Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison IDPosteriorErrorProbability.xml @ 14:986e03d3201e 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 18:59:09 +0000
parents 711a081d80ba
children 93e6ec445d5d
comparison
equal deleted inserted replaced
13:111c3a00136d 14:986e03d3201e
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description> 5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> 7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</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@
52 <configfiles> 50 <configfiles>
53 <inputs name="args_json" data_style="paths"/> 51 <inputs name="args_json" data_style="paths"/>
54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
55 </configfiles> 53 </configfiles>
56 <inputs> 54 <inputs>
57 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 55 <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
58 <param name="split_charge" argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/> 56 <param argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/>
59 <param name="top_hits_only" argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/> 57 <param argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/>
60 <param name="ignore_bad_data" argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/> 58 <param argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
61 <param name="prob_correct" argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/> 59 <param argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
62 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false"> 60 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
63 <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="true" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/> 61 <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="true" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
64 <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" display="radio" type="select" optional="false" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used"> 62 <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" optional="true" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
65 <option value="Gumbel" selected="true">Gumbel</option> 63 <option value="Gumbel" selected="true">Gumbel</option>
66 <option value="Gauss">Gauss</option> 64 <option value="Gauss">Gauss</option>
67 <expand macro="list_string_san"/> 65 <expand macro="list_string_san" name="incorrectly_assigned"/>
68 </param> 66 </param>
69 <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="true" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/> 67 <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="true" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
70 <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="true" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/> 68 <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="true" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
71 <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" display="radio" type="select" optional="false" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing"> 69 <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" optional="true" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
72 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option> 70 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
73 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option> 71 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
74 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option> 72 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
75 <option value="none">none</option> 73 <option value="none">none</option>
76 <expand macro="list_string_san"/> 74 <expand macro="list_string_san" name="outlier_handling"/>
77 </param> 75 </param>
78 </section> 76 </section>
79 <expand macro="adv_opts_macro"> 77 <expand macro="adv_opts_macro">
80 <param name="fdr_for_targets_smaller" argument="-fdr_for_targets_smaller" type="float" optional="true" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/> 78 <param argument="-fdr_for_targets_smaller" type="float" optional="true" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
81 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 79 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
82 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 80 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
83 <expand macro="list_string_san"/> 81 <expand macro="list_string_san" name="test"/>
84 </param> 82 </param>
85 </expand> 83 </expand>
86 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 84 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
87 <option value="out_plot_FLAG">out_plot (txt file (if gnuplot is available, a corresponding PDF will be created as well.))</option> 85 <option value="out_plot_FLAG">out_plot (txt file (if gnuplot is available, a corresponding PDF will be created as well.))</option>
88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 86 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
95 </data> 93 </data>
96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 94 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 95 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
98 </data> 96 </data>
99 </outputs> 97 </outputs>
100 <tests> 98 <tests><!-- TOPP_IDPosteriorErrorProbability_1 -->
101 <expand macro="autotest_IDPosteriorErrorProbability"/> 99 <test expect_num_outputs="2">
102 <expand macro="manutest_IDPosteriorErrorProbability"/> 100 <section name="adv_opts">
101 <param name="fdr_for_targets_smaller" value="0.05"/>
102 <param name="force" value="false"/>
103 <param name="test" value="true"/>
104 </section>
105 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
106 <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
107 <param name="split_charge" value="false"/>
108 <param name="top_hits_only" value="false"/>
109 <param name="ignore_bad_data" value="false"/>
110 <param name="prob_correct" value="false"/>
111 <section name="fit_algorithm">
112 <param name="number_of_bins" value="100"/>
113 <param name="incorrectly_assigned" value="Gumbel"/>
114 <param name="max_nr_iterations" value="1000"/>
115 <param name="neg_log_delta" value="6"/>
116 <param name="outlier_handling" value="ignore_iqr_outliers"/>
117 </section>
118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
119 <output name="ctd_out" ftype="xml">
120 <assert_contents>
121 <is_valid_xml/>
122 </assert_contents>
123 </output>
124 </test>
125 <!-- TOPP_IDPosteriorErrorProbability_2 -->
126 <test expect_num_outputs="2">
127 <section name="adv_opts">
128 <param name="fdr_for_targets_smaller" value="0.05"/>
129 <param name="force" value="false"/>
130 <param name="test" value="true"/>
131 </section>
132 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
133 <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
134 <param name="split_charge" value="false"/>
135 <param name="top_hits_only" value="false"/>
136 <param name="ignore_bad_data" value="false"/>
137 <param name="prob_correct" value="false"/>
138 <section name="fit_algorithm">
139 <param name="number_of_bins" value="100"/>
140 <param name="incorrectly_assigned" value="Gumbel"/>
141 <param name="max_nr_iterations" value="1000"/>
142 <param name="neg_log_delta" value="6"/>
143 <param name="outlier_handling" value="ignore_iqr_outliers"/>
144 </section>
145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
146 <output name="ctd_out" ftype="xml">
147 <assert_contents>
148 <is_valid_xml/>
149 </assert_contents>
150 </output>
151 </test>
152 <!-- TOPP_IDPosteriorErrorProbability_3 -->
153 <test expect_num_outputs="2">
154 <section name="adv_opts">
155 <param name="fdr_for_targets_smaller" value="0.05"/>
156 <param name="force" value="false"/>
157 <param name="test" value="true"/>
158 </section>
159 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
160 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
161 <param name="split_charge" value="false"/>
162 <param name="top_hits_only" value="false"/>
163 <param name="ignore_bad_data" value="false"/>
164 <param name="prob_correct" value="false"/>
165 <section name="fit_algorithm">
166 <param name="number_of_bins" value="100"/>
167 <param name="incorrectly_assigned" value="Gumbel"/>
168 <param name="max_nr_iterations" value="1000"/>
169 <param name="neg_log_delta" value="6"/>
170 <param name="outlier_handling" value="ignore_iqr_outliers"/>
171 </section>
172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
173 <output name="ctd_out" ftype="xml">
174 <assert_contents>
175 <is_valid_xml/>
176 </assert_contents>
177 </output>
178 </test>
179 <!-- TOPP_IDPosteriorErrorProbability_4 -->
180 <test expect_num_outputs="2">
181 <section name="adv_opts">
182 <param name="fdr_for_targets_smaller" value="0.05"/>
183 <param name="force" value="false"/>
184 <param name="test" value="true"/>
185 </section>
186 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
187 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
188 <param name="split_charge" value="true"/>
189 <param name="top_hits_only" value="false"/>
190 <param name="ignore_bad_data" value="false"/>
191 <param name="prob_correct" value="false"/>
192 <section name="fit_algorithm">
193 <param name="number_of_bins" value="100"/>
194 <param name="incorrectly_assigned" value="Gumbel"/>
195 <param name="max_nr_iterations" value="1000"/>
196 <param name="neg_log_delta" value="6"/>
197 <param name="outlier_handling" value="ignore_iqr_outliers"/>
198 </section>
199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
200 <output name="ctd_out" ftype="xml">
201 <assert_contents>
202 <is_valid_xml/>
203 </assert_contents>
204 </output>
205 </test>
206 <!-- TOPP_IDPosteriorErrorProbability_5 -->
207 <test expect_num_outputs="2">
208 <section name="adv_opts">
209 <param name="fdr_for_targets_smaller" value="0.05"/>
210 <param name="force" value="false"/>
211 <param name="test" value="true"/>
212 </section>
213 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
214 <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
215 <param name="split_charge" value="true"/>
216 <param name="top_hits_only" value="false"/>
217 <param name="ignore_bad_data" value="false"/>
218 <param name="prob_correct" value="false"/>
219 <section name="fit_algorithm">
220 <param name="number_of_bins" value="100"/>
221 <param name="incorrectly_assigned" value="Gumbel"/>
222 <param name="max_nr_iterations" value="1000"/>
223 <param name="neg_log_delta" value="6"/>
224 <param name="outlier_handling" value="ignore_iqr_outliers"/>
225 </section>
226 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
227 <output name="ctd_out" ftype="xml">
228 <assert_contents>
229 <is_valid_xml/>
230 </assert_contents>
231 </output>
232 </test>
233 <!-- TOPP_IDPosteriorErrorProbability_6 -->
234 <test expect_num_outputs="2">
235 <section name="adv_opts">
236 <param name="fdr_for_targets_smaller" value="0.05"/>
237 <param name="force" value="false"/>
238 <param name="test" value="true"/>
239 </section>
240 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
241 <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
242 <param name="split_charge" value="true"/>
243 <param name="top_hits_only" value="false"/>
244 <param name="ignore_bad_data" value="false"/>
245 <param name="prob_correct" value="false"/>
246 <section name="fit_algorithm">
247 <param name="number_of_bins" value="100"/>
248 <param name="incorrectly_assigned" value="Gumbel"/>
249 <param name="max_nr_iterations" value="1000"/>
250 <param name="neg_log_delta" value="6"/>
251 <param name="outlier_handling" value="ignore_iqr_outliers"/>
252 </section>
253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
254 <output name="ctd_out" ftype="xml">
255 <assert_contents>
256 <is_valid_xml/>
257 </assert_contents>
258 </output>
259 </test>
260 <!-- TOPP_IDPosteriorErrorProbability_7 -->
261 <test expect_num_outputs="2">
262 <section name="adv_opts">
263 <param name="fdr_for_targets_smaller" value="0.05"/>
264 <param name="force" value="false"/>
265 <param name="test" value="true"/>
266 </section>
267 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
268 <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
269 <param name="split_charge" value="false"/>
270 <param name="top_hits_only" value="false"/>
271 <param name="ignore_bad_data" value="true"/>
272 <param name="prob_correct" value="false"/>
273 <section name="fit_algorithm">
274 <param name="number_of_bins" value="100"/>
275 <param name="incorrectly_assigned" value="Gumbel"/>
276 <param name="max_nr_iterations" value="1000"/>
277 <param name="neg_log_delta" value="6"/>
278 <param name="outlier_handling" value="ignore_iqr_outliers"/>
279 </section>
280 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
281 <output name="ctd_out" ftype="xml">
282 <assert_contents>
283 <is_valid_xml/>
284 </assert_contents>
285 </output>
286 </test>
287 <!-- TOPP_IDPosteriorErrorProbability_8 -->
288 <test expect_num_outputs="2">
289 <section name="adv_opts">
290 <param name="fdr_for_targets_smaller" value="0.05"/>
291 <param name="force" value="false"/>
292 <param name="test" value="true"/>
293 </section>
294 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
295 <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
296 <param name="split_charge" value="false"/>
297 <param name="top_hits_only" value="false"/>
298 <param name="ignore_bad_data" value="false"/>
299 <param name="prob_correct" value="true"/>
300 <section name="fit_algorithm">
301 <param name="number_of_bins" value="100"/>
302 <param name="incorrectly_assigned" value="Gumbel"/>
303 <param name="max_nr_iterations" value="1000"/>
304 <param name="neg_log_delta" value="6"/>
305 <param name="outlier_handling" value="ignore_iqr_outliers"/>
306 </section>
307 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
308 <output name="ctd_out" ftype="xml">
309 <assert_contents>
310 <is_valid_xml/>
311 </assert_contents>
312 </output>
313 </test>
103 </tests> 314 </tests>
104 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 315 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
105 316
106 317
107 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDPosteriorErrorProbability.html]]></help> 318 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
108 <expand macro="references"/> 319 <expand macro="references"/>
109 </tool> 320 </tool>