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comparison FalseDiscoveryRate.xml @ 15:6ccbf9a2072c 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 19:02:41 +0000
parents 469690558892
children 4138acdeedfb
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14:c9eff69a7c62 15:6ccbf9a2072c
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="FalseDiscoveryRate" name="FalseDiscoveryRate" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token> 7 <token name="@EXECUTABLE@">FalseDiscoveryRate</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/> 42 <param argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
45 <param name="PSM" argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/> 43 <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
46 <param name="protein" 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=""/>
47 <section name="FDR" title="FDR control" help="" expanded="false"> 45 <section name="FDR" title="FDR control" help="" expanded="false">
48 <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" 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)"/>
49 <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" 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)"/>
50 <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">
51 <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=""/>
61 <param name="add_decoy_peptides" argument="-algorithm:add_decoy_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy peptides will be written to output file, too" help="The q-value is set to the closest target score"/> 59 <param name="add_decoy_peptides" argument="-algorithm:add_decoy_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy peptides will be written to output file, too" help="The q-value is set to the closest target score"/>
62 <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"/>
63 <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=""/>
64 </section> 62 </section>
65 <expand macro="adv_opts_macro"> 63 <expand macro="adv_opts_macro">
66 <param name="force" 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=""/>
67 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
68 <expand macro="list_string_san"/> 66 <expand macro="list_string_san" name="test"/>
69 </param> 67 </param>
70 </expand> 68 </expand>
71 <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">
72 <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>
73 </param> 71 </param>
76 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 74 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
78 <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>
79 </data> 77 </data>
80 </outputs> 78 </outputs>
81 <tests> 79 <tests><!-- TOPP_FalseDiscoveryRate_1 -->
82 <expand macro="autotest_FalseDiscoveryRate"/> 80 <test expect_num_outputs="2">
83 <expand macro="manutest_FalseDiscoveryRate"/> 81 <section name="adv_opts">
82 <param name="force" value="false"/>
83 <param name="test" value="true"/>
84 </section>
85 <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 <param name="PSM" value="true"/>
88 <param name="protein" value="false"/>
89 <section name="FDR">
90 <param name="PSM" value="1.0"/>
91 <param name="protein" value="1.0"/>
92 <section name="cleanup">
93 <param name="remove_proteins_without_psms" value="true"/>
94 <param name="remove_psms_without_proteins" value="true"/>
95 <param name="remove_spectra_without_psms" value="true"/>
96 </section>
97 </section>
98 <section name="algorithm">
99 <param name="no_qvalues" value="false"/>
100 <param name="use_all_hits" value="false"/>
101 <param name="split_charge_variants" value="false"/>
102 <param name="treat_runs_separately" value="false"/>
103 <param name="add_decoy_peptides" value="false"/>
104 <param name="add_decoy_proteins" value="false"/>
105 <param name="conservative" value="true"/>
106 </section>
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
108 <output name="ctd_out" ftype="xml">
109 <assert_contents>
110 <is_valid_xml/>
111 </assert_contents>
112 </output>
113 </test>
114 <!-- TOPP_FalseDiscoveryRate_2 -->
115 <test expect_num_outputs="2">
116 <section name="adv_opts">
117 <param name="force" value="false"/>
118 <param name="test" value="true"/>
119 </section>
120 <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"/>
122 <param name="PSM" value="true"/>
123 <param name="protein" value="false"/>
124 <section name="FDR">
125 <param name="PSM" value="1.0"/>
126 <param name="protein" value="1.0"/>
127 <section name="cleanup">
128 <param name="remove_proteins_without_psms" value="true"/>
129 <param name="remove_psms_without_proteins" value="true"/>
130 <param name="remove_spectra_without_psms" value="true"/>
131 </section>
132 </section>
133 <section name="algorithm">
134 <param name="no_qvalues" value="false"/>
135 <param name="use_all_hits" value="false"/>
136 <param name="split_charge_variants" value="false"/>
137 <param name="treat_runs_separately" value="true"/>
138 <param name="add_decoy_peptides" value="false"/>
139 <param name="add_decoy_proteins" value="false"/>
140 <param name="conservative" value="true"/>
141 </section>
142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
143 <output name="ctd_out" ftype="xml">
144 <assert_contents>
145 <is_valid_xml/>
146 </assert_contents>
147 </output>
148 </test>
149 <!-- TOPP_FalseDiscoveryRate_3 -->
150 <test expect_num_outputs="2">
151 <section name="adv_opts">
152 <param name="force" value="false"/>
153 <param name="test" value="true"/>
154 </section>
155 <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"/>
157 <param name="PSM" value="true"/>
158 <param name="protein" value="false"/>
159 <section name="FDR">
160 <param name="PSM" value="1.0"/>
161 <param name="protein" value="1.0"/>
162 <section name="cleanup">
163 <param name="remove_proteins_without_psms" value="true"/>
164 <param name="remove_psms_without_proteins" value="true"/>
165 <param name="remove_spectra_without_psms" value="true"/>
166 </section>
167 </section>
168 <section name="algorithm">
169 <param name="no_qvalues" value="false"/>
170 <param name="use_all_hits" value="false"/>
171 <param name="split_charge_variants" value="true"/>
172 <param name="treat_runs_separately" value="false"/>
173 <param name="add_decoy_peptides" value="false"/>
174 <param name="add_decoy_proteins" value="false"/>
175 <param name="conservative" value="true"/>
176 </section>
177 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
178 <output name="ctd_out" ftype="xml">
179 <assert_contents>
180 <is_valid_xml/>
181 </assert_contents>
182 </output>
183 </test>
184 <!-- TOPP_FalseDiscoveryRate_4 -->
185 <test expect_num_outputs="2">
186 <section name="adv_opts">
187 <param name="force" value="false"/>
188 <param name="test" value="true"/>
189 </section>
190 <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"/>
192 <param name="PSM" value="true"/>
193 <param name="protein" value="false"/>
194 <section name="FDR">
195 <param name="PSM" value="1.0"/>
196 <param name="protein" value="1.0"/>
197 <section name="cleanup">
198 <param name="remove_proteins_without_psms" value="true"/>
199 <param name="remove_psms_without_proteins" value="true"/>
200 <param name="remove_spectra_without_psms" value="true"/>
201 </section>
202 </section>
203 <section name="algorithm">
204 <param name="no_qvalues" value="false"/>
205 <param name="use_all_hits" value="false"/>
206 <param name="split_charge_variants" value="true"/>
207 <param name="treat_runs_separately" value="false"/>
208 <param name="add_decoy_peptides" value="false"/>
209 <param name="add_decoy_proteins" value="false"/>
210 <param name="conservative" value="true"/>
211 </section>
212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
213 <output name="ctd_out" ftype="xml">
214 <assert_contents>
215 <is_valid_xml/>
216 </assert_contents>
217 </output>
218 </test>
219 <!-- TOPP_FalseDiscoveryRate_5 -->
220 <test expect_num_outputs="2">
221 <section name="adv_opts">
222 <param name="force" value="true"/>
223 <param name="test" value="true"/>
224 </section>
225 <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"/>
227 <param name="PSM" value="false"/>
228 <param name="protein" value="true"/>
229 <section name="FDR">
230 <param name="PSM" value="1.0"/>
231 <param name="protein" value="1.0"/>
232 <section name="cleanup">
233 <param name="remove_proteins_without_psms" value="true"/>
234 <param name="remove_psms_without_proteins" value="true"/>
235 <param name="remove_spectra_without_psms" value="true"/>
236 </section>
237 </section>
238 <section name="algorithm">
239 <param name="no_qvalues" value="false"/>
240 <param name="use_all_hits" value="false"/>
241 <param name="split_charge_variants" value="false"/>
242 <param name="treat_runs_separately" value="false"/>
243 <param name="add_decoy_peptides" value="false"/>
244 <param name="add_decoy_proteins" value="true"/>
245 <param name="conservative" value="true"/>
246 </section>
247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
248 <output name="ctd_out" ftype="xml">
249 <assert_contents>
250 <is_valid_xml/>
251 </assert_contents>
252 </output>
253 </test>
254 <!-- TOPP_FalseDiscoveryRate_6 -->
255 <test expect_num_outputs="2">
256 <section name="adv_opts">
257 <param name="force" value="false"/>
258 <param name="test" value="true"/>
259 </section>
260 <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"/>
262 <param name="PSM" value="true"/>
263 <param name="protein" value="false"/>
264 <section name="FDR">
265 <param name="PSM" value="0.05"/>
266 <param name="protein" value="1.0"/>
267 <section name="cleanup">
268 <param name="remove_proteins_without_psms" value="true"/>
269 <param name="remove_psms_without_proteins" value="true"/>
270 <param name="remove_spectra_without_psms" value="true"/>
271 </section>
272 </section>
273 <section name="algorithm">
274 <param name="no_qvalues" value="false"/>
275 <param name="use_all_hits" value="false"/>
276 <param name="split_charge_variants" value="false"/>
277 <param name="treat_runs_separately" value="false"/>
278 <param name="add_decoy_peptides" value="false"/>
279 <param name="add_decoy_proteins" value="false"/>
280 <param name="conservative" value="true"/>
281 </section>
282 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
283 <output name="ctd_out" ftype="xml">
284 <assert_contents>
285 <is_valid_xml/>
286 </assert_contents>
287 </output>
288 </test>
289 <!-- TOPP_FalseDiscoveryRate_7 -->
290 <test expect_num_outputs="2">
291 <section name="adv_opts">
292 <param name="force" value="true"/>
293 <param name="test" value="true"/>
294 </section>
295 <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"/>
297 <param name="PSM" value="false"/>
298 <param name="protein" value="true"/>
299 <section name="FDR">
300 <param name="PSM" value="1.0"/>
301 <param name="protein" value="0.3"/>
302 <section name="cleanup">
303 <param name="remove_proteins_without_psms" value="true"/>
304 <param name="remove_psms_without_proteins" value="true"/>
305 <param name="remove_spectra_without_psms" value="true"/>
306 </section>
307 </section>
308 <section name="algorithm">
309 <param name="no_qvalues" value="false"/>
310 <param name="use_all_hits" value="false"/>
311 <param name="split_charge_variants" value="false"/>
312 <param name="treat_runs_separately" value="false"/>
313 <param name="add_decoy_peptides" value="false"/>
314 <param name="add_decoy_proteins" value="false"/>
315 <param name="conservative" value="true"/>
316 </section>
317 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
318 <output name="ctd_out" ftype="xml">
319 <assert_contents>
320 <is_valid_xml/>
321 </assert_contents>
322 </output>
323 </test>
84 </tests> 324 </tests>
85 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches. 325 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
86 326
87 327
88 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FalseDiscoveryRate.html]]></help> 328 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FalseDiscoveryRate.html]]></help>
89 <expand macro="references"/> 329 <expand macro="references"/>
90 </tool> 330 </tool>