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comparison ProteinQuantifier.xml @ 13:d426affe977c draft default tip

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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 19:18:55 +0000
parents bb1e75938909
children
comparison
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12:16026cdb1330 13:d426affe977c
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: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compute peptide and protein abundances</description> 5 <description>Compute peptide and protein abundances</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ProteinQuantifier</token> 7 <token name="@EXECUTABLE@">ProteinQuantifier</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@
84 <configfiles> 82 <configfiles>
85 <inputs name="args_json" data_style="paths"/> 83 <inputs name="args_json" data_style="paths"/>
86 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
87 </configfiles> 85 </configfiles>
88 <inputs> 86 <inputs>
89 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> 87 <param argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
90 <param name="protein_groups" argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/> 88 <param argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
91 <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> 89 <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
92 <param name="top" argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/> 90 <param argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
93 <param name="average" argument="-average" display="radio" type="select" optional="false" label="Averaging method used to compute protein abundances from peptide abundances" help=""> 91 <param argument="-average" type="select" optional="true" label="Averaging method used to compute protein abundances from peptide abundances" help="">
94 <option value="median" selected="true">median</option> 92 <option value="median" selected="true">median</option>
95 <option value="mean">mean</option> 93 <option value="mean">mean</option>
96 <option value="weighted_mean">weighted_mean</option> 94 <option value="weighted_mean">weighted_mean</option>
97 <option value="sum">sum</option> 95 <option value="sum">sum</option>
98 <expand macro="list_string_san"/> 96 <expand macro="list_string_san" name="average"/>
99 </param> 97 </param>
100 <param name="include_all" argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/> 98 <param argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
101 <param name="best_charge_and_fraction" argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/> 99 <param argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
102 <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/> 100 <param argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
103 <param name="ratios" argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/> 101 <param argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
104 <param name="ratiosSILAC" argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/> 102 <param argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
105 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false"> 103 <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
106 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/> 104 <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
107 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0', all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> 105 <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0',all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
108 </section> 106 </section>
109 <section name="format" title="Output formatting options" help="" expanded="false"> 107 <section name="format" title="Output formatting options" help="" expanded="false">
110 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help=""> 108 <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
111 <expand macro="list_string_san"/> 109 <expand macro="list_string_san" name="separator"/>
112 </param> 110 </param>
113 <param name="quoting" argument="-format:quoting" display="radio" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes"> 111 <param name="quoting" argument="-format:quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
114 <option value="none">none</option> 112 <option value="none">none</option>
115 <option value="double" selected="true">double</option> 113 <option value="double" selected="true">double</option>
116 <option value="escape">escape</option> 114 <option value="escape">escape</option>
117 <expand macro="list_string_san"/> 115 <expand macro="list_string_san" name="quoting"/>
118 </param> 116 </param>
119 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help=""> 117 <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
120 <expand macro="list_string_san"/> 118 <expand macro="list_string_san" name="replacement"/>
121 </param> 119 </param>
122 </section> 120 </section>
123 <expand macro="adv_opts_macro"> 121 <expand macro="adv_opts_macro">
124 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 122 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
125 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 123 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
126 <expand macro="list_string_san"/> 124 <expand macro="list_string_san" name="test"/>
127 </param> 125 </param>
128 </expand> 126 </expand>
129 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 127 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
130 <option value="out_FLAG">out (Output file for protein abundances)</option> 128 <option value="out_FLAG">out (Output file for protein abundances)</option>
131 <option value="peptide_out_FLAG">peptide_out (Output file for peptide abundances)</option> 129 <option value="peptide_out_FLAG">peptide_out (Output file for peptide abundances)</option>
148 </data> 146 </data>
149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 147 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 148 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data> 149 </data>
152 </outputs> 150 </outputs>
153 <tests> 151 <tests><!-- TOPP_ProteinQuantifier_1 -->
154 <expand macro="autotest_ProteinQuantifier"/> 152 <test expect_num_outputs="3">
155 <expand macro="manutest_ProteinQuantifier"/> 153 <section name="adv_opts">
154 <param name="force" value="false"/>
155 <param name="test" value="true"/>
156 </section>
157 <param name="in" value="ProteinQuantifier_input.featureXML"/>
158 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
159 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
160 <param name="top" value="3"/>
161 <param name="average" value="median"/>
162 <param name="include_all" value="false"/>
163 <param name="best_charge_and_fraction" value="false"/>
164 <param name="greedy_group_resolution" value="false"/>
165 <param name="ratios" value="false"/>
166 <param name="ratiosSILAC" value="false"/>
167 <section name="consensus">
168 <param name="normalize" value="false"/>
169 <param name="fix_peptides" value="false"/>
170 </section>
171 <section name="format">
172 <param name="separator" value=""/>
173 <param name="quoting" value="double"/>
174 <param name="replacement" value="_"/>
175 </section>
176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
177 <output name="ctd_out" ftype="xml">
178 <assert_contents>
179 <is_valid_xml/>
180 </assert_contents>
181 </output>
182 </test>
183 <!-- TOPP_ProteinQuantifier_2 -->
184 <test expect_num_outputs="3">
185 <section name="adv_opts">
186 <param name="force" value="false"/>
187 <param name="test" value="true"/>
188 </section>
189 <param name="in" value="ProteinQuantifier_input.featureXML"/>
190 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
191 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
192 <param name="top" value="2"/>
193 <param name="average" value="sum"/>
194 <param name="include_all" value="true"/>
195 <param name="best_charge_and_fraction" value="true"/>
196 <param name="greedy_group_resolution" value="false"/>
197 <param name="ratios" value="false"/>
198 <param name="ratiosSILAC" value="false"/>
199 <section name="consensus">
200 <param name="normalize" value="false"/>
201 <param name="fix_peptides" value="false"/>
202 </section>
203 <section name="format">
204 <param name="separator" value=""/>
205 <param name="quoting" value="double"/>
206 <param name="replacement" value="_"/>
207 </section>
208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
209 <output name="ctd_out" ftype="xml">
210 <assert_contents>
211 <is_valid_xml/>
212 </assert_contents>
213 </output>
214 </test>
215 <!-- TOPP_ProteinQuantifier_3 -->
216 <test expect_num_outputs="3">
217 <section name="adv_opts">
218 <param name="force" value="false"/>
219 <param name="test" value="true"/>
220 </section>
221 <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
222 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
223 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
224 <param name="top" value="2"/>
225 <param name="average" value="mean"/>
226 <param name="include_all" value="true"/>
227 <param name="best_charge_and_fraction" value="false"/>
228 <param name="greedy_group_resolution" value="false"/>
229 <param name="ratios" value="false"/>
230 <param name="ratiosSILAC" value="false"/>
231 <section name="consensus">
232 <param name="normalize" value="false"/>
233 <param name="fix_peptides" value="false"/>
234 </section>
235 <section name="format">
236 <param name="separator" value=""/>
237 <param name="quoting" value="double"/>
238 <param name="replacement" value="_"/>
239 </section>
240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
241 <output name="ctd_out" ftype="xml">
242 <assert_contents>
243 <is_valid_xml/>
244 </assert_contents>
245 </output>
246 </test>
247 <!-- TOPP_ProteinQuantifier_4 -->
248 <test expect_num_outputs="2">
249 <section name="adv_opts">
250 <param name="force" value="false"/>
251 <param name="test" value="true"/>
252 </section>
253 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
254 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
255 <param name="top" value="0"/>
256 <param name="average" value="sum"/>
257 <param name="include_all" value="false"/>
258 <param name="best_charge_and_fraction" value="false"/>
259 <param name="greedy_group_resolution" value="false"/>
260 <param name="ratios" value="false"/>
261 <param name="ratiosSILAC" value="false"/>
262 <section name="consensus">
263 <param name="normalize" value="false"/>
264 <param name="fix_peptides" value="false"/>
265 </section>
266 <section name="format">
267 <param name="separator" value=""/>
268 <param name="quoting" value="double"/>
269 <param name="replacement" value="_"/>
270 </section>
271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
272 <output name="ctd_out" ftype="xml">
273 <assert_contents>
274 <is_valid_xml/>
275 </assert_contents>
276 </output>
277 </test>
278 <!-- TOPP_ProteinQuantifier_5 -->
279 <test expect_num_outputs="2">
280 <section name="adv_opts">
281 <param name="force" value="false"/>
282 <param name="test" value="true"/>
283 </section>
284 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
285 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
286 <param name="top" value="3"/>
287 <param name="average" value="sum"/>
288 <param name="include_all" value="false"/>
289 <param name="best_charge_and_fraction" value="false"/>
290 <param name="greedy_group_resolution" value="false"/>
291 <param name="ratios" value="false"/>
292 <param name="ratiosSILAC" value="false"/>
293 <section name="consensus">
294 <param name="normalize" value="false"/>
295 <param name="fix_peptides" value="false"/>
296 </section>
297 <section name="format">
298 <param name="separator" value=""/>
299 <param name="quoting" value="double"/>
300 <param name="replacement" value="_"/>
301 </section>
302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
303 <output name="ctd_out" ftype="xml">
304 <assert_contents>
305 <is_valid_xml/>
306 </assert_contents>
307 </output>
308 </test>
309 <!-- TOPP_ProteinQuantifier_6 -->
310 <test expect_num_outputs="2">
311 <section name="adv_opts">
312 <param name="force" value="false"/>
313 <param name="test" value="true"/>
314 </section>
315 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
316 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
317 <param name="top" value="3"/>
318 <param name="average" value="sum"/>
319 <param name="include_all" value="true"/>
320 <param name="best_charge_and_fraction" value="false"/>
321 <param name="greedy_group_resolution" value="false"/>
322 <param name="ratios" value="false"/>
323 <param name="ratiosSILAC" value="false"/>
324 <section name="consensus">
325 <param name="normalize" value="false"/>
326 <param name="fix_peptides" value="false"/>
327 </section>
328 <section name="format">
329 <param name="separator" value=""/>
330 <param name="quoting" value="double"/>
331 <param name="replacement" value="_"/>
332 </section>
333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
334 <output name="ctd_out" ftype="xml">
335 <assert_contents>
336 <is_valid_xml/>
337 </assert_contents>
338 </output>
339 </test>
340 <!-- TOPP_ProteinQuantifier_7 -->
341 <test expect_num_outputs="2">
342 <section name="adv_opts">
343 <param name="force" value="false"/>
344 <param name="test" value="true"/>
345 </section>
346 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
347 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
348 <param name="top" value="0"/>
349 <param name="average" value="sum"/>
350 <param name="include_all" value="false"/>
351 <param name="best_charge_and_fraction" value="false"/>
352 <param name="greedy_group_resolution" value="false"/>
353 <param name="ratios" value="false"/>
354 <param name="ratiosSILAC" value="false"/>
355 <section name="consensus">
356 <param name="normalize" value="false"/>
357 <param name="fix_peptides" value="true"/>
358 </section>
359 <section name="format">
360 <param name="separator" value=""/>
361 <param name="quoting" value="double"/>
362 <param name="replacement" value="_"/>
363 </section>
364 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
365 <output name="ctd_out" ftype="xml">
366 <assert_contents>
367 <is_valid_xml/>
368 </assert_contents>
369 </output>
370 </test>
371 <!-- TOPP_ProteinQuantifier_8 -->
372 <test expect_num_outputs="2">
373 <section name="adv_opts">
374 <param name="force" value="false"/>
375 <param name="test" value="true"/>
376 </section>
377 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
378 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
379 <param name="top" value="3"/>
380 <param name="average" value="sum"/>
381 <param name="include_all" value="false"/>
382 <param name="best_charge_and_fraction" value="false"/>
383 <param name="greedy_group_resolution" value="false"/>
384 <param name="ratios" value="false"/>
385 <param name="ratiosSILAC" value="false"/>
386 <section name="consensus">
387 <param name="normalize" value="false"/>
388 <param name="fix_peptides" value="true"/>
389 </section>
390 <section name="format">
391 <param name="separator" value=""/>
392 <param name="quoting" value="double"/>
393 <param name="replacement" value="_"/>
394 </section>
395 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
396 <output name="ctd_out" ftype="xml">
397 <assert_contents>
398 <is_valid_xml/>
399 </assert_contents>
400 </output>
401 </test>
402 <!-- TOPP_ProteinQuantifier_9 -->
403 <test expect_num_outputs="3">
404 <section name="adv_opts">
405 <param name="force" value="false"/>
406 <param name="test" value="true"/>
407 </section>
408 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
409 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
410 <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
411 <param name="top" value="3"/>
412 <param name="average" value="sum"/>
413 <param name="include_all" value="true"/>
414 <param name="best_charge_and_fraction" value="false"/>
415 <param name="greedy_group_resolution" value="false"/>
416 <param name="ratios" value="false"/>
417 <param name="ratiosSILAC" value="false"/>
418 <section name="consensus">
419 <param name="normalize" value="false"/>
420 <param name="fix_peptides" value="true"/>
421 </section>
422 <section name="format">
423 <param name="separator" value=""/>
424 <param name="quoting" value="double"/>
425 <param name="replacement" value="_"/>
426 </section>
427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
428 <output name="ctd_out" ftype="xml">
429 <assert_contents>
430 <is_valid_xml/>
431 </assert_contents>
432 </output>
433 </test>
434 <!-- TOPP_ProteinQuantifier_12 -->
435 <test expect_num_outputs="2">
436 <section name="adv_opts">
437 <param name="force" value="false"/>
438 <param name="test" value="true"/>
439 </section>
440 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
441 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
442 <param name="top" value="3"/>
443 <param name="average" value="sum"/>
444 <param name="include_all" value="true"/>
445 <param name="best_charge_and_fraction" value="false"/>
446 <param name="greedy_group_resolution" value="false"/>
447 <param name="ratios" value="true"/>
448 <param name="ratiosSILAC" value="false"/>
449 <section name="consensus">
450 <param name="normalize" value="false"/>
451 <param name="fix_peptides" value="true"/>
452 </section>
453 <section name="format">
454 <param name="separator" value=""/>
455 <param name="quoting" value="double"/>
456 <param name="replacement" value="_"/>
457 </section>
458 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
459 <output name="ctd_out" ftype="xml">
460 <assert_contents>
461 <is_valid_xml/>
462 </assert_contents>
463 </output>
464 </test>
465 <!-- TOPP_ProteinQuantifier_13 -->
466 <test expect_num_outputs="2">
467 <section name="adv_opts">
468 <param name="force" value="false"/>
469 <param name="test" value="true"/>
470 </section>
471 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
472 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
473 <param name="top" value="3"/>
474 <param name="average" value="sum"/>
475 <param name="include_all" value="true"/>
476 <param name="best_charge_and_fraction" value="false"/>
477 <param name="greedy_group_resolution" value="false"/>
478 <param name="ratios" value="false"/>
479 <param name="ratiosSILAC" value="true"/>
480 <section name="consensus">
481 <param name="normalize" value="false"/>
482 <param name="fix_peptides" value="true"/>
483 </section>
484 <section name="format">
485 <param name="separator" value=""/>
486 <param name="quoting" value="double"/>
487 <param name="replacement" value="_"/>
488 </section>
489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
490 <output name="ctd_out" ftype="xml">
491 <assert_contents>
492 <is_valid_xml/>
493 </assert_contents>
494 </output>
495 </test>
496 <!-- TOPP_ProteinQuantifier_14 -->
497 <test expect_num_outputs="3">
498 <section name="adv_opts">
499 <param name="force" value="false"/>
500 <param name="test" value="true"/>
501 </section>
502 <param name="in" value="ProteinQuantifier_input.idXML"/>
503 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
504 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
505 <param name="top" value="0"/>
506 <param name="average" value="sum"/>
507 <param name="include_all" value="false"/>
508 <param name="best_charge_and_fraction" value="false"/>
509 <param name="greedy_group_resolution" value="false"/>
510 <param name="ratios" value="false"/>
511 <param name="ratiosSILAC" value="false"/>
512 <section name="consensus">
513 <param name="normalize" value="false"/>
514 <param name="fix_peptides" value="false"/>
515 </section>
516 <section name="format">
517 <param name="separator" value=""/>
518 <param name="quoting" value="double"/>
519 <param name="replacement" value="_"/>
520 </section>
521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
522 <output name="ctd_out" ftype="xml">
523 <assert_contents>
524 <is_valid_xml/>
525 </assert_contents>
526 </output>
527 </test>
156 </tests> 528 </tests>
157 <help><![CDATA[Compute peptide and protein abundances 529 <help><![CDATA[Compute peptide and protein abundances
158 530
159 531
160 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ProteinQuantifier.html]]></help> 532 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ProteinQuantifier.html]]></help>
161 <expand macro="references"/> 533 <expand macro="references"/>
162 </tool> 534 </tool>