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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 21:39:03 +0000
parents 6ccbf9a2072c
children
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15:6ccbf9a2072c 16:4138acdeedfb
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="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> 4 <description>Estimates the false discovery rate on peptide and protein level using decoy searches</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token> 6 <token name="@EXECUTABLE@">FalseDiscoveryRate</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 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/> 41 <param argument="-in" type="data" format="idxml" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
43 <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/> 42 <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
43 <param argument="-peptide" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform FDR calculation on peptide level and annotates it as meta value" help="(Note: if set, also calculates FDR/q-value on PSM level.)"/>
44 <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/> 44 <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
45 <section name="FDR" title="FDR control" help="" expanded="false"> 45 <section name="FDR" title="FDR control" help="" expanded="false">
46 <param name="PSM" argument="-FDR:PSM" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/> 46 <param name="PSM" argument="-FDR:PSM" type="float" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
47 <param name="protein" argument="-FDR:protein" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/> 47 <param name="protein" argument="-FDR:protein" type="float" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
48 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false"> 48 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
49 <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/> 49 <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/>
50 <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/> 50 <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/>
51 <param name="remove_spectra_without_psms" argument="-FDR:cleanup:remove_spectra_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove spectra without PSMs (due to being decoy or below protein FDR threshold)" help="Caution: if remove_psms_without_proteins is false, protein level filtering does not propagate"/> 51 <param name="remove_spectra_without_psms" argument="-FDR:cleanup:remove_spectra_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove spectra without PSMs (due to being decoy or below protein FDR threshold)" help="Caution: if remove_psms_without_proteins is false, protein level filtering does not propagate"/>
52 </section> 52 </section>
60 <param name="add_decoy_proteins" argument="-algorithm:add_decoy_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy proteins will be written to output file, too" help="The q-value is set to the closest target score"/> 60 <param name="add_decoy_proteins" argument="-algorithm:add_decoy_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy proteins will be written to output file, too" help="The q-value is set to the closest target score"/>
61 <param name="conservative" argument="-algorithm:conservative" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula" help=""/> 61 <param name="conservative" argument="-algorithm:conservative" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula" help=""/>
62 </section> 62 </section>
63 <expand macro="adv_opts_macro"> 63 <expand macro="adv_opts_macro">
64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
65 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 65 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
66 <expand macro="list_string_san" name="test"/> 66 <expand macro="list_string_san" name="test"/>
67 </param> 67 </param>
68 </expand> 68 </expand>
69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
74 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 74 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
77 </data> 77 </data>
78 </outputs> 78 </outputs>
79 <tests><!-- TOPP_FalseDiscoveryRate_1 --> 79 <tests>
80 <!-- TOPP_FalseDiscoveryRate_1 -->
80 <test expect_num_outputs="2"> 81 <test expect_num_outputs="2">
81 <section name="adv_opts"> 82 <section name="adv_opts">
82 <param name="force" value="false"/> 83 <param name="force" value="false"/>
83 <param name="test" value="true"/> 84 <param name="test" value="true"/>
84 </section> 85 </section>
85 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> 86 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
86 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 87 <output name="out" value="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
87 <param name="PSM" value="true"/> 88 <param name="PSM" value="true"/>
88 <param name="protein" value="false"/> 89 <param name="peptide" value="false"/>
89 <section name="FDR"> 90 <param name="protein" value="false"/>
90 <param name="PSM" value="1.0"/> 91 <section name="FDR">
91 <param name="protein" value="1.0"/> 92 <param name="PSM" value="1.0"/>
92 <section name="cleanup"> 93 <param name="protein" value="1.0"/>
93 <param name="remove_proteins_without_psms" value="true"/> 94 <section name="cleanup">
94 <param name="remove_psms_without_proteins" value="true"/> 95 <param name="remove_proteins_without_psms" value="true"/>
95 <param name="remove_spectra_without_psms" value="true"/> 96 <param name="remove_psms_without_proteins" value="true"/>
96 </section> 97 <param name="remove_spectra_without_psms" value="true"/>
97 </section> 98 </section>
98 <section name="algorithm"> 99 </section>
99 <param name="no_qvalues" value="false"/> 100 <section name="algorithm">
100 <param name="use_all_hits" value="false"/> 101 <param name="no_qvalues" value="false"/>
101 <param name="split_charge_variants" value="false"/> 102 <param name="use_all_hits" value="false"/>
102 <param name="treat_runs_separately" value="false"/> 103 <param name="split_charge_variants" value="false"/>
103 <param name="add_decoy_peptides" value="false"/> 104 <param name="treat_runs_separately" value="false"/>
104 <param name="add_decoy_proteins" value="false"/> 105 <param name="add_decoy_peptides" value="false"/>
105 <param name="conservative" value="true"/> 106 <param name="add_decoy_proteins" value="false"/>
106 </section> 107 <param name="conservative" value="true"/>
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 108 </section>
108 <output name="ctd_out" ftype="xml"> 109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
109 <assert_contents> 110 <output name="ctd_out" ftype="xml">
110 <is_valid_xml/> 111 <assert_contents>
111 </assert_contents> 112 <is_valid_xml/>
112 </output> 113 </assert_contents>
114 </output>
115 <assert_stdout>
116 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
117 </assert_stdout>
113 </test> 118 </test>
114 <!-- TOPP_FalseDiscoveryRate_2 --> 119 <!-- TOPP_FalseDiscoveryRate_2 -->
115 <test expect_num_outputs="2"> 120 <test expect_num_outputs="2">
116 <section name="adv_opts"> 121 <section name="adv_opts">
117 <param name="force" value="false"/> 122 <param name="force" value="false"/>
118 <param name="test" value="true"/> 123 <param name="test" value="true"/>
119 </section> 124 </section>
120 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> 125 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
121 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 126 <output name="out" value="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
122 <param name="PSM" value="true"/> 127 <param name="PSM" value="true"/>
128 <param name="peptide" value="false"/>
123 <param name="protein" value="false"/> 129 <param name="protein" value="false"/>
124 <section name="FDR"> 130 <section name="FDR">
125 <param name="PSM" value="1.0"/> 131 <param name="PSM" value="1.0"/>
126 <param name="protein" value="1.0"/> 132 <param name="protein" value="1.0"/>
127 <section name="cleanup"> 133 <section name="cleanup">
143 <output name="ctd_out" ftype="xml"> 149 <output name="ctd_out" ftype="xml">
144 <assert_contents> 150 <assert_contents>
145 <is_valid_xml/> 151 <is_valid_xml/>
146 </assert_contents> 152 </assert_contents>
147 </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>
148 </test> 157 </test>
149 <!-- TOPP_FalseDiscoveryRate_3 --> 158 <!-- TOPP_FalseDiscoveryRate_3 -->
150 <test expect_num_outputs="2"> 159 <test expect_num_outputs="2">
151 <section name="adv_opts"> 160 <section name="adv_opts">
152 <param name="force" value="false"/> 161 <param name="force" value="false"/>
153 <param name="test" value="true"/> 162 <param name="test" value="true"/>
154 </section> 163 </section>
155 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> 164 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
156 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 165 <output name="out" value="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
157 <param name="PSM" value="true"/> 166 <param name="PSM" value="true"/>
167 <param name="peptide" value="false"/>
158 <param name="protein" value="false"/> 168 <param name="protein" value="false"/>
159 <section name="FDR"> 169 <section name="FDR">
160 <param name="PSM" value="1.0"/> 170 <param name="PSM" value="1.0"/>
161 <param name="protein" value="1.0"/> 171 <param name="protein" value="1.0"/>
162 <section name="cleanup"> 172 <section name="cleanup">
178 <output name="ctd_out" ftype="xml"> 188 <output name="ctd_out" ftype="xml">
179 <assert_contents> 189 <assert_contents>
180 <is_valid_xml/> 190 <is_valid_xml/>
181 </assert_contents> 191 </assert_contents>
182 </output> 192 </output>
193 <assert_stdout>
194 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
195 </assert_stdout>
183 </test> 196 </test>
184 <!-- TOPP_FalseDiscoveryRate_4 --> 197 <!-- TOPP_FalseDiscoveryRate_4 -->
185 <test expect_num_outputs="2"> 198 <test expect_num_outputs="2">
186 <section name="adv_opts"> 199 <section name="adv_opts">
187 <param name="force" value="false"/> 200 <param name="force" value="false"/>
188 <param name="test" value="true"/> 201 <param name="test" value="true"/>
189 </section> 202 </section>
190 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> 203 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
191 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 204 <output name="out" value="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
192 <param name="PSM" value="true"/> 205 <param name="PSM" value="true"/>
206 <param name="peptide" value="false"/>
193 <param name="protein" value="false"/> 207 <param name="protein" value="false"/>
194 <section name="FDR"> 208 <section name="FDR">
195 <param name="PSM" value="1.0"/> 209 <param name="PSM" value="1.0"/>
196 <param name="protein" value="1.0"/> 210 <param name="protein" value="1.0"/>
197 <section name="cleanup"> 211 <section name="cleanup">
213 <output name="ctd_out" ftype="xml"> 227 <output name="ctd_out" ftype="xml">
214 <assert_contents> 228 <assert_contents>
215 <is_valid_xml/> 229 <is_valid_xml/>
216 </assert_contents> 230 </assert_contents>
217 </output> 231 </output>
232 <assert_stdout>
233 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
234 </assert_stdout>
218 </test> 235 </test>
219 <!-- TOPP_FalseDiscoveryRate_5 --> 236 <!-- TOPP_FalseDiscoveryRate_5 -->
220 <test expect_num_outputs="2"> 237 <test expect_num_outputs="2">
221 <section name="adv_opts"> 238 <section name="adv_opts">
222 <param name="force" value="true"/> 239 <param name="force" value="true"/>
223 <param name="test" value="true"/> 240 <param name="test" value="true"/>
224 </section> 241 </section>
225 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> 242 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
226 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 243 <output name="out" value="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
227 <param name="PSM" value="false"/> 244 <param name="PSM" value="false"/>
245 <param name="peptide" value="false"/>
228 <param name="protein" value="true"/> 246 <param name="protein" value="true"/>
229 <section name="FDR"> 247 <section name="FDR">
230 <param name="PSM" value="1.0"/> 248 <param name="PSM" value="1.0"/>
231 <param name="protein" value="1.0"/> 249 <param name="protein" value="1.0"/>
232 <section name="cleanup"> 250 <section name="cleanup">
248 <output name="ctd_out" ftype="xml"> 266 <output name="ctd_out" ftype="xml">
249 <assert_contents> 267 <assert_contents>
250 <is_valid_xml/> 268 <is_valid_xml/>
251 </assert_contents> 269 </assert_contents>
252 </output> 270 </output>
271 <assert_stdout>
272 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
273 </assert_stdout>
253 </test> 274 </test>
254 <!-- TOPP_FalseDiscoveryRate_6 --> 275 <!-- TOPP_FalseDiscoveryRate_6 -->
255 <test expect_num_outputs="2"> 276 <test expect_num_outputs="2">
256 <section name="adv_opts"> 277 <section name="adv_opts">
257 <param name="force" value="false"/> 278 <param name="force" value="false"/>
258 <param name="test" value="true"/> 279 <param name="test" value="true"/>
259 </section> 280 </section>
260 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> 281 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
261 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 282 <output name="out" value="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
262 <param name="PSM" value="true"/> 283 <param name="PSM" value="true"/>
284 <param name="peptide" value="false"/>
263 <param name="protein" value="false"/> 285 <param name="protein" value="false"/>
264 <section name="FDR"> 286 <section name="FDR">
265 <param name="PSM" value="0.05"/> 287 <param name="PSM" value="0.05"/>
266 <param name="protein" value="1.0"/> 288 <param name="protein" value="1.0"/>
267 <section name="cleanup"> 289 <section name="cleanup">
283 <output name="ctd_out" ftype="xml"> 305 <output name="ctd_out" ftype="xml">
284 <assert_contents> 306 <assert_contents>
285 <is_valid_xml/> 307 <is_valid_xml/>
286 </assert_contents> 308 </assert_contents>
287 </output> 309 </output>
310 <assert_stdout>
311 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
312 </assert_stdout>
288 </test> 313 </test>
289 <!-- TOPP_FalseDiscoveryRate_7 --> 314 <!-- TOPP_FalseDiscoveryRate_7 -->
290 <test expect_num_outputs="2"> 315 <test expect_num_outputs="2">
291 <section name="adv_opts"> 316 <section name="adv_opts">
292 <param name="force" value="true"/> 317 <param name="force" value="true"/>
293 <param name="test" value="true"/> 318 <param name="test" value="true"/>
294 </section> 319 </section>
295 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> 320 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
296 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 321 <output name="out" value="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
297 <param name="PSM" value="false"/> 322 <param name="PSM" value="false"/>
323 <param name="peptide" value="false"/>
298 <param name="protein" value="true"/> 324 <param name="protein" value="true"/>
299 <section name="FDR"> 325 <section name="FDR">
300 <param name="PSM" value="1.0"/> 326 <param name="PSM" value="1.0"/>
301 <param name="protein" value="0.3"/> 327 <param name="protein" value="0.3"/>
302 <section name="cleanup"> 328 <section name="cleanup">
318 <output name="ctd_out" ftype="xml"> 344 <output name="ctd_out" ftype="xml">
319 <assert_contents> 345 <assert_contents>
320 <is_valid_xml/> 346 <is_valid_xml/>
321 </assert_contents> 347 </assert_contents>
322 </output> 348 </output>
349 <assert_stdout>
350 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
351 </assert_stdout>
323 </test> 352 </test>
324 </tests> 353 </tests>
325 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches. 354 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
326 355
327 356
328 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FalseDiscoveryRate.html]]></help> 357 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FalseDiscoveryRate.html]]></help>
329 <expand macro="references"/> 358 <expand macro="references"/>
330 </tool> 359 </tool>