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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:40:19 +0000
parents 986e03d3201e
children
comparison
equal deleted inserted replaced
14:986e03d3201e 15:93e6ec445d5d
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> 6 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 19 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
21 mkdir out_plot && 20 mkdir out_plot &&
22 #end if 21 #end if
23 22
50 <configfiles> 49 <configfiles>
51 <inputs name="args_json" data_style="paths"/> 50 <inputs name="args_json" data_style="paths"/>
52 <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>
53 </configfiles> 52 </configfiles>
54 <inputs> 53 <inputs>
55 <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 54 <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
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"/> 55 <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"/>
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=""/> 56 <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=""/>
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"/> 57 <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"/>
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=""/> 58 <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=""/>
60 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false"> 59 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
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"/> 60 <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
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"> 61 <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" type="select" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
63 <option value="Gumbel" selected="true">Gumbel</option> 62 <option value="Gumbel" selected="true">Gumbel</option>
64 <option value="Gauss">Gauss</option> 63 <option value="Gauss">Gauss</option>
65 <expand macro="list_string_san" name="incorrectly_assigned"/> 64 <expand macro="list_string_san" name="incorrectly_assigned"/>
66 </param> 65 </param>
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=""/> 66 <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" 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=""/> 67 <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
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"> 68 <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" type="select" 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">
70 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option> 69 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
71 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option> 70 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
72 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option> 71 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
73 <option value="none">none</option> 72 <option value="none">none</option>
74 <expand macro="list_string_san" name="outlier_handling"/> 73 <expand macro="list_string_san" name="outlier_handling"/>
75 </param> 74 </param>
76 </section> 75 </section>
77 <expand macro="adv_opts_macro"> 76 <expand macro="adv_opts_macro">
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"/> 77 <param argument="-fdr_for_targets_smaller" type="float" 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"/>
79 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 78 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
80 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 79 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
81 <expand macro="list_string_san" name="test"/> 80 <expand macro="list_string_san" name="test"/>
82 </param> 81 </param>
83 </expand> 82 </expand>
84 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 83 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
85 <option value="out_plot_FLAG">out_plot (txt file (if gnuplot is available, a corresponding PDF will be created as well.))</option> 84 <option value="out_plot_FLAG">out_plot (txt file (if gnuplot is available, a corresponding PDF will be created as well.))</option>
93 </data> 92 </data>
94 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
95 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
96 </data> 95 </data>
97 </outputs> 96 </outputs>
98 <tests><!-- TOPP_IDPosteriorErrorProbability_1 --> 97 <tests>
98 <!-- TOPP_IDPosteriorErrorProbability_1 -->
99 <test expect_num_outputs="2"> 99 <test expect_num_outputs="2">
100 <section name="adv_opts"> 100 <section name="adv_opts">
101 <param name="fdr_for_targets_smaller" value="0.05"/> 101 <param name="fdr_for_targets_smaller" value="0.05"/>
102 <param name="force" value="false"/> 102 <param name="force" value="false"/>
103 <param name="test" value="true"/> 103 <param name="test" value="true"/>
104 </section> 104 </section>
105 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> 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"/> 106 <output name="out" value="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
107 <param name="split_charge" value="false"/> 107 <param name="split_charge" value="false"/>
108 <param name="top_hits_only" value="false"/> 108 <param name="top_hits_only" value="false"/>
109 <param name="ignore_bad_data" value="false"/> 109 <param name="ignore_bad_data" value="false"/>
110 <param name="prob_correct" value="false"/> 110 <param name="prob_correct" value="false"/>
111 <section name="fit_algorithm"> 111 <section name="fit_algorithm">
112 <param name="number_of_bins" value="100"/> 112 <param name="number_of_bins" value="100"/>
113 <param name="incorrectly_assigned" value="Gumbel"/> 113 <param name="incorrectly_assigned" value="Gumbel"/>
114 <param name="max_nr_iterations" value="1000"/> 114 <param name="max_nr_iterations" value="1000"/>
115 <param name="neg_log_delta" value="6"/> 115 <param name="neg_log_delta" value="6"/>
116 <param name="outlier_handling" value="ignore_iqr_outliers"/> 116 <param name="outlier_handling" value="ignore_iqr_outliers"/>
117 </section> 117 </section>
118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
119 <output name="ctd_out" ftype="xml"> 119 <output name="ctd_out" ftype="xml">
120 <assert_contents> 120 <assert_contents>
121 <is_valid_xml/> 121 <is_valid_xml/>
122 </assert_contents> 122 </assert_contents>
123 </output> 123 </output>
124 <assert_stdout>
125 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
126 </assert_stdout>
124 </test> 127 </test>
125 <!-- TOPP_IDPosteriorErrorProbability_2 --> 128 <!-- TOPP_IDPosteriorErrorProbability_2 -->
126 <test expect_num_outputs="2"> 129 <test expect_num_outputs="2">
127 <section name="adv_opts"> 130 <section name="adv_opts">
128 <param name="fdr_for_targets_smaller" value="0.05"/> 131 <param name="fdr_for_targets_smaller" value="0.05"/>
129 <param name="force" value="false"/> 132 <param name="force" value="false"/>
130 <param name="test" value="true"/> 133 <param name="test" value="true"/>
131 </section> 134 </section>
132 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> 135 <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"/> 136 <output name="out" value="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
134 <param name="split_charge" value="false"/> 137 <param name="split_charge" value="false"/>
135 <param name="top_hits_only" value="false"/> 138 <param name="top_hits_only" value="false"/>
136 <param name="ignore_bad_data" value="false"/> 139 <param name="ignore_bad_data" value="false"/>
137 <param name="prob_correct" value="false"/> 140 <param name="prob_correct" value="false"/>
138 <section name="fit_algorithm"> 141 <section name="fit_algorithm">
139 <param name="number_of_bins" value="100"/> 142 <param name="number_of_bins" value="100"/>
140 <param name="incorrectly_assigned" value="Gumbel"/> 143 <param name="incorrectly_assigned" value="Gumbel"/>
141 <param name="max_nr_iterations" value="1000"/> 144 <param name="max_nr_iterations" value="1000"/>
142 <param name="neg_log_delta" value="6"/> 145 <param name="neg_log_delta" value="6"/>
143 <param name="outlier_handling" value="ignore_iqr_outliers"/> 146 <param name="outlier_handling" value="ignore_iqr_outliers"/>
144 </section> 147 </section>
145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 148 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
146 <output name="ctd_out" ftype="xml"> 149 <output name="ctd_out" ftype="xml">
147 <assert_contents> 150 <assert_contents>
148 <is_valid_xml/> 151 <is_valid_xml/>
149 </assert_contents> 152 </assert_contents>
150 </output> 153 </output>
154 <assert_stdout>
155 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
156 </assert_stdout>
151 </test> 157 </test>
152 <!-- TOPP_IDPosteriorErrorProbability_3 --> 158 <!-- TOPP_IDPosteriorErrorProbability_3 -->
153 <test expect_num_outputs="2"> 159 <test expect_num_outputs="2">
154 <section name="adv_opts"> 160 <section name="adv_opts">
155 <param name="fdr_for_targets_smaller" value="0.05"/> 161 <param name="fdr_for_targets_smaller" value="0.05"/>
156 <param name="force" value="false"/> 162 <param name="force" value="false"/>
157 <param name="test" value="true"/> 163 <param name="test" value="true"/>
158 </section> 164 </section>
159 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> 165 <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"/> 166 <output name="out" value="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
161 <param name="split_charge" value="false"/> 167 <param name="split_charge" value="false"/>
162 <param name="top_hits_only" value="false"/> 168 <param name="top_hits_only" value="false"/>
163 <param name="ignore_bad_data" value="false"/> 169 <param name="ignore_bad_data" value="false"/>
164 <param name="prob_correct" value="false"/> 170 <param name="prob_correct" value="false"/>
165 <section name="fit_algorithm"> 171 <section name="fit_algorithm">
166 <param name="number_of_bins" value="100"/> 172 <param name="number_of_bins" value="100"/>
167 <param name="incorrectly_assigned" value="Gumbel"/> 173 <param name="incorrectly_assigned" value="Gumbel"/>
168 <param name="max_nr_iterations" value="1000"/> 174 <param name="max_nr_iterations" value="1000"/>
169 <param name="neg_log_delta" value="6"/> 175 <param name="neg_log_delta" value="6"/>
170 <param name="outlier_handling" value="ignore_iqr_outliers"/> 176 <param name="outlier_handling" value="ignore_iqr_outliers"/>
171 </section> 177 </section>
172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 178 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
173 <output name="ctd_out" ftype="xml"> 179 <output name="ctd_out" ftype="xml">
174 <assert_contents> 180 <assert_contents>
175 <is_valid_xml/> 181 <is_valid_xml/>
176 </assert_contents> 182 </assert_contents>
177 </output> 183 </output>
184 <assert_stdout>
185 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
186 </assert_stdout>
178 </test> 187 </test>
179 <!-- TOPP_IDPosteriorErrorProbability_4 --> 188 <!-- TOPP_IDPosteriorErrorProbability_4 -->
180 <test expect_num_outputs="2"> 189 <test expect_num_outputs="2">
181 <section name="adv_opts"> 190 <section name="adv_opts">
182 <param name="fdr_for_targets_smaller" value="0.05"/> 191 <param name="fdr_for_targets_smaller" value="0.05"/>
183 <param name="force" value="false"/> 192 <param name="force" value="false"/>
184 <param name="test" value="true"/> 193 <param name="test" value="true"/>
185 </section> 194 </section>
186 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> 195 <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"/> 196 <output name="out" value="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
188 <param name="split_charge" value="true"/> 197 <param name="split_charge" value="true"/>
189 <param name="top_hits_only" value="false"/> 198 <param name="top_hits_only" value="false"/>
190 <param name="ignore_bad_data" value="false"/> 199 <param name="ignore_bad_data" value="false"/>
191 <param name="prob_correct" value="false"/> 200 <param name="prob_correct" value="false"/>
192 <section name="fit_algorithm"> 201 <section name="fit_algorithm">
200 <output name="ctd_out" ftype="xml"> 209 <output name="ctd_out" ftype="xml">
201 <assert_contents> 210 <assert_contents>
202 <is_valid_xml/> 211 <is_valid_xml/>
203 </assert_contents> 212 </assert_contents>
204 </output> 213 </output>
214 <assert_stdout>
215 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
216 </assert_stdout>
205 </test> 217 </test>
206 <!-- TOPP_IDPosteriorErrorProbability_5 --> 218 <!-- TOPP_IDPosteriorErrorProbability_5 -->
207 <test expect_num_outputs="2"> 219 <test expect_num_outputs="2">
208 <section name="adv_opts"> 220 <section name="adv_opts">
209 <param name="fdr_for_targets_smaller" value="0.05"/> 221 <param name="fdr_for_targets_smaller" value="0.05"/>
210 <param name="force" value="false"/> 222 <param name="force" value="false"/>
211 <param name="test" value="true"/> 223 <param name="test" value="true"/>
212 </section> 224 </section>
213 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> 225 <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"/> 226 <output name="out" value="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
215 <param name="split_charge" value="true"/> 227 <param name="split_charge" value="true"/>
216 <param name="top_hits_only" value="false"/> 228 <param name="top_hits_only" value="false"/>
217 <param name="ignore_bad_data" value="false"/> 229 <param name="ignore_bad_data" value="false"/>
218 <param name="prob_correct" value="false"/> 230 <param name="prob_correct" value="false"/>
219 <section name="fit_algorithm"> 231 <section name="fit_algorithm">
227 <output name="ctd_out" ftype="xml"> 239 <output name="ctd_out" ftype="xml">
228 <assert_contents> 240 <assert_contents>
229 <is_valid_xml/> 241 <is_valid_xml/>
230 </assert_contents> 242 </assert_contents>
231 </output> 243 </output>
244 <assert_stdout>
245 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
246 </assert_stdout>
232 </test> 247 </test>
233 <!-- TOPP_IDPosteriorErrorProbability_6 --> 248 <!-- TOPP_IDPosteriorErrorProbability_6 -->
234 <test expect_num_outputs="2"> 249 <test expect_num_outputs="2">
235 <section name="adv_opts"> 250 <section name="adv_opts">
236 <param name="fdr_for_targets_smaller" value="0.05"/> 251 <param name="fdr_for_targets_smaller" value="0.05"/>
237 <param name="force" value="false"/> 252 <param name="force" value="false"/>
238 <param name="test" value="true"/> 253 <param name="test" value="true"/>
239 </section> 254 </section>
240 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> 255 <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"/> 256 <output name="out" value="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
242 <param name="split_charge" value="true"/> 257 <param name="split_charge" value="true"/>
243 <param name="top_hits_only" value="false"/> 258 <param name="top_hits_only" value="false"/>
244 <param name="ignore_bad_data" value="false"/> 259 <param name="ignore_bad_data" value="false"/>
245 <param name="prob_correct" value="false"/> 260 <param name="prob_correct" value="false"/>
246 <section name="fit_algorithm"> 261 <section name="fit_algorithm">
254 <output name="ctd_out" ftype="xml"> 269 <output name="ctd_out" ftype="xml">
255 <assert_contents> 270 <assert_contents>
256 <is_valid_xml/> 271 <is_valid_xml/>
257 </assert_contents> 272 </assert_contents>
258 </output> 273 </output>
274 <assert_stdout>
275 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
276 </assert_stdout>
259 </test> 277 </test>
260 <!-- TOPP_IDPosteriorErrorProbability_7 --> 278 <!-- TOPP_IDPosteriorErrorProbability_7 -->
261 <test expect_num_outputs="2"> 279 <test expect_num_outputs="2">
262 <section name="adv_opts"> 280 <section name="adv_opts">
263 <param name="fdr_for_targets_smaller" value="0.05"/> 281 <param name="fdr_for_targets_smaller" value="0.05"/>
264 <param name="force" value="false"/> 282 <param name="force" value="false"/>
265 <param name="test" value="true"/> 283 <param name="test" value="true"/>
266 </section> 284 </section>
267 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> 285 <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"/> 286 <output name="out" value="IDPosteriorErrorProbability_bad_data_output.tmp" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
269 <param name="split_charge" value="false"/> 287 <param name="split_charge" value="false"/>
270 <param name="top_hits_only" value="false"/> 288 <param name="top_hits_only" value="false"/>
271 <param name="ignore_bad_data" value="true"/> 289 <param name="ignore_bad_data" value="true"/>
272 <param name="prob_correct" value="false"/> 290 <param name="prob_correct" value="false"/>
273 <section name="fit_algorithm"> 291 <section name="fit_algorithm">
281 <output name="ctd_out" ftype="xml"> 299 <output name="ctd_out" ftype="xml">
282 <assert_contents> 300 <assert_contents>
283 <is_valid_xml/> 301 <is_valid_xml/>
284 </assert_contents> 302 </assert_contents>
285 </output> 303 </output>
304 <assert_stdout>
305 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
306 </assert_stdout>
286 </test> 307 </test>
287 <!-- TOPP_IDPosteriorErrorProbability_8 --> 308 <!-- TOPP_IDPosteriorErrorProbability_8 -->
288 <test expect_num_outputs="2"> 309 <test expect_num_outputs="2">
289 <section name="adv_opts"> 310 <section name="adv_opts">
290 <param name="fdr_for_targets_smaller" value="0.05"/> 311 <param name="fdr_for_targets_smaller" value="0.05"/>
291 <param name="force" value="false"/> 312 <param name="force" value="false"/>
292 <param name="test" value="true"/> 313 <param name="test" value="true"/>
293 </section> 314 </section>
294 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> 315 <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"/> 316 <output name="out" value="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
296 <param name="split_charge" value="false"/> 317 <param name="split_charge" value="false"/>
297 <param name="top_hits_only" value="false"/> 318 <param name="top_hits_only" value="false"/>
298 <param name="ignore_bad_data" value="false"/> 319 <param name="ignore_bad_data" value="false"/>
299 <param name="prob_correct" value="true"/> 320 <param name="prob_correct" value="true"/>
300 <section name="fit_algorithm"> 321 <section name="fit_algorithm">
308 <output name="ctd_out" ftype="xml"> 329 <output name="ctd_out" ftype="xml">
309 <assert_contents> 330 <assert_contents>
310 <is_valid_xml/> 331 <is_valid_xml/>
311 </assert_contents> 332 </assert_contents>
312 </output> 333 </output>
334 <assert_stdout>
335 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
336 </assert_stdout>
313 </test> 337 </test>
314 </tests> 338 </tests>
315 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 339 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
316 340
317 341
318 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDPosteriorErrorProbability.html]]></help> 342 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDPosteriorErrorProbability.html]]></help>
319 <expand macro="references"/> 343 <expand macro="references"/>
320 </tool> 344 </tool>