Mercurial > repos > galaxyp > openms_tofcalibration
comparison TOFCalibration.xml @ 13:9f0e189d093c draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:03:51 +0000 |
parents | 90f459a4da0e |
children | b6f7cec6cc9e |
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12:cfd9c633de6b | 13:9f0e189d093c |
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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: [Signal processing and preprocessing]--> | 3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
4 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="TOFCalibration" name="TOFCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Applies time of flight calibration.</description> | 5 <description>Applies time of flight calibration.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">TOFCalibration</token> | 7 <token name="@EXECUTABLE@">TOFCalibration</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@ |
51 <configfiles> | 49 <configfiles> |
52 <inputs name="args_json" data_style="paths"/> | 50 <inputs name="args_json" data_style="paths"/> |
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 51 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
54 </configfiles> | 52 </configfiles> |
55 <inputs> | 53 <inputs> |
56 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> | 54 <param argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> |
57 <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/> | 55 <param argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/> |
58 <param name="ref_masses" argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/> | 56 <param argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/> |
59 <param name="tof_const" argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/> | 57 <param argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/> |
60 <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/> | 58 <param argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/> |
61 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> | 59 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> |
62 <section name="PeakPicker" title="" help="" expanded="false"> | 60 <section name="PeakPicker" title="" help="" expanded="false"> |
63 <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> | 61 <param name="signal_to_noise" argument="-algorithm:PeakPicker:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> |
64 <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/> | 62 <param name="centroid_percentage" argument="-algorithm:PeakPicker:centroid_percentage" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/> |
65 <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> | 63 <param name="peak_width" argument="-algorithm:PeakPicker:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> |
120 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> | 118 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> |
121 </section> | 119 </section> |
122 </section> | 120 </section> |
123 </section> | 121 </section> |
124 <expand macro="adv_opts_macro"> | 122 <expand macro="adv_opts_macro"> |
125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 123 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 124 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
127 <expand macro="list_string_san"/> | 125 <expand macro="list_string_san" name="test"/> |
128 </param> | 126 </param> |
129 </expand> | 127 </expand> |
130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 129 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
132 </param> | 130 </param> |
135 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 133 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
136 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 134 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
137 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 135 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
138 </data> | 136 </data> |
139 </outputs> | 137 </outputs> |
140 <tests> | 138 <tests><!-- TOPP_TOFCalibration_1 --> |
141 <expand macro="autotest_TOFCalibration"/> | 139 <test expect_num_outputs="2"> |
142 <expand macro="manutest_TOFCalibration"/> | 140 <section name="adv_opts"> |
141 <param name="force" value="false"/> | |
142 <param name="test" value="true"/> | |
143 </section> | |
144 <param name="in" value="TOFCalibration_1_input.mzML"/> | |
145 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | |
146 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> | |
147 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> | |
148 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> | |
149 <param name="peak_data" value="false"/> | |
150 <section name="algorithm"> | |
151 <section name="PeakPicker"> | |
152 <param name="signal_to_noise" value="3.0"/> | |
153 <param name="centroid_percentage" value="0.6"/> | |
154 <param name="peak_width" value="0.15"/> | |
155 <param name="estimate_peak_width" value="false"/> | |
156 <param name="fwhm_lower_bound_factor" value="0.7"/> | |
157 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
158 <section name="optimization"> | |
159 <param name="iterations" value="400"/> | |
160 <section name="penalties"> | |
161 <param name="position" value="0.0"/> | |
162 <param name="left_width" value="1.0"/> | |
163 <param name="right_width" value="1.0"/> | |
164 <param name="height" value="1.0"/> | |
165 </section> | |
166 <section name="2d"> | |
167 <param name="tolerance_mz" value="2.2"/> | |
168 <param name="max_peak_distance" value="1.2"/> | |
169 </section> | |
170 </section> | |
171 <section name="thresholds"> | |
172 <param name="peak_bound" value="400.0"/> | |
173 <param name="peak_bound_ms2_level" value="10.0"/> | |
174 <param name="correlation" value="0.0"/> | |
175 <param name="noise_level" value="0.1"/> | |
176 <param name="search_radius" value="3"/> | |
177 </section> | |
178 <section name="wavelet_transform"> | |
179 <param name="spacing" value="0.001"/> | |
180 </section> | |
181 <section name="deconvolution"> | |
182 <param name="deconvolution" value="false"/> | |
183 <param name="asym_threshold" value="0.3"/> | |
184 <param name="left_width" value="2.0"/> | |
185 <param name="right_width" value="2.0"/> | |
186 <param name="scaling" value="0.12"/> | |
187 <section name="fitting"> | |
188 <param name="fwhm_threshold" value="0.7"/> | |
189 <param name="eps_abs" value="9.999999747378752e-06"/> | |
190 <param name="eps_rel" value="9.999999747378752e-06"/> | |
191 <param name="max_iteration" value="10"/> | |
192 <section name="penalties"> | |
193 <param name="position" value="0.0"/> | |
194 <param name="height" value="1.0"/> | |
195 <param name="left_width" value="0.0"/> | |
196 <param name="right_width" value="0.0"/> | |
197 </section> | |
198 </section> | |
199 </section> | |
200 <section name="SignalToNoiseEstimationParameter"> | |
201 <param name="max_intensity" value="-1"/> | |
202 <param name="auto_max_stdev_factor" value="3.0"/> | |
203 <param name="auto_max_percentile" value="95"/> | |
204 <param name="auto_mode" value="0"/> | |
205 <param name="win_len" value="200.0"/> | |
206 <param name="bin_count" value="30"/> | |
207 <param name="stdev_mp" value="3.0"/> | |
208 <param name="min_required_elements" value="10"/> | |
209 <param name="noise_for_empty_window" value="1e+20"/> | |
210 </section> | |
211 </section> | |
212 </section> | |
213 <param name="OPTIONAL_OUTPUTS" value="ctd_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_TOFCalibration_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="TOFCalibration_2_input.mzML"/> | |
227 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> | |
228 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> | |
229 <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> | |
230 <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> | |
231 <param name="peak_data" value="true"/> | |
232 <section name="algorithm"> | |
233 <section name="PeakPicker"> | |
234 <param name="signal_to_noise" value="3.0"/> | |
235 <param name="centroid_percentage" value="0.6"/> | |
236 <param name="peak_width" value="0.15"/> | |
237 <param name="estimate_peak_width" value="false"/> | |
238 <param name="fwhm_lower_bound_factor" value="0.7"/> | |
239 <param name="fwhm_upper_bound_factor" value="20.0"/> | |
240 <section name="optimization"> | |
241 <param name="iterations" value="400"/> | |
242 <section name="penalties"> | |
243 <param name="position" value="0.0"/> | |
244 <param name="left_width" value="1.0"/> | |
245 <param name="right_width" value="1.0"/> | |
246 <param name="height" value="1.0"/> | |
247 </section> | |
248 <section name="2d"> | |
249 <param name="tolerance_mz" value="2.2"/> | |
250 <param name="max_peak_distance" value="1.2"/> | |
251 </section> | |
252 </section> | |
253 <section name="thresholds"> | |
254 <param name="peak_bound" value="400.0"/> | |
255 <param name="peak_bound_ms2_level" value="10.0"/> | |
256 <param name="correlation" value="0.0"/> | |
257 <param name="noise_level" value="0.1"/> | |
258 <param name="search_radius" value="3"/> | |
259 </section> | |
260 <section name="wavelet_transform"> | |
261 <param name="spacing" value="0.001"/> | |
262 </section> | |
263 <section name="deconvolution"> | |
264 <param name="deconvolution" value="false"/> | |
265 <param name="asym_threshold" value="0.3"/> | |
266 <param name="left_width" value="2.0"/> | |
267 <param name="right_width" value="2.0"/> | |
268 <param name="scaling" value="0.12"/> | |
269 <section name="fitting"> | |
270 <param name="fwhm_threshold" value="0.7"/> | |
271 <param name="eps_abs" value="9.999999747378752e-06"/> | |
272 <param name="eps_rel" value="9.999999747378752e-06"/> | |
273 <param name="max_iteration" value="10"/> | |
274 <section name="penalties"> | |
275 <param name="position" value="0.0"/> | |
276 <param name="height" value="1.0"/> | |
277 <param name="left_width" value="0.0"/> | |
278 <param name="right_width" value="0.0"/> | |
279 </section> | |
280 </section> | |
281 </section> | |
282 <section name="SignalToNoiseEstimationParameter"> | |
283 <param name="max_intensity" value="-1"/> | |
284 <param name="auto_max_stdev_factor" value="3.0"/> | |
285 <param name="auto_max_percentile" value="95"/> | |
286 <param name="auto_mode" value="0"/> | |
287 <param name="win_len" value="200.0"/> | |
288 <param name="bin_count" value="30"/> | |
289 <param name="stdev_mp" value="3.0"/> | |
290 <param name="min_required_elements" value="10"/> | |
291 <param name="noise_for_empty_window" value="1e+20"/> | |
292 </section> | |
293 </section> | |
294 </section> | |
295 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
296 <output name="ctd_out" ftype="xml"> | |
297 <assert_contents> | |
298 <is_valid_xml/> | |
299 </assert_contents> | |
300 </output> | |
301 </test> | |
143 </tests> | 302 </tests> |
144 <help><![CDATA[Applies time of flight calibration. | 303 <help><![CDATA[Applies time of flight calibration. |
145 | 304 |
146 | 305 |
147 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TOFCalibration.html]]></help> | 306 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TOFCalibration.html]]></help> |
148 <expand macro="references"/> | 307 <expand macro="references"/> |
149 </tool> | 308 </tool> |