 <param name="span" value="0.666666666666667"/>
250 <param name="num_iterations" value="3"/>
251 <param name="delta" value="-1.0"/>
252 <param name="interpolation_type" value="cspline"/>
253 <param name="extrapolation_type" value="four-point-linear"/>
254 </section>
255 <section name="interpolated">
256 <param name="interpolation_type" value="cspline"/>
257 <param name="extrapolation_type" value="two-point-linear"/>
258 </section>
259 </section>
260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
261 <output name="ctd_out" ftype="xml">
262 <assert_contents>
263 <is_valid_xml/>
264 </assert_contents>
265 </output>
266 </test>
267 <!-- TOPP_MapRTTransformer_3 -->
268 <test expect_num_outputs="2">
269 <section name="adv_opts">
270 <param name="force" value="false"/>
271 <param name="test" value="true"/>
272 </section>
273 <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
274 <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta_frac="0.7" ftype="trafoxml"/>
275 <param name="invert" value="true"/>
276 <param name="store_original_rt" value="false"/>
277 <section name="model">
278 <param name="type" value="none"/>
279 <section name="linear">
280 <param name="symmetric_regression" value="false"/>
281 <param name="x_weight"/>
282 <param name="y_weight"/>
283 <param name="x_datum_min" value="1e-15"/>
284 <param name="x_datum_max" value="1000000000000000.0"/>
285 <param name="y_datum_min" value="1e-15"/>
286 <param name="y_datum_max" value="1000000000000000.0"/>
287 </section>
288 <section name="b_spline">
289 <param name="wavelength" value="0.0"/>
290 <param name="num_nodes" value="5"/>
291 <param name="extrapolate" value="linear"/>
292 <param name="boundary_condition" value="2"/>
293 </section>
294 <section name="lowess">
295 <param name="span" value="0.666666666666667"/>
296 <param name="num_iterations" value="3"/>
297 <param name="delta" value="-1.0"/>
298 <param name="interpolation_type" value="cspline"/>
299 <param name="extrapolation_type" value="four-point-linear"/>
300 </section>
301 <section name="interpolated">
302 <param name="interpolation_type" value="cspline"/>
303 <param name="extrapolation_type" value="two-point-linear"/>
304 </section>
305 </section>
306 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
307 <output name="ctd_out" ftype="xml">
308 <assert_contents>
309 <is_valid_xml/>
310 </assert_contents>
311 </output>
312 </test>
313 <!-- TOPP_MapRTTransformer_4 -->
314 <test expect_num_outputs="2">
315 <section name="adv_opts">
316 <param name="force" value="false"/>
317 <param name="test" value="true"/>
318 </section>
319 <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
320 <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
321 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
322 <param name="invert" value="false"/>
323 <param name="store_original_rt" value="false"/>
324 <section name="model">
325 <param name="type" value="none"/>
326 <section name="linear">
327 <param name="symmetric_regression" value="false"/>
328 <param name="x_weight"/>
329 <param name="y_weight"/>
330 <param name="x_datum_min" value="1e-15"/>
331 <param name="x_datum_max" value="1000000000000000.0"/>
332 <param name="y_datum_min" value="1e-15"/>
333 <param name="y_datum_max" value="1000000000000000.0"/>
334 </section>
335 <section name="b_spline">
336 <param name="wavelength" value="0.0"/>
337 <param name="num_nodes" value="5"/>
338 <param name="extrapolate" value="linear"/>
339 <param name="boundary_condition" value="2"/>
340 </section>
341 <section name="lowess">
342 <param name="span" value="0.666666666666667"/>
343 <param name="num_iterations" value="3"/>
344 <param name="delta" value="-1.0"/>
345 <param name="interpolation_type" value="cspline"/>
346 <param name="extrapolation_type" value="four-point-linear"/>
347 </section>
348 <section name="interpolated">
349 <param name="interpolation_type" value="cspline"/>
350 <param name="extrapolation_type" value="two-point-linear"/>
351 </section>
352 </section>
353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
354 <output name="ctd_out" ftype="xml">
355 <assert_contents>
356 <is_valid_xml/>
357 </assert_contents>
358 </output>
359 </test>
360 <!-- TOPP_MapRTTransformer_5 -->
361 <test expect_num_outputs="2">
362 <section name="adv_opts">
363 <param name="force" value="false"/>
364 <param name="test" value="true"/>
365 </section>
366 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
367 <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
368 <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
369 <param name="invert" value="false"/>
370 <param name="store_original_rt" value="false"/>
371 <section name="model">
372 <param name="type" value="none"/>
373 <section name="linear">
374 <param name="symmetric_regression" value="false"/>
375 <param name="x_weight"/>
376 <param name="y_weight"/>
377 <param name="x_datum_min" value="1e-15"/>
378 <param name="x_datum_max" value="1000000000000000.0"/>
379 <param name="y_datum_min" value="1e-15"/>
380 <param name="y_datum_max" value="1000000000000000.0"/>
381 </section>
382 <section name="b_spline">
383 <param name="wavelength" value="0.0"/>
384 <param name="num_nodes" value="5"/>
385 <param name="extrapolate" value="linear"/>
386 <param name="boundary_condition" value="2"/>
387 </section>
388 <section name="lowess">
389 <param name="span" value="0.666666666666667"/>
390 <param name="num_iterations" value="3"/>
391 <param name="delta" value="-1.0"/>
392 <param name="interpolation_type" value="cspline"/>
393 <param name="extrapolation_type" value="four-point-linear"/>
394 </section>
395 <section name="interpolated">
396 <param name="interpolation_type" value="cspline"/>
397 <param name="extrapolation_type" value="two-point-linear"/>
398 </section>
399 </section>
400 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
401 <output name="ctd_out" ftype="xml">
402 <assert_contents>
403 <is_valid_xml/>
404 </assert_contents>
405 </output>
406 </test>
407 <!-- TOPP_MapRTTransformer_6 -->
408 <test expect_num_outputs="2">
409 <section name="adv_opts">
410 <param name="force" value="false"/>
411 <param name="test" value="true"/>
412 </section>
413 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
414 <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
415 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
416 <param name="invert" value="false"/>
417 <param name="store_original_rt" value="true"/>
418 <section name="model">
419 <param name="type" value="none"/>
420 <section name="linear">
421 <param name="symmetric_regression" value="false"/>
422 <param name="x_weight"/>
423 <param name="y_weight"/>
424 <param name="x_datum_min" value="1e-15"/>
425 <param name="x_datum_max" value="1000000000000000.0"/>
426 <param name="y_datum_min" value="1e-15"/>
427 <param name="y_datum_max" value="1000000000000000.0"/>
428 </section>
429 <section name="b_spline">
430 <param name="wavelength" value="0.0"/>
431 <param name="num_nodes" value="5"/>
432 <param name="extrapolate" value="linear"/>
433 <param name="boundary_condition" value="2"/>
434 </section>
435 <section name="lowess">
436 <param name="span" value="0.666666666666667"/>
437 <param name="num_iterations" value="3"/>
438 <param name="delta" value="-1.0"/>
439 <param name="interpolation_type" value="cspline"/>
440 <param name="extrapolation_type" value="four-point-linear"/>
441 </section>
442 <section name="interpolated">
443 <param name="interpolation_type" value="cspline"/>
444 <param name="extrapolation_type" value="two-point-linear"/>
445 </section>
446 </section>
447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
448 <output name="ctd_out" ftype="xml">
449 <assert_contents>
450 <is_valid_xml/>
451 </assert_contents>
452 </output>
453 </test>
180 </tests> 454 </tests>
181 <help><![CDATA[Applies retention time transformations to maps. 455 <help><![CDATA[Applies retention time transformations to maps.
182 456
183 457
184 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapRTTransformer.html]]></help> 458 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapRTTransformer.html]]></help>
185 <expand macro="references"/> 459 <expand macro="references"/>
186 </tool> 460 </tool>