comparison macros_autotest.xml @ 11:36c84cb92e46 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:54:16 -0400
parents
children 55f3c74f6ce6
comparison
equal deleted inserted replaced
10:9cc4b157e2fb 11:36c84cb92e46
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <xml name="autotest_AccurateMassSearch">
4 <test expect_num_outputs="2">
5 <conditional name="adv_opts_cond">
6 <param name="adv_opts_selector" value="advanced"/>
7 <param name="force" value="false"/>
8 <param name="test" value="true"/>
9 </conditional>
10 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
11 <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
12 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
13 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
14 <section name="db">
15 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
16 <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
17 </section>
18 <section name="algorithm">
19 <param name="mass_error_value" value="5.0"/>
20 <param name="mass_error_unit" value="ppm"/>
21 <param name="ionization_mode" value="positive"/>
22 <param name="isotopic_similarity" value="false"/>
23 <param name="use_feature_adducts" value="false"/>
24 <param name="keep_unidentified_masses" value="false"/>
25 <section name="mzTab">
26 <param name="exportIsotopeIntensities" value="false"/>
27 </section>
28 </section>
29 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
30 <output name="ctd_out" ftype="xml">
31 <assert_contents>
32 <is_valid_xml/>
33 </assert_contents>
34 </output>
35 </test>
36 <test expect_num_outputs="3">
37 <conditional name="adv_opts_cond">
38 <param name="adv_opts_selector" value="advanced"/>
39 <param name="force" value="false"/>
40 <param name="test" value="true"/>
41 </conditional>
42 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
43 <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
44 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
45 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
46 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
47 <section name="db">
48 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
49 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
50 </section>
51 <section name="algorithm">
52 <param name="mass_error_value" value="5.0"/>
53 <param name="mass_error_unit" value="ppm"/>
54 <param name="ionization_mode" value="positive"/>
55 <param name="isotopic_similarity" value="false"/>
56 <param name="use_feature_adducts" value="false"/>
57 <param name="keep_unidentified_masses" value="false"/>
58 <section name="mzTab">
59 <param name="exportIsotopeIntensities" value="true"/>
60 </section>
61 </section>
62 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
63 <output name="ctd_out" ftype="xml">
64 <assert_contents>
65 <is_valid_xml/>
66 </assert_contents>
67 </output>
68 </test>
69 <test expect_num_outputs="3">
70 <conditional name="adv_opts_cond">
71 <param name="adv_opts_selector" value="advanced"/>
72 <param name="force" value="false"/>
73 <param name="test" value="true"/>
74 </conditional>
75 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
76 <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
77 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
78 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
79 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
80 <section name="db">
81 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
82 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
83 </section>
84 <section name="algorithm">
85 <param name="mass_error_value" value="5.0"/>
86 <param name="mass_error_unit" value="ppm"/>
87 <param name="ionization_mode" value="positive"/>
88 <param name="isotopic_similarity" value="false"/>
89 <param name="use_feature_adducts" value="false"/>
90 <param name="keep_unidentified_masses" value="false"/>
91 <section name="mzTab">
92 <param name="exportIsotopeIntensities" value="false"/>
93 </section>
94 </section>
95 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
96 <output name="ctd_out" ftype="xml">
97 <assert_contents>
98 <is_valid_xml/>
99 </assert_contents>
100 </output>
101 </test>
102 </xml>
103 <xml name="autotest_AssayGeneratorMetabo">
104 <test expect_num_outputs="2">
105 <conditional name="adv_opts_cond">
106 <param name="adv_opts_selector" value="advanced"/>
107 <param name="precursor_recalibration_window" value="0.1"/>
108 <param name="precursor_recalibration_window_unit" value="Da"/>
109 <param name="min_fragment_mz" value="0.0"/>
110 <param name="max_fragment_mz" value="2000.0"/>
111 <param name="force" value="false"/>
112 <param name="test" value="true"/>
113 </conditional>
114 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
115 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
116 <param name="out_type" value="tsv"/>
117 <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
118 <param name="fragment_annotation" value="none"/>
119 <param name="method" value="highest_intensity"/>
120 <param name="use_exact_mass" value="false"/>
121 <param name="exclude_ms2_precursor" value="false"/>
122 <param name="precursor_mz_distance" value="0.0001"/>
123 <param name="precursor_rt_tolerance" value="5.0"/>
124 <param name="use_known_unknowns" value="false"/>
125 <param name="min_transitions" value="1"/>
126 <param name="max_transitions" value="3"/>
127 <param name="cosine_similarity_threshold" value="0.98"/>
128 <param name="transition_threshold" value="5.0"/>
129 <param name="out_workspace_directory" value=""/>
130 <section name="deisotoping">
131 <param name="use_deisotoper" value="false"/>
132 <param name="fragment_tolerance" value="1.0"/>
133 <param name="fragment_unit" value="ppm"/>
134 <param name="min_charge" value="1"/>
135 <param name="max_charge" value="1"/>
136 <param name="min_isopeaks" value="2"/>
137 <param name="max_isopeaks" value="3"/>
138 <param name="keep_only_deisotoped" value="false"/>
139 <param name="annotate_charge" value="false"/>
140 </section>
141 <section name="preprocessing">
142 <param name="filter_by_num_masstraces" value="1"/>
143 <param name="precursor_mz_tolerance" value="0.005"/>
144 <param name="precursor_mz_tolerance_unit" value="Da"/>
145 <param name="precursor_rt_tolerance" value="5"/>
146 <param name="isotope_pattern_iterations" value="3"/>
147 <param name="feature_only" value="false"/>
148 <param name="no_masstrace_info_isotope_pattern" value="false"/>
149 </section>
150 <section name="sirius">
151 <param name="profile" value="qtof"/>
152 <param name="candidates" value="5"/>
153 <param name="database" value="all"/>
154 <param name="noise" value="0"/>
155 <param name="ppm_max" value="10"/>
156 <param name="isotope" value="both"/>
157 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
158 <param name="compound_timeout" value="10"/>
159 <param name="tree_timeout" value="0"/>
160 <param name="top_n_hits" value="10"/>
161 <param name="cores" value="1"/>
162 <param name="auto_charge" value="false"/>
163 <param name="ion_tree" value="false"/>
164 <param name="no_recalibration" value="false"/>
165 <param name="most_intense_ms2" value="false"/>
166 </section>
167 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
168 <output name="ctd_out" ftype="xml">
169 <assert_contents>
170 <is_valid_xml/>
171 </assert_contents>
172 </output>
173 </test>
174 <test expect_num_outputs="2">
175 <conditional name="adv_opts_cond">
176 <param name="adv_opts_selector" value="advanced"/>
177 <param name="precursor_recalibration_window" value="0.1"/>
178 <param name="precursor_recalibration_window_unit" value="Da"/>
179 <param name="min_fragment_mz" value="0.0"/>
180 <param name="max_fragment_mz" value="2000.0"/>
181 <param name="force" value="false"/>
182 <param name="test" value="true"/>
183 </conditional>
184 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
185 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
186 <param name="out_type" value="tsv"/>
187 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
188 <param name="fragment_annotation" value="none"/>
189 <param name="method" value="highest_intensity"/>
190 <param name="use_exact_mass" value="false"/>
191 <param name="exclude_ms2_precursor" value="false"/>
192 <param name="precursor_mz_distance" value="0.0001"/>
193 <param name="precursor_rt_tolerance" value="5.0"/>
194 <param name="use_known_unknowns" value="false"/>
195 <param name="min_transitions" value="1"/>
196 <param name="max_transitions" value="3"/>
197 <param name="cosine_similarity_threshold" value="0.98"/>
198 <param name="transition_threshold" value="5.0"/>
199 <param name="out_workspace_directory" value=""/>
200 <section name="deisotoping">
201 <param name="use_deisotoper" value="false"/>
202 <param name="fragment_tolerance" value="1.0"/>
203 <param name="fragment_unit" value="ppm"/>
204 <param name="min_charge" value="1"/>
205 <param name="max_charge" value="1"/>
206 <param name="min_isopeaks" value="2"/>
207 <param name="max_isopeaks" value="3"/>
208 <param name="keep_only_deisotoped" value="false"/>
209 <param name="annotate_charge" value="false"/>
210 </section>
211 <section name="preprocessing">
212 <param name="filter_by_num_masstraces" value="1"/>
213 <param name="precursor_mz_tolerance" value="0.005"/>
214 <param name="precursor_mz_tolerance_unit" value="Da"/>
215 <param name="precursor_rt_tolerance" value="5"/>
216 <param name="isotope_pattern_iterations" value="3"/>
217 <param name="feature_only" value="false"/>
218 <param name="no_masstrace_info_isotope_pattern" value="false"/>
219 </section>
220 <section name="sirius">
221 <param name="profile" value="qtof"/>
222 <param name="candidates" value="5"/>
223 <param name="database" value="all"/>
224 <param name="noise" value="0"/>
225 <param name="ppm_max" value="10"/>
226 <param name="isotope" value="both"/>
227 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
228 <param name="compound_timeout" value="10"/>
229 <param name="tree_timeout" value="0"/>
230 <param name="top_n_hits" value="10"/>
231 <param name="cores" value="1"/>
232 <param name="auto_charge" value="false"/>
233 <param name="ion_tree" value="false"/>
234 <param name="no_recalibration" value="false"/>
235 <param name="most_intense_ms2" value="false"/>
236 </section>
237 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
238 <output name="ctd_out" ftype="xml">
239 <assert_contents>
240 <is_valid_xml/>
241 </assert_contents>
242 </output>
243 </test>
244 <test expect_num_outputs="2">
245 <conditional name="adv_opts_cond">
246 <param name="adv_opts_selector" value="advanced"/>
247 <param name="precursor_recalibration_window" value="0.1"/>
248 <param name="precursor_recalibration_window_unit" value="Da"/>
249 <param name="min_fragment_mz" value="0.0"/>
250 <param name="max_fragment_mz" value="2000.0"/>
251 <param name="force" value="false"/>
252 <param name="test" value="true"/>
253 </conditional>
254 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
255 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
256 <param name="out_type" value="tsv"/>
257 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
258 <param name="fragment_annotation" value="none"/>
259 <param name="method" value="consensus_spectrum"/>
260 <param name="use_exact_mass" value="false"/>
261 <param name="exclude_ms2_precursor" value="false"/>
262 <param name="precursor_mz_distance" value="0.0001"/>
263 <param name="precursor_rt_tolerance" value="5.0"/>
264 <param name="use_known_unknowns" value="false"/>
265 <param name="min_transitions" value="1"/>
266 <param name="max_transitions" value="3"/>
267 <param name="cosine_similarity_threshold" value="0.98"/>
268 <param name="transition_threshold" value="5.0"/>
269 <param name="out_workspace_directory" value=""/>
270 <section name="deisotoping">
271 <param name="use_deisotoper" value="false"/>
272 <param name="fragment_tolerance" value="1.0"/>
273 <param name="fragment_unit" value="ppm"/>
274 <param name="min_charge" value="1"/>
275 <param name="max_charge" value="1"/>
276 <param name="min_isopeaks" value="2"/>
277 <param name="max_isopeaks" value="3"/>
278 <param name="keep_only_deisotoped" value="false"/>
279 <param name="annotate_charge" value="false"/>
280 </section>
281 <section name="preprocessing">
282 <param name="filter_by_num_masstraces" value="1"/>
283 <param name="precursor_mz_tolerance" value="0.005"/>
284 <param name="precursor_mz_tolerance_unit" value="Da"/>
285 <param name="precursor_rt_tolerance" value="5"/>
286 <param name="isotope_pattern_iterations" value="3"/>
287 <param name="feature_only" value="false"/>
288 <param name="no_masstrace_info_isotope_pattern" value="false"/>
289 </section>
290 <section name="sirius">
291 <param name="profile" value="qtof"/>
292 <param name="candidates" value="5"/>
293 <param name="database" value="all"/>
294 <param name="noise" value="0"/>
295 <param name="ppm_max" value="10"/>
296 <param name="isotope" value="both"/>
297 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
298 <param name="compound_timeout" value="10"/>
299 <param name="tree_timeout" value="0"/>
300 <param name="top_n_hits" value="10"/>
301 <param name="cores" value="1"/>
302 <param name="auto_charge" value="false"/>
303 <param name="ion_tree" value="false"/>
304 <param name="no_recalibration" value="false"/>
305 <param name="most_intense_ms2" value="false"/>
306 </section>
307 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
308 <output name="ctd_out" ftype="xml">
309 <assert_contents>
310 <is_valid_xml/>
311 </assert_contents>
312 </output>
313 </test>
314 <test expect_num_outputs="2">
315 <conditional name="adv_opts_cond">
316 <param name="adv_opts_selector" value="advanced"/>
317 <param name="precursor_recalibration_window" value="0.1"/>
318 <param name="precursor_recalibration_window_unit" value="Da"/>
319 <param name="min_fragment_mz" value="0.0"/>
320 <param name="max_fragment_mz" value="2000.0"/>
321 <param name="force" value="false"/>
322 <param name="test" value="true"/>
323 </conditional>
324 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
325 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
326 <param name="out_type" value="tsv"/>
327 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
328 <param name="fragment_annotation" value="none"/>
329 <param name="method" value="consensus_spectrum"/>
330 <param name="use_exact_mass" value="false"/>
331 <param name="exclude_ms2_precursor" value="false"/>
332 <param name="precursor_mz_distance" value="0.0001"/>
333 <param name="precursor_rt_tolerance" value="5.0"/>
334 <param name="use_known_unknowns" value="false"/>
335 <param name="min_transitions" value="1"/>
336 <param name="max_transitions" value="3"/>
337 <param name="cosine_similarity_threshold" value="0.98"/>
338 <param name="transition_threshold" value="5.0"/>
339 <param name="out_workspace_directory" value=""/>
340 <section name="deisotoping">
341 <param name="use_deisotoper" value="false"/>
342 <param name="fragment_tolerance" value="1.0"/>
343 <param name="fragment_unit" value="ppm"/>
344 <param name="min_charge" value="1"/>
345 <param name="max_charge" value="1"/>
346 <param name="min_isopeaks" value="2"/>
347 <param name="max_isopeaks" value="3"/>
348 <param name="keep_only_deisotoped" value="false"/>
349 <param name="annotate_charge" value="false"/>
350 </section>
351 <section name="preprocessing">
352 <param name="filter_by_num_masstraces" value="1"/>
353 <param name="precursor_mz_tolerance" value="0.005"/>
354 <param name="precursor_mz_tolerance_unit" value="Da"/>
355 <param name="precursor_rt_tolerance" value="5"/>
356 <param name="isotope_pattern_iterations" value="3"/>
357 <param name="feature_only" value="false"/>
358 <param name="no_masstrace_info_isotope_pattern" value="false"/>
359 </section>
360 <section name="sirius">
361 <param name="profile" value="qtof"/>
362 <param name="candidates" value="5"/>
363 <param name="database" value="all"/>
364 <param name="noise" value="0"/>
365 <param name="ppm_max" value="10"/>
366 <param name="isotope" value="both"/>
367 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
368 <param name="compound_timeout" value="10"/>
369 <param name="tree_timeout" value="0"/>
370 <param name="top_n_hits" value="10"/>
371 <param name="cores" value="1"/>
372 <param name="auto_charge" value="false"/>
373 <param name="ion_tree" value="false"/>
374 <param name="no_recalibration" value="false"/>
375 <param name="most_intense_ms2" value="false"/>
376 </section>
377 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
378 <output name="ctd_out" ftype="xml">
379 <assert_contents>
380 <is_valid_xml/>
381 </assert_contents>
382 </output>
383 </test>
384 <test expect_num_outputs="2">
385 <conditional name="adv_opts_cond">
386 <param name="adv_opts_selector" value="advanced"/>
387 <param name="precursor_recalibration_window" value="0.1"/>
388 <param name="precursor_recalibration_window_unit" value="Da"/>
389 <param name="min_fragment_mz" value="0.0"/>
390 <param name="max_fragment_mz" value="2000.0"/>
391 <param name="force" value="false"/>
392 <param name="test" value="true"/>
393 </conditional>
394 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
395 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
396 <param name="out_type" value="tsv"/>
397 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
398 <param name="fragment_annotation" value="none"/>
399 <param name="method" value="consensus_spectrum"/>
400 <param name="use_exact_mass" value="false"/>
401 <param name="exclude_ms2_precursor" value="false"/>
402 <param name="precursor_mz_distance" value="0.0001"/>
403 <param name="precursor_rt_tolerance" value="5.0"/>
404 <param name="use_known_unknowns" value="true"/>
405 <param name="min_transitions" value="1"/>
406 <param name="max_transitions" value="3"/>
407 <param name="cosine_similarity_threshold" value="0.98"/>
408 <param name="transition_threshold" value="5.0"/>
409 <param name="out_workspace_directory" value=""/>
410 <section name="deisotoping">
411 <param name="use_deisotoper" value="false"/>
412 <param name="fragment_tolerance" value="1.0"/>
413 <param name="fragment_unit" value="ppm"/>
414 <param name="min_charge" value="1"/>
415 <param name="max_charge" value="1"/>
416 <param name="min_isopeaks" value="2"/>
417 <param name="max_isopeaks" value="3"/>
418 <param name="keep_only_deisotoped" value="false"/>
419 <param name="annotate_charge" value="false"/>
420 </section>
421 <section name="preprocessing">
422 <param name="filter_by_num_masstraces" value="1"/>
423 <param name="precursor_mz_tolerance" value="0.005"/>
424 <param name="precursor_mz_tolerance_unit" value="Da"/>
425 <param name="precursor_rt_tolerance" value="5"/>
426 <param name="isotope_pattern_iterations" value="3"/>
427 <param name="feature_only" value="false"/>
428 <param name="no_masstrace_info_isotope_pattern" value="false"/>
429 </section>
430 <section name="sirius">
431 <param name="profile" value="qtof"/>
432 <param name="candidates" value="5"/>
433 <param name="database" value="all"/>
434 <param name="noise" value="0"/>
435 <param name="ppm_max" value="10"/>
436 <param name="isotope" value="both"/>
437 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
438 <param name="compound_timeout" value="10"/>
439 <param name="tree_timeout" value="0"/>
440 <param name="top_n_hits" value="10"/>
441 <param name="cores" value="1"/>
442 <param name="auto_charge" value="false"/>
443 <param name="ion_tree" value="false"/>
444 <param name="no_recalibration" value="false"/>
445 <param name="most_intense_ms2" value="false"/>
446 </section>
447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
448 <output name="ctd_out" ftype="xml">
449 <assert_contents>
450 <is_valid_xml/>
451 </assert_contents>
452 </output>
453 </test>
454 <test expect_num_outputs="2">
455 <conditional name="adv_opts_cond">
456 <param name="adv_opts_selector" value="advanced"/>
457 <param name="precursor_recalibration_window" value="0.1"/>
458 <param name="precursor_recalibration_window_unit" value="Da"/>
459 <param name="min_fragment_mz" value="0.0"/>
460 <param name="max_fragment_mz" value="2000.0"/>
461 <param name="force" value="false"/>
462 <param name="test" value="true"/>
463 </conditional>
464 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
465 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
466 <param name="out_type" value="tsv"/>
467 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
468 <param name="fragment_annotation" value="sirius"/>
469 <param name="method" value="highest_intensity"/>
470 <param name="use_exact_mass" value="true"/>
471 <param name="exclude_ms2_precursor" value="false"/>
472 <param name="precursor_mz_distance" value="0.0001"/>
473 <param name="precursor_rt_tolerance" value="5.0"/>
474 <param name="use_known_unknowns" value="false"/>
475 <param name="min_transitions" value="2"/>
476 <param name="max_transitions" value="3"/>
477 <param name="cosine_similarity_threshold" value="0.98"/>
478 <param name="transition_threshold" value="3.0"/>
479 <param name="out_workspace_directory" value=""/>
480 <section name="deisotoping">
481 <param name="use_deisotoper" value="false"/>
482 <param name="fragment_tolerance" value="1.0"/>
483 <param name="fragment_unit" value="ppm"/>
484 <param name="min_charge" value="1"/>
485 <param name="max_charge" value="1"/>
486 <param name="min_isopeaks" value="2"/>
487 <param name="max_isopeaks" value="3"/>
488 <param name="keep_only_deisotoped" value="false"/>
489 <param name="annotate_charge" value="false"/>
490 </section>
491 <section name="preprocessing">
492 <param name="filter_by_num_masstraces" value="1"/>
493 <param name="precursor_mz_tolerance" value="10.0"/>
494 <param name="precursor_mz_tolerance_unit" value="ppm"/>
495 <param name="precursor_rt_tolerance" value="5"/>
496 <param name="isotope_pattern_iterations" value="3"/>
497 <param name="feature_only" value="true"/>
498 <param name="no_masstrace_info_isotope_pattern" value="false"/>
499 </section>
500 <section name="sirius">
501 <param name="profile" value="qtof"/>
502 <param name="candidates" value="5"/>
503 <param name="database" value="all"/>
504 <param name="noise" value="0"/>
505 <param name="ppm_max" value="10"/>
506 <param name="isotope" value="both"/>
507 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
508 <param name="compound_timeout" value="100"/>
509 <param name="tree_timeout" value="0"/>
510 <param name="top_n_hits" value="10"/>
511 <param name="cores" value="1"/>
512 <param name="auto_charge" value="false"/>
513 <param name="ion_tree" value="false"/>
514 <param name="no_recalibration" value="false"/>
515 <param name="most_intense_ms2" value="false"/>
516 </section>
517 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
518 <output name="ctd_out" ftype="xml">
519 <assert_contents>
520 <is_valid_xml/>
521 </assert_contents>
522 </output>
523 </test>
524 <test expect_num_outputs="2">
525 <conditional name="adv_opts_cond">
526 <param name="adv_opts_selector" value="advanced"/>
527 <param name="precursor_recalibration_window" value="0.1"/>
528 <param name="precursor_recalibration_window_unit" value="Da"/>
529 <param name="min_fragment_mz" value="0.0"/>
530 <param name="max_fragment_mz" value="2000.0"/>
531 <param name="force" value="false"/>
532 <param name="test" value="true"/>
533 </conditional>
534 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
535 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
536 <param name="out_type" value="tsv"/>
537 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
538 <param name="fragment_annotation" value="sirius"/>
539 <param name="method" value="highest_intensity"/>
540 <param name="use_exact_mass" value="true"/>
541 <param name="exclude_ms2_precursor" value="false"/>
542 <param name="precursor_mz_distance" value="0.0001"/>
543 <param name="precursor_rt_tolerance" value="5.0"/>
544 <param name="use_known_unknowns" value="true"/>
545 <param name="min_transitions" value="2"/>
546 <param name="max_transitions" value="3"/>
547 <param name="cosine_similarity_threshold" value="0.98"/>
548 <param name="transition_threshold" value="3.0"/>
549 <param name="out_workspace_directory" value=""/>
550 <section name="deisotoping">
551 <param name="use_deisotoper" value="false"/>
552 <param name="fragment_tolerance" value="1.0"/>
553 <param name="fragment_unit" value="ppm"/>
554 <param name="min_charge" value="1"/>
555 <param name="max_charge" value="1"/>
556 <param name="min_isopeaks" value="2"/>
557 <param name="max_isopeaks" value="3"/>
558 <param name="keep_only_deisotoped" value="false"/>
559 <param name="annotate_charge" value="false"/>
560 </section>
561 <section name="preprocessing">
562 <param name="filter_by_num_masstraces" value="1"/>
563 <param name="precursor_mz_tolerance" value="10.0"/>
564 <param name="precursor_mz_tolerance_unit" value="ppm"/>
565 <param name="precursor_rt_tolerance" value="5"/>
566 <param name="isotope_pattern_iterations" value="3"/>
567 <param name="feature_only" value="true"/>
568 <param name="no_masstrace_info_isotope_pattern" value="false"/>
569 </section>
570 <section name="sirius">
571 <param name="profile" value="qtof"/>
572 <param name="candidates" value="5"/>
573 <param name="database" value="all"/>
574 <param name="noise" value="0"/>
575 <param name="ppm_max" value="10"/>
576 <param name="isotope" value="both"/>
577 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
578 <param name="compound_timeout" value="100"/>
579 <param name="tree_timeout" value="0"/>
580 <param name="top_n_hits" value="10"/>
581 <param name="cores" value="1"/>
582 <param name="auto_charge" value="false"/>
583 <param name="ion_tree" value="false"/>
584 <param name="no_recalibration" value="false"/>
585 <param name="most_intense_ms2" value="false"/>
586 </section>
587 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
588 <output name="ctd_out" ftype="xml">
589 <assert_contents>
590 <is_valid_xml/>
591 </assert_contents>
592 </output>
593 </test>
594 <test expect_num_outputs="2">
595 <conditional name="adv_opts_cond">
596 <param name="adv_opts_selector" value="advanced"/>
597 <param name="precursor_recalibration_window" value="0.1"/>
598 <param name="precursor_recalibration_window_unit" value="Da"/>
599 <param name="min_fragment_mz" value="0.0"/>
600 <param name="max_fragment_mz" value="2000.0"/>
601 <param name="force" value="false"/>
602 <param name="test" value="true"/>
603 </conditional>
604 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
605 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
606 <param name="out_type" value="tsv"/>
607 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
608 <param name="fragment_annotation" value="sirius"/>
609 <param name="method" value="highest_intensity"/>
610 <param name="use_exact_mass" value="true"/>
611 <param name="exclude_ms2_precursor" value="false"/>
612 <param name="precursor_mz_distance" value="0.0001"/>
613 <param name="precursor_rt_tolerance" value="5.0"/>
614 <param name="use_known_unknowns" value="false"/>
615 <param name="min_transitions" value="2"/>
616 <param name="max_transitions" value="3"/>
617 <param name="cosine_similarity_threshold" value="0.98"/>
618 <param name="transition_threshold" value="3.0"/>
619 <param name="out_workspace_directory" value=""/>
620 <section name="deisotoping">
621 <param name="use_deisotoper" value="false"/>
622 <param name="fragment_tolerance" value="1.0"/>
623 <param name="fragment_unit" value="ppm"/>
624 <param name="min_charge" value="1"/>
625 <param name="max_charge" value="1"/>
626 <param name="min_isopeaks" value="2"/>
627 <param name="max_isopeaks" value="3"/>
628 <param name="keep_only_deisotoped" value="false"/>
629 <param name="annotate_charge" value="false"/>
630 </section>
631 <section name="preprocessing">
632 <param name="filter_by_num_masstraces" value="1"/>
633 <param name="precursor_mz_tolerance" value="10.0"/>
634 <param name="precursor_mz_tolerance_unit" value="ppm"/>
635 <param name="precursor_rt_tolerance" value="5"/>
636 <param name="isotope_pattern_iterations" value="3"/>
637 <param name="feature_only" value="true"/>
638 <param name="no_masstrace_info_isotope_pattern" value="false"/>
639 </section>
640 <section name="sirius">
641 <param name="profile" value="qtof"/>
642 <param name="candidates" value="5"/>
643 <param name="database" value="all"/>
644 <param name="noise" value="0"/>
645 <param name="ppm_max" value="10"/>
646 <param name="isotope" value="both"/>
647 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
648 <param name="compound_timeout" value="100"/>
649 <param name="tree_timeout" value="0"/>
650 <param name="top_n_hits" value="10"/>
651 <param name="cores" value="1"/>
652 <param name="auto_charge" value="false"/>
653 <param name="ion_tree" value="false"/>
654 <param name="no_recalibration" value="false"/>
655 <param name="most_intense_ms2" value="false"/>
656 </section>
657 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
658 <output name="ctd_out" ftype="xml">
659 <assert_contents>
660 <is_valid_xml/>
661 </assert_contents>
662 </output>
663 </test>
664 <test expect_num_outputs="2">
665 <conditional name="adv_opts_cond">
666 <param name="adv_opts_selector" value="advanced"/>
667 <param name="precursor_recalibration_window" value="0.1"/>
668 <param name="precursor_recalibration_window_unit" value="Da"/>
669 <param name="min_fragment_mz" value="100.0"/>
670 <param name="max_fragment_mz" value="900.0"/>
671 <param name="force" value="false"/>
672 <param name="test" value="true"/>
673 </conditional>
674 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
675 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
676 <param name="out_type" value="tsv"/>
677 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
678 <param name="fragment_annotation" value="sirius"/>
679 <param name="method" value="highest_intensity"/>
680 <param name="use_exact_mass" value="true"/>
681 <param name="exclude_ms2_precursor" value="false"/>
682 <param name="precursor_mz_distance" value="0.0001"/>
683 <param name="precursor_rt_tolerance" value="5.0"/>
684 <param name="use_known_unknowns" value="false"/>
685 <param name="min_transitions" value="2"/>
686 <param name="max_transitions" value="3"/>
687 <param name="cosine_similarity_threshold" value="0.98"/>
688 <param name="transition_threshold" value="3.0"/>
689 <param name="out_workspace_directory" value=""/>
690 <section name="deisotoping">
691 <param name="use_deisotoper" value="false"/>
692 <param name="fragment_tolerance" value="1.0"/>
693 <param name="fragment_unit" value="ppm"/>
694 <param name="min_charge" value="1"/>
695 <param name="max_charge" value="1"/>
696 <param name="min_isopeaks" value="2"/>
697 <param name="max_isopeaks" value="3"/>
698 <param name="keep_only_deisotoped" value="false"/>
699 <param name="annotate_charge" value="false"/>
700 </section>
701 <section name="preprocessing">
702 <param name="filter_by_num_masstraces" value="1"/>
703 <param name="precursor_mz_tolerance" value="10.0"/>
704 <param name="precursor_mz_tolerance_unit" value="ppm"/>
705 <param name="precursor_rt_tolerance" value="5"/>
706 <param name="isotope_pattern_iterations" value="3"/>
707 <param name="feature_only" value="true"/>
708 <param name="no_masstrace_info_isotope_pattern" value="false"/>
709 </section>
710 <section name="sirius">
711 <param name="profile" value="qtof"/>
712 <param name="candidates" value="5"/>
713 <param name="database" value="all"/>
714 <param name="noise" value="0"/>
715 <param name="ppm_max" value="10"/>
716 <param name="isotope" value="both"/>
717 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
718 <param name="compound_timeout" value="100"/>
719 <param name="tree_timeout" value="0"/>
720 <param name="top_n_hits" value="10"/>
721 <param name="cores" value="1"/>
722 <param name="auto_charge" value="false"/>
723 <param name="ion_tree" value="false"/>
724 <param name="no_recalibration" value="false"/>
725 <param name="most_intense_ms2" value="false"/>
726 </section>
727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
728 <output name="ctd_out" ftype="xml">
729 <assert_contents>
730 <is_valid_xml/>
731 </assert_contents>
732 </output>
733 </test>
734 </xml>
735 <xml name="autotest_BaselineFilter">
736 <test expect_num_outputs="2">
737 <conditional name="adv_opts_cond">
738 <param name="adv_opts_selector" value="advanced"/>
739 <param name="force" value="false"/>
740 <param name="test" value="true"/>
741 </conditional>
742 <param name="in" value="BaselineFilter_input.mzML"/>
743 <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
744 <param name="struc_elem_length" value="1.5"/>
745 <param name="struc_elem_unit" value="Thomson"/>
746 <param name="method" value="tophat"/>
747 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
748 <output name="ctd_out" ftype="xml">
749 <assert_contents>
750 <is_valid_xml/>
751 </assert_contents>
752 </output>
753 </test>
754 </xml>
755 <xml name="autotest_ClusterMassTracesByPrecursor">
756 </xml>
757 <xml name="autotest_ClusterMassTraces">
758 </xml>
759 <xml name="autotest_CometAdapter">
760 <test expect_num_outputs="3">
761 <conditional name="adv_opts_cond">
762 <param name="adv_opts_selector" value="advanced"/>
763 <param name="fragment_bin_tolerance" value="1.0005"/>
764 <param name="fragment_bin_offset" value="0.25"/>
765 <param name="instrument" value="high_res"/>
766 <param name="use_A_ions" value="false"/>
767 <param name="use_B_ions" value="true"/>
768 <param name="use_C_ions" value="false"/>
769 <param name="use_X_ions" value="false"/>
770 <param name="use_Y_ions" value="true"/>
771 <param name="use_Z_ions" value="false"/>
772 <param name="use_NL_ions" value="false"/>
773 <param name="digest_mass_range" value="600:5000"/>
774 <param name="max_precursor_charge" value="5"/>
775 <param name="spectrum_batch_size" value="1000"/>
776 <param name="mass_offsets" value="0.0"/>
777 <param name="minimum_peaks" value="10"/>
778 <param name="minimum_intensity" value="0.0"/>
779 <param name="remove_precursor_peak" value="no"/>
780 <param name="remove_precursor_tolerance" value="1.5"/>
781 <param name="clear_mz_range" value="0:0"/>
782 <param name="max_variable_mods_in_peptide" value="5"/>
783 <param name="require_variable_mod" value="false"/>
784 <param name="force" value="false"/>
785 <param name="test" value="true"/>
786 </conditional>
787 <param name="in" value="spectra_comet.mzML"/>
788 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
789 <param name="database" value="proteins.fasta"/>
790 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
791 <param name="precursor_mass_tolerance" value="3.0"/>
792 <param name="precursor_error_units" value="ppm"/>
793 <param name="isotope_error" value="off"/>
794 <param name="enzyme" value="Trypsin"/>
795 <param name="num_enzyme_termini" value="fully"/>
796 <param name="allowed_missed_cleavages" value="1"/>
797 <param name="num_hits" value="5"/>
798 <param name="precursor_charge" value="0:0"/>
799 <param name="override_charge" value="keep any known"/>
800 <param name="ms_level" value="2"/>
801 <param name="activation_method" value="ALL"/>
802 <param name="max_fragment_charge" value="3"/>
803 <param name="clip_nterm_methionine" value="false"/>
804 <param name="fixed_modifications" value=""/>
805 <param name="variable_modifications" value=""/>
806 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
807 <output name="ctd_out" ftype="xml">
808 <assert_contents>
809 <is_valid_xml/>
810 </assert_contents>
811 </output>
812 </test>
813 <test expect_num_outputs="3">
814 <conditional name="adv_opts_cond">
815 <param name="adv_opts_selector" value="advanced"/>
816 <param name="fragment_bin_tolerance" value="1.0005"/>
817 <param name="fragment_bin_offset" value="0.25"/>
818 <param name="instrument" value="high_res"/>
819 <param name="use_A_ions" value="false"/>
820 <param name="use_B_ions" value="true"/>
821 <param name="use_C_ions" value="false"/>
822 <param name="use_X_ions" value="false"/>
823 <param name="use_Y_ions" value="true"/>
824 <param name="use_Z_ions" value="false"/>
825 <param name="use_NL_ions" value="false"/>
826 <param name="digest_mass_range" value="600:5000"/>
827 <param name="max_precursor_charge" value="5"/>
828 <param name="spectrum_batch_size" value="1000"/>
829 <param name="mass_offsets" value="0.0"/>
830 <param name="minimum_peaks" value="10"/>
831 <param name="minimum_intensity" value="0.0"/>
832 <param name="remove_precursor_peak" value="no"/>
833 <param name="remove_precursor_tolerance" value="1.5"/>
834 <param name="clear_mz_range" value="0:0"/>
835 <param name="max_variable_mods_in_peptide" value="5"/>
836 <param name="require_variable_mod" value="false"/>
837 <param name="force" value="false"/>
838 <param name="test" value="true"/>
839 </conditional>
840 <param name="in" value="CometAdapter_2_prepared.mzML"/>
841 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
842 <param name="database" value="CometAdapter_2_in.fasta"/>
843 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
844 <param name="precursor_mass_tolerance" value="3.0"/>
845 <param name="precursor_error_units" value="Da"/>
846 <param name="isotope_error" value="off"/>
847 <param name="enzyme" value="Trypsin"/>
848 <param name="num_enzyme_termini" value="fully"/>
849 <param name="allowed_missed_cleavages" value="1"/>
850 <param name="num_hits" value="5"/>
851 <param name="precursor_charge" value="0:0"/>
852 <param name="override_charge" value="keep any known"/>
853 <param name="ms_level" value="2"/>
854 <param name="activation_method" value="ALL"/>
855 <param name="max_fragment_charge" value="3"/>
856 <param name="clip_nterm_methionine" value="false"/>
857 <param name="fixed_modifications" value=""/>
858 <param name="variable_modifications" value=""/>
859 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
860 <output name="ctd_out" ftype="xml">
861 <assert_contents>
862 <is_valid_xml/>
863 </assert_contents>
864 </output>
865 </test>
866 <test expect_num_outputs="3">
867 <conditional name="adv_opts_cond">
868 <param name="adv_opts_selector" value="advanced"/>
869 <param name="fragment_bin_tolerance" value="0.02"/>
870 <param name="fragment_bin_offset" value="0.0"/>
871 <param name="instrument" value="high_res"/>
872 <param name="use_A_ions" value="false"/>
873 <param name="use_B_ions" value="true"/>
874 <param name="use_C_ions" value="false"/>
875 <param name="use_X_ions" value="false"/>
876 <param name="use_Y_ions" value="true"/>
877 <param name="use_Z_ions" value="false"/>
878 <param name="use_NL_ions" value="false"/>
879 <param name="digest_mass_range" value="600:5000"/>
880 <param name="max_precursor_charge" value="5"/>
881 <param name="spectrum_batch_size" value="20000"/>
882 <param name="mass_offsets" value="0.0"/>
883 <param name="minimum_peaks" value="10"/>
884 <param name="minimum_intensity" value="0.0"/>
885 <param name="remove_precursor_peak" value="no"/>
886 <param name="remove_precursor_tolerance" value="1.5"/>
887 <param name="clear_mz_range" value="0:0"/>
888 <param name="max_variable_mods_in_peptide" value="3"/>
889 <param name="require_variable_mod" value="false"/>
890 <param name="force" value="false"/>
891 <param name="test" value="true"/>
892 </conditional>
893 <param name="in" value="CometAdapter_3.mzML"/>
894 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
895 <param name="database" value="CometAdapter_3.fasta"/>
896 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
897 <param name="precursor_mass_tolerance" value="5.0"/>
898 <param name="precursor_error_units" value="ppm"/>
899 <param name="isotope_error" value="off"/>
900 <param name="enzyme" value="Trypsin"/>
901 <param name="num_enzyme_termini" value="fully"/>
902 <param name="allowed_missed_cleavages" value="3"/>
903 <param name="num_hits" value="5"/>
904 <param name="precursor_charge" value="0:0"/>
905 <param name="override_charge" value="keep known search unknown"/>
906 <param name="ms_level" value="2"/>
907 <param name="activation_method" value="ALL"/>
908 <param name="max_fragment_charge" value="3"/>
909 <param name="clip_nterm_methionine" value="false"/>
910 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
911 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
912 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
913 <output name="ctd_out" ftype="xml">
914 <assert_contents>
915 <is_valid_xml/>
916 </assert_contents>
917 </output>
918 </test>
919 </xml>
920 <xml name="autotest_CompNovoCID">
921 <test expect_num_outputs="2">
922 <conditional name="adv_opts_cond">
923 <param name="adv_opts_selector" value="advanced"/>
924 <param name="force" value="false"/>
925 <param name="test" value="true"/>
926 </conditional>
927 <param name="in" value="CompNovoCID_1_input.mzML"/>
928 <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
929 <section name="algorithm">
930 <param name="max_number_aa_per_decomp" value="4"/>
931 <param name="tryptic_only" value="true"/>
932 <param name="precursor_mass_tolerance" value="0.3"/>
933 <param name="fragment_mass_tolerance" value="0.3"/>
934 <param name="max_number_pivot" value="9"/>
935 <param name="max_subscore_number" value="40"/>
936 <param name="decomp_weights_precision" value="0.01"/>
937 <param name="double_charged_iso_threshold" value="0.6"/>
938 <param name="max_mz" value="2000.0"/>
939 <param name="min_mz" value="200.0"/>
940 <param name="max_isotope_to_score" value="3"/>
941 <param name="max_decomp_weight" value="450.0"/>
942 <param name="max_isotope" value="3"/>
943 <param name="missed_cleavages" value="1"/>
944 <param name="number_of_hits" value="1"/>
945 <param name="estimate_precursor_mz" value="true"/>
946 <param name="number_of_prescoring_hits" value="250"/>
947 <param name="fixed_modifications" value=""/>
948 <param name="variable_modifications" value=""/>
949 <param name="residue_set" value="Natural19WithoutI"/>
950 </section>
951 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
952 <output name="ctd_out" ftype="xml">
953 <assert_contents>
954 <is_valid_xml/>
955 </assert_contents>
956 </output>
957 </test>
958 </xml>
959 <xml name="autotest_CompNovo">
960 <test expect_num_outputs="2">
961 <conditional name="adv_opts_cond">
962 <param name="adv_opts_selector" value="advanced"/>
963 <param name="force" value="false"/>
964 <param name="test" value="true"/>
965 </conditional>
966 <param name="in" value="CompNovo_1_input.mzML"/>
967 <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
968 <section name="algorithm">
969 <param name="max_number_aa_per_decomp" value="4"/>
970 <param name="tryptic_only" value="true"/>
971 <param name="precursor_mass_tolerance" value="0.3"/>
972 <param name="fragment_mass_tolerance" value="0.3"/>
973 <param name="max_number_pivot" value="9"/>
974 <param name="max_subscore_number" value="40"/>
975 <param name="decomp_weights_precision" value="0.01"/>
976 <param name="double_charged_iso_threshold" value="0.6"/>
977 <param name="max_mz" value="2000.0"/>
978 <param name="min_mz" value="200.0"/>
979 <param name="max_isotope_to_score" value="3"/>
980 <param name="max_decomp_weight" value="450.0"/>
981 <param name="max_isotope" value="3"/>
982 <param name="missed_cleavages" value="1"/>
983 <param name="number_of_hits" value="1"/>
984 <param name="estimate_precursor_mz" value="true"/>
985 <param name="number_of_prescoring_hits" value="250"/>
986 <param name="fixed_modifications" value=""/>
987 <param name="variable_modifications" value=""/>
988 <param name="residue_set" value="Natural19WithoutI"/>
989 </section>
990 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
991 <output name="ctd_out" ftype="xml">
992 <assert_contents>
993 <is_valid_xml/>
994 </assert_contents>
995 </output>
996 </test>
997 </xml>
998 <xml name="autotest_ConsensusID">
999 <test expect_num_outputs="2">
1000 <conditional name="adv_opts_cond">
1001 <param name="adv_opts_selector" value="advanced"/>
1002 <param name="force" value="false"/>
1003 <param name="test" value="true"/>
1004 </conditional>
1005 <param name="in" value="ConsensusID_1_input.idXML"/>
1006 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1007 <param name="rt_delta" value="0.1"/>
1008 <param name="mz_delta" value="0.1"/>
1009 <param name="algorithm" value="PEPMatrix"/>
1010 <section name="filter">
1011 <param name="considered_hits" value="0"/>
1012 <param name="min_support" value="0.0"/>
1013 <param name="count_empty" value="false"/>
1014 </section>
1015 <section name="PEPIons">
1016 <param name="mass_tolerance" value="0.5"/>
1017 <param name="min_shared" value="2"/>
1018 </section>
1019 <section name="PEPMatrix">
1020 <param name="matrix" value="PAM30MS"/>
1021 <param name="penalty" value="5"/>
1022 </section>
1023 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1024 <output name="ctd_out" ftype="xml">
1025 <assert_contents>
1026 <is_valid_xml/>
1027 </assert_contents>
1028 </output>
1029 </test>
1030 <test expect_num_outputs="2">
1031 <conditional name="adv_opts_cond">
1032 <param name="adv_opts_selector" value="advanced"/>
1033 <param name="force" value="false"/>
1034 <param name="test" value="true"/>
1035 </conditional>
1036 <param name="in" value="ConsensusID_2_input.featureXML"/>
1037 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1038 <param name="rt_delta" value="0.1"/>
1039 <param name="mz_delta" value="0.1"/>
1040 <param name="algorithm" value="average"/>
1041 <section name="filter">
1042 <param name="considered_hits" value="0"/>
1043 <param name="min_support" value="0.0"/>
1044 <param name="count_empty" value="false"/>
1045 </section>
1046 <section name="PEPIons">
1047 <param name="mass_tolerance" value="0.5"/>
1048 <param name="min_shared" value="2"/>
1049 </section>
1050 <section name="PEPMatrix">
1051 <param name="matrix" value="identity"/>
1052 <param name="penalty" value="5"/>
1053 </section>
1054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1055 <output name="ctd_out" ftype="xml">
1056 <assert_contents>
1057 <is_valid_xml/>
1058 </assert_contents>
1059 </output>
1060 </test>
1061 <test expect_num_outputs="2">
1062 <conditional name="adv_opts_cond">
1063 <param name="adv_opts_selector" value="advanced"/>
1064 <param name="force" value="false"/>
1065 <param name="test" value="true"/>
1066 </conditional>
1067 <param name="in" value="ConsensusID_3_input.consensusXML"/>
1068 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1069 <param name="rt_delta" value="0.1"/>
1070 <param name="mz_delta" value="0.1"/>
1071 <param name="algorithm" value="best"/>
1072 <section name="filter">
1073 <param name="considered_hits" value="0"/>
1074 <param name="min_support" value="0.0"/>
1075 <param name="count_empty" value="false"/>
1076 </section>
1077 <section name="PEPIons">
1078 <param name="mass_tolerance" value="0.5"/>
1079 <param name="min_shared" value="2"/>
1080 </section>
1081 <section name="PEPMatrix">
1082 <param name="matrix" value="identity"/>
1083 <param name="penalty" value="5"/>
1084 </section>
1085 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1086 <output name="ctd_out" ftype="xml">
1087 <assert_contents>
1088 <is_valid_xml/>
1089 </assert_contents>
1090 </output>
1091 </test>
1092 <test expect_num_outputs="2">
1093 <conditional name="adv_opts_cond">
1094 <param name="adv_opts_selector" value="advanced"/>
1095 <param name="force" value="false"/>
1096 <param name="test" value="true"/>
1097 </conditional>
1098 <param name="in" value="ConsensusID_1_input.idXML"/>
1099 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1100 <param name="rt_delta" value="0.1"/>
1101 <param name="mz_delta" value="0.1"/>
1102 <param name="algorithm" value="PEPMatrix"/>
1103 <section name="filter">
1104 <param name="considered_hits" value="6"/>
1105 <param name="min_support" value="0.0"/>
1106 <param name="count_empty" value="false"/>
1107 </section>
1108 <section name="PEPIons">
1109 <param name="mass_tolerance" value="0.5"/>
1110 <param name="min_shared" value="2"/>
1111 </section>
1112 <section name="PEPMatrix">
1113 <param name="matrix" value="identity"/>
1114 <param name="penalty" value="5"/>
1115 </section>
1116 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1117 <output name="ctd_out" ftype="xml">
1118 <assert_contents>
1119 <is_valid_xml/>
1120 </assert_contents>
1121 </output>
1122 </test>
1123 <test expect_num_outputs="2">
1124 <conditional name="adv_opts_cond">
1125 <param name="adv_opts_selector" value="advanced"/>
1126 <param name="force" value="false"/>
1127 <param name="test" value="true"/>
1128 </conditional>
1129 <param name="in" value="ConsensusID_1_input.idXML"/>
1130 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1131 <param name="rt_delta" value="0.1"/>
1132 <param name="mz_delta" value="0.1"/>
1133 <param name="algorithm" value="PEPIons"/>
1134 <section name="filter">
1135 <param name="considered_hits" value="0"/>
1136 <param name="min_support" value="0.0"/>
1137 <param name="count_empty" value="false"/>
1138 </section>
1139 <section name="PEPIons">
1140 <param name="mass_tolerance" value="0.5"/>
1141 <param name="min_shared" value="2"/>
1142 </section>
1143 <section name="PEPMatrix">
1144 <param name="matrix" value="identity"/>
1145 <param name="penalty" value="5"/>
1146 </section>
1147 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1148 <output name="ctd_out" ftype="xml">
1149 <assert_contents>
1150 <is_valid_xml/>
1151 </assert_contents>
1152 </output>
1153 </test>
1154 <test expect_num_outputs="2">
1155 <conditional name="adv_opts_cond">
1156 <param name="adv_opts_selector" value="advanced"/>
1157 <param name="force" value="false"/>
1158 <param name="test" value="true"/>
1159 </conditional>
1160 <param name="in" value="ConsensusID_1_input.idXML"/>
1161 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1162 <param name="rt_delta" value="0.1"/>
1163 <param name="mz_delta" value="0.1"/>
1164 <param name="algorithm" value="best"/>
1165 <section name="filter">
1166 <param name="considered_hits" value="0"/>
1167 <param name="min_support" value="0.5"/>
1168 <param name="count_empty" value="false"/>
1169 </section>
1170 <section name="PEPIons">
1171 <param name="mass_tolerance" value="0.5"/>
1172 <param name="min_shared" value="2"/>
1173 </section>
1174 <section name="PEPMatrix">
1175 <param name="matrix" value="identity"/>
1176 <param name="penalty" value="5"/>
1177 </section>
1178 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1179 <output name="ctd_out" ftype="xml">
1180 <assert_contents>
1181 <is_valid_xml/>
1182 </assert_contents>
1183 </output>
1184 </test>
1185 </xml>
1186 <xml name="autotest_ConsensusMapNormalizer">
1187 <test expect_num_outputs="2">
1188 <conditional name="adv_opts_cond">
1189 <param name="adv_opts_selector" value="advanced"/>
1190 <param name="accession_filter" value=""/>
1191 <param name="description_filter" value=""/>
1192 <param name="force" value="false"/>
1193 <param name="test" value="true"/>
1194 </conditional>
1195 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
1196 <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1197 <param name="algorithm_type" value="robust_regression"/>
1198 <param name="ratio_threshold" value="0.67"/>
1199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1200 <output name="ctd_out" ftype="xml">
1201 <assert_contents>
1202 <is_valid_xml/>
1203 </assert_contents>
1204 </output>
1205 </test>
1206 </xml>
1207 <xml name="autotest_CruxAdapter">
1208 <test expect_num_outputs="2">
1209 <conditional name="adv_opts_cond">
1210 <param name="adv_opts_selector" value="advanced"/>
1211 <param name="custom_enzyme" value=""/>
1212 <param name="decoy_prefix" value="decoy_"/>
1213 <param name="deisotope" value="false"/>
1214 <param name="report_decoys" value="false"/>
1215 <param name="force" value="false"/>
1216 <param name="test" value="true"/>
1217 </conditional>
1218 <param name="in" value="spectra_comet.mzML"/>
1219 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1220 <param name="database" value="proteins.fasta"/>
1221 <param name="extra_index_args" value=""/>
1222 <param name="extra_search_args" value=""/>
1223 <param name="extra_percolator_args" value=""/>
1224 <param name="precursor_mass_tolerance" value="10.0"/>
1225 <param name="precursor_mass_units" value="ppm"/>
1226 <param name="fragment_bin_offset" value="0.0"/>
1227 <param name="fragment_bin_width" value="0.02"/>
1228 <param name="isotope_error" value=""/>
1229 <param name="run_percolator" value="false"/>
1230 <param name="enzyme" value="trypsin"/>
1231 <param name="digestion" value="full-digest"/>
1232 <param name="allowed_missed_cleavages" value="0"/>
1233 <param name="decoy_format" value="shuffle"/>
1234 <param name="keep_terminal_aminos" value="NC"/>
1235 <param name="cterm_modifications" value=""/>
1236 <param name="nterm_modifications" value=""/>
1237 <param name="modifications" value=""/>
1238 <param name="test_fdr" value="0.01"/>
1239 <param name="train_fdr" value="0.01"/>
1240 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1241 <output name="ctd_out" ftype="xml">
1242 <assert_contents>
1243 <is_valid_xml/>
1244 </assert_contents>
1245 </output>
1246 </test>
1247 </xml>
1248 <xml name="autotest_CVInspector">
1249 </xml>
1250 <xml name="autotest_DatabaseFilter">
1251 <test expect_num_outputs="2">
1252 <conditional name="adv_opts_cond">
1253 <param name="adv_opts_selector" value="advanced"/>
1254 <param name="force" value="false"/>
1255 <param name="test" value="true"/>
1256 </conditional>
1257 <param name="in" value="DatabaseFilter_1.fasta"/>
1258 <param name="id" value="DatabaseFilter_1.idXML"/>
1259 <param name="method" value="whitelist"/>
1260 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1261 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1262 <output name="ctd_out" ftype="xml">
1263 <assert_contents>
1264 <is_valid_xml/>
1265 </assert_contents>
1266 </output>
1267 </test>
1268 <test expect_num_outputs="2">
1269 <conditional name="adv_opts_cond">
1270 <param name="adv_opts_selector" value="advanced"/>
1271 <param name="force" value="false"/>
1272 <param name="test" value="true"/>
1273 </conditional>
1274 <param name="in" value="DatabaseFilter_1.fasta"/>
1275 <param name="id" value="DatabaseFilter_1.idXML"/>
1276 <param name="method" value="blacklist"/>
1277 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1278 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1279 <output name="ctd_out" ftype="xml">
1280 <assert_contents>
1281 <is_valid_xml/>
1282 </assert_contents>
1283 </output>
1284 </test>
1285 <test expect_num_outputs="2">
1286 <conditional name="adv_opts_cond">
1287 <param name="adv_opts_selector" value="advanced"/>
1288 <param name="force" value="false"/>
1289 <param name="test" value="true"/>
1290 </conditional>
1291 <param name="in" value="DatabaseFilter_3.fasta"/>
1292 <param name="id" value="DatabaseFilter_3.mzid"/>
1293 <param name="method" value="whitelist"/>
1294 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1295 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1296 <output name="ctd_out" ftype="xml">
1297 <assert_contents>
1298 <is_valid_xml/>
1299 </assert_contents>
1300 </output>
1301 </test>
1302 <test expect_num_outputs="2">
1303 <conditional name="adv_opts_cond">
1304 <param name="adv_opts_selector" value="advanced"/>
1305 <param name="force" value="false"/>
1306 <param name="test" value="true"/>
1307 </conditional>
1308 <param name="in" value="DatabaseFilter_3.fasta"/>
1309 <param name="id" value="DatabaseFilter_3.mzid"/>
1310 <param name="method" value="blacklist"/>
1311 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1312 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1313 <output name="ctd_out" ftype="xml">
1314 <assert_contents>
1315 <is_valid_xml/>
1316 </assert_contents>
1317 </output>
1318 </test>
1319 </xml>
1320 <xml name="autotest_Decharger">
1321 <test expect_num_outputs="4">
1322 <conditional name="adv_opts_cond">
1323 <param name="adv_opts_selector" value="advanced"/>
1324 <param name="force" value="false"/>
1325 <param name="test" value="true"/>
1326 </conditional>
1327 <param name="in" value="Decharger_input.featureXML"/>
1328 <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1329 <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
1330 <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
1331 <section name="algorithm">
1332 <section name="FeatureDeconvolution">
1333 <param name="charge_min" value="1"/>
1334 <param name="charge_max" value="10"/>
1335 <param name="charge_span_max" value="4"/>
1336 <param name="q_try" value="feature"/>
1337 <param name="retention_max_diff" value="1.0"/>
1338 <param name="retention_max_diff_local" value="1.0"/>
1339 <param name="mass_max_diff" value="0.1"/>
1340 <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
1341 <param name="max_neutrals" value="0"/>
1342 <param name="max_minority_bound" value="2"/>
1343 <param name="min_rt_overlap" value="0.66"/>
1344 <param name="intensity_filter" value="false"/>
1345 <param name="negative_mode" value="false"/>
1346 <param name="default_map_label" value="decharged features"/>
1347 <param name="verbose_level" value="0"/>
1348 </section>
1349 </section>
1350 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
1351 <output name="ctd_out" ftype="xml">
1352 <assert_contents>
1353 <is_valid_xml/>
1354 </assert_contents>
1355 </output>
1356 </test>
1357 </xml>
1358 <xml name="autotest_DecoyDatabase">
1359 <test expect_num_outputs="2">
1360 <conditional name="adv_opts_cond">
1361 <param name="adv_opts_selector" value="advanced"/>
1362 <param name="shuffle_max_attempts" value="30"/>
1363 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1364 <param name="seed" value="1"/>
1365 <param name="force" value="false"/>
1366 <param name="test" value="true"/>
1367 </conditional>
1368 <param name="in" value="DecoyDatabase_1.fasta"/>
1369 <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1370 <param name="decoy_string" value="DECOY_"/>
1371 <param name="decoy_string_position" value="prefix"/>
1372 <param name="only_decoy" value="true"/>
1373 <param name="type" value="protein"/>
1374 <param name="method" value="reverse"/>
1375 <param name="enzyme" value="Trypsin"/>
1376 <section name="Decoy">
1377 <param name="non_shuffle_pattern" value=""/>
1378 <param name="keepPeptideNTerm" value="true"/>
1379 <param name="keepPeptideCTerm" value="true"/>
1380 </section>
1381 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1382 <output name="ctd_out" ftype="xml">
1383 <assert_contents>
1384 <is_valid_xml/>
1385 </assert_contents>
1386 </output>
1387 </test>
1388 <test expect_num_outputs="2">
1389 <conditional name="adv_opts_cond">
1390 <param name="adv_opts_selector" value="advanced"/>
1391 <param name="shuffle_max_attempts" value="30"/>
1392 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1393 <param name="seed" value="42"/>
1394 <param name="force" value="false"/>
1395 <param name="test" value="true"/>
1396 </conditional>
1397 <param name="in" value="DecoyDatabase_1.fasta"/>
1398 <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1399 <param name="decoy_string" value="blabla"/>
1400 <param name="decoy_string_position" value="prefix"/>
1401 <param name="only_decoy" value="false"/>
1402 <param name="type" value="protein"/>
1403 <param name="method" value="shuffle"/>
1404 <param name="enzyme" value="Trypsin"/>
1405 <section name="Decoy">
1406 <param name="non_shuffle_pattern" value="KRP"/>
1407 <param name="keepPeptideNTerm" value="true"/>
1408 <param name="keepPeptideCTerm" value="true"/>
1409 </section>
1410 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1411 <output name="ctd_out" ftype="xml">
1412 <assert_contents>
1413 <is_valid_xml/>
1414 </assert_contents>
1415 </output>
1416 </test>
1417 <test expect_num_outputs="2">
1418 <conditional name="adv_opts_cond">
1419 <param name="adv_opts_selector" value="advanced"/>
1420 <param name="shuffle_max_attempts" value="30"/>
1421 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1422 <param name="seed" value="42"/>
1423 <param name="force" value="false"/>
1424 <param name="test" value="true"/>
1425 </conditional>
1426 <param name="in" value="DecoyDatabase_1.fasta"/>
1427 <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1428 <param name="decoy_string" value="blabla"/>
1429 <param name="decoy_string_position" value="prefix"/>
1430 <param name="only_decoy" value="false"/>
1431 <param name="type" value="protein"/>
1432 <param name="method" value="shuffle"/>
1433 <param name="enzyme" value="Chymotrypsin"/>
1434 <section name="Decoy">
1435 <param name="non_shuffle_pattern" value="KR"/>
1436 <param name="keepPeptideNTerm" value="true"/>
1437 <param name="keepPeptideCTerm" value="true"/>
1438 </section>
1439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1440 <output name="ctd_out" ftype="xml">
1441 <assert_contents>
1442 <is_valid_xml/>
1443 </assert_contents>
1444 </output>
1445 </test>
1446 <test expect_num_outputs="2">
1447 <conditional name="adv_opts_cond">
1448 <param name="adv_opts_selector" value="advanced"/>
1449 <param name="shuffle_max_attempts" value="30"/>
1450 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1451 <param name="seed" value="42"/>
1452 <param name="force" value="false"/>
1453 <param name="test" value="true"/>
1454 </conditional>
1455 <param name="in" value="DecoyDatabase_4.fasta"/>
1456 <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1457 <param name="decoy_string" value="blabla"/>
1458 <param name="decoy_string_position" value="prefix"/>
1459 <param name="only_decoy" value="false"/>
1460 <param name="type" value="RNA"/>
1461 <param name="method" value="reverse"/>
1462 <param name="enzyme" value="Trypsin"/>
1463 <section name="Decoy">
1464 <param name="non_shuffle_pattern" value=""/>
1465 <param name="keepPeptideNTerm" value="true"/>
1466 <param name="keepPeptideCTerm" value="true"/>
1467 </section>
1468 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1469 <output name="ctd_out" ftype="xml">
1470 <assert_contents>
1471 <is_valid_xml/>
1472 </assert_contents>
1473 </output>
1474 </test>
1475 </xml>
1476 <xml name="autotest_DeMeanderize">
1477 </xml>
1478 <xml name="autotest_DTAExtractor">
1479 <test expect_num_outputs="1">
1480 <conditional name="adv_opts_cond">
1481 <param name="adv_opts_selector" value="advanced"/>
1482 <param name="force" value="false"/>
1483 <param name="test" value="true"/>
1484 </conditional>
1485 <param name="in" value="DTAExtractor_1_input.mzML"/>
1486 <param name="out" value="DTAExtractor"/>
1487 <param name="mz" value=":"/>
1488 <param name="rt" value=":61"/>
1489 <param name="level" value="1,2,3"/>
1490 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1491 <output name="ctd_out" ftype="xml">
1492 <assert_contents>
1493 <is_valid_xml/>
1494 </assert_contents>
1495 </output>
1496 </test>
1497 <test expect_num_outputs="1">
1498 <conditional name="adv_opts_cond">
1499 <param name="adv_opts_selector" value="advanced"/>
1500 <param name="force" value="false"/>
1501 <param name="test" value="true"/>
1502 </conditional>
1503 <param name="in" value="DTAExtractor_1_input.mzML"/>
1504 <param name="out" value="DTAExtractor"/>
1505 <param name="mz" value=":"/>
1506 <param name="rt" value=":"/>
1507 <param name="level" value="1"/>
1508 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1509 <output name="ctd_out" ftype="xml">
1510 <assert_contents>
1511 <is_valid_xml/>
1512 </assert_contents>
1513 </output>
1514 </test>
1515 <test expect_num_outputs="1">
1516 <conditional name="adv_opts_cond">
1517 <param name="adv_opts_selector" value="advanced"/>
1518 <param name="force" value="false"/>
1519 <param name="test" value="true"/>
1520 </conditional>
1521 <param name="in" value="DTAExtractor_1_input.mzML"/>
1522 <param name="out" value="DTAExtractor"/>
1523 <param name="mz" value=":1000"/>
1524 <param name="rt" value=":"/>
1525 <param name="level" value="2"/>
1526 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1527 <output name="ctd_out" ftype="xml">
1528 <assert_contents>
1529 <is_valid_xml/>
1530 </assert_contents>
1531 </output>
1532 </test>
1533 </xml>
1534 <xml name="autotest_EICExtractor">
1535 </xml>
1536 <xml name="autotest_Epifany">
1537 <test expect_num_outputs="2">
1538 <conditional name="adv_opts_cond">
1539 <param name="adv_opts_selector" value="advanced"/>
1540 <param name="conservative_fdr" value="true"/>
1541 <param name="min_psms_extreme_probability" value="0.0"/>
1542 <param name="force" value="false"/>
1543 <param name="test" value="true"/>
1544 </conditional>
1545 <param name="in" value="FidoAdapter_1_input.idXML"/>
1546 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1547 <param name="protein_fdr" value="false"/>
1548 <param name="greedy_group_resolution" value="none"/>
1549 <param name="max_psms_extreme_probability" value="1.0"/>
1550 <section name="algorithm">
1551 <param name="psm_probability_cutoff" value="0.001"/>
1552 <param name="top_PSMs" value="1"/>
1553 <param name="update_PSM_probabilities" value="true"/>
1554 <param name="user_defined_priors" value="false"/>
1555 <param name="annotate_group_probabilities" value="true"/>
1556 <param name="use_ids_outside_features" value="false"/>
1557 <section name="model_parameters">
1558 <param name="prot_prior" value="0.7"/>
1559 <param name="pep_emission" value="0.1"/>
1560 <param name="pep_spurious_emission" value="0.001"/>
1561 <param name="pep_prior" value="0.1"/>
1562 <param name="regularize" value="false"/>
1563 <param name="extended_model" value="false"/>
1564 </section>
1565 <section name="loopy_belief_propagation">
1566 <param name="scheduling_type" value="priority"/>
1567 <param name="convergence_threshold" value="1e-05"/>
1568 <param name="dampening_lambda" value="0.001"/>
1569 <param name="max_nr_iterations" value="2147483647"/>
1570 <param name="p_norm_inference" value="1.0"/>
1571 </section>
1572 <section name="param_optimize">
1573 <param name="aucweight" value="0.3"/>
1574 <param name="conservative_fdr" value="true"/>
1575 </section>
1576 </section>
1577 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1578 <output name="ctd_out" ftype="xml">
1579 <assert_contents>
1580 <is_valid_xml/>
1581 </assert_contents>
1582 </output>
1583 </test>
1584 </xml>
1585 <xml name="autotest_ERPairFinder">
1586 </xml>
1587 <xml name="autotest_ExternalCalibration">
1588 <test expect_num_outputs="2">
1589 <conditional name="adv_opts_cond">
1590 <param name="adv_opts_selector" value="advanced"/>
1591 <param name="force" value="false"/>
1592 <param name="test" value="true"/>
1593 </conditional>
1594 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1595 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1596 <param name="offset" value="-5.5"/>
1597 <param name="slope" value="0.0001"/>
1598 <param name="power" value="0.0"/>
1599 <param name="ms_level" value="1"/>
1600 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1601 <output name="ctd_out" ftype="xml">
1602 <assert_contents>
1603 <is_valid_xml/>
1604 </assert_contents>
1605 </output>
1606 </test>
1607 <test expect_num_outputs="2">
1608 <conditional name="adv_opts_cond">
1609 <param name="adv_opts_selector" value="advanced"/>
1610 <param name="force" value="false"/>
1611 <param name="test" value="true"/>
1612 </conditional>
1613 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1614 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1615 <param name="offset" value="-5.5"/>
1616 <param name="slope" value="0.0001"/>
1617 <param name="power" value="0.0"/>
1618 <param name="ms_level" value="2"/>
1619 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1620 <output name="ctd_out" ftype="xml">
1621 <assert_contents>
1622 <is_valid_xml/>
1623 </assert_contents>
1624 </output>
1625 </test>
1626 </xml>
1627 <xml name="autotest_FalseDiscoveryRate">
1628 <test expect_num_outputs="2">
1629 <conditional name="adv_opts_cond">
1630 <param name="adv_opts_selector" value="advanced"/>
1631 <param name="force" value="false"/>
1632 <param name="test" value="true"/>
1633 </conditional>
1634 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1635 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1636 <param name="PSM" value="true"/>
1637 <param name="protein" value="false"/>
1638 <section name="FDR">
1639 <param name="PSM" value="1.0"/>
1640 <param name="protein" value="1.0"/>
1641 <section name="cleanup">
1642 <param name="remove_proteins_without_psms" value="true"/>
1643 <param name="remove_psms_without_proteins" value="true"/>
1644 <param name="remove_spectra_without_psms" value="true"/>
1645 </section>
1646 </section>
1647 <section name="algorithm">
1648 <param name="no_qvalues" value="false"/>
1649 <param name="use_all_hits" value="false"/>
1650 <param name="split_charge_variants" value="false"/>
1651 <param name="treat_runs_separately" value="false"/>
1652 <param name="add_decoy_peptides" value="false"/>
1653 <param name="add_decoy_proteins" value="false"/>
1654 <param name="conservative" value="true"/>
1655 </section>
1656 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1657 <output name="ctd_out" ftype="xml">
1658 <assert_contents>
1659 <is_valid_xml/>
1660 </assert_contents>
1661 </output>
1662 </test>
1663 <test expect_num_outputs="2">
1664 <conditional name="adv_opts_cond">
1665 <param name="adv_opts_selector" value="advanced"/>
1666 <param name="force" value="false"/>
1667 <param name="test" value="true"/>
1668 </conditional>
1669 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1670 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1671 <param name="PSM" value="true"/>
1672 <param name="protein" value="false"/>
1673 <section name="FDR">
1674 <param name="PSM" value="1.0"/>
1675 <param name="protein" value="1.0"/>
1676 <section name="cleanup">
1677 <param name="remove_proteins_without_psms" value="true"/>
1678 <param name="remove_psms_without_proteins" value="true"/>
1679 <param name="remove_spectra_without_psms" value="true"/>
1680 </section>
1681 </section>
1682 <section name="algorithm">
1683 <param name="no_qvalues" value="false"/>
1684 <param name="use_all_hits" value="false"/>
1685 <param name="split_charge_variants" value="false"/>
1686 <param name="treat_runs_separately" value="true"/>
1687 <param name="add_decoy_peptides" value="false"/>
1688 <param name="add_decoy_proteins" value="false"/>
1689 <param name="conservative" value="true"/>
1690 </section>
1691 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1692 <output name="ctd_out" ftype="xml">
1693 <assert_contents>
1694 <is_valid_xml/>
1695 </assert_contents>
1696 </output>
1697 </test>
1698 <test expect_num_outputs="2">
1699 <conditional name="adv_opts_cond">
1700 <param name="adv_opts_selector" value="advanced"/>
1701 <param name="force" value="false"/>
1702 <param name="test" value="true"/>
1703 </conditional>
1704 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1705 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1706 <param name="PSM" value="true"/>
1707 <param name="protein" value="false"/>
1708 <section name="FDR">
1709 <param name="PSM" value="1.0"/>
1710 <param name="protein" value="1.0"/>
1711 <section name="cleanup">
1712 <param name="remove_proteins_without_psms" value="true"/>
1713 <param name="remove_psms_without_proteins" value="true"/>
1714 <param name="remove_spectra_without_psms" value="true"/>
1715 </section>
1716 </section>
1717 <section name="algorithm">
1718 <param name="no_qvalues" value="false"/>
1719 <param name="use_all_hits" value="false"/>
1720 <param name="split_charge_variants" value="true"/>
1721 <param name="treat_runs_separately" value="false"/>
1722 <param name="add_decoy_peptides" value="false"/>
1723 <param name="add_decoy_proteins" value="false"/>
1724 <param name="conservative" value="true"/>
1725 </section>
1726 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1727 <output name="ctd_out" ftype="xml">
1728 <assert_contents>
1729 <is_valid_xml/>
1730 </assert_contents>
1731 </output>
1732 </test>
1733 <test expect_num_outputs="2">
1734 <conditional name="adv_opts_cond">
1735 <param name="adv_opts_selector" value="advanced"/>
1736 <param name="force" value="false"/>
1737 <param name="test" value="true"/>
1738 </conditional>
1739 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
1740 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1741 <param name="PSM" value="true"/>
1742 <param name="protein" value="false"/>
1743 <section name="FDR">
1744 <param name="PSM" value="1.0"/>
1745 <param name="protein" value="1.0"/>
1746 <section name="cleanup">
1747 <param name="remove_proteins_without_psms" value="true"/>
1748 <param name="remove_psms_without_proteins" value="true"/>
1749 <param name="remove_spectra_without_psms" value="true"/>
1750 </section>
1751 </section>
1752 <section name="algorithm">
1753 <param name="no_qvalues" value="false"/>
1754 <param name="use_all_hits" value="false"/>
1755 <param name="split_charge_variants" value="true"/>
1756 <param name="treat_runs_separately" value="false"/>
1757 <param name="add_decoy_peptides" value="false"/>
1758 <param name="add_decoy_proteins" value="false"/>
1759 <param name="conservative" value="true"/>
1760 </section>
1761 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1762 <output name="ctd_out" ftype="xml">
1763 <assert_contents>
1764 <is_valid_xml/>
1765 </assert_contents>
1766 </output>
1767 </test>
1768 <test expect_num_outputs="2">
1769 <conditional name="adv_opts_cond">
1770 <param name="adv_opts_selector" value="advanced"/>
1771 <param name="force" value="true"/>
1772 <param name="test" value="true"/>
1773 </conditional>
1774 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
1775 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1776 <param name="PSM" value="false"/>
1777 <param name="protein" value="true"/>
1778 <section name="FDR">
1779 <param name="PSM" value="1.0"/>
1780 <param name="protein" value="1.0"/>
1781 <section name="cleanup">
1782 <param name="remove_proteins_without_psms" value="true"/>
1783 <param name="remove_psms_without_proteins" value="true"/>
1784 <param name="remove_spectra_without_psms" value="true"/>
1785 </section>
1786 </section>
1787 <section name="algorithm">
1788 <param name="no_qvalues" value="false"/>
1789 <param name="use_all_hits" value="false"/>
1790 <param name="split_charge_variants" value="false"/>
1791 <param name="treat_runs_separately" value="false"/>
1792 <param name="add_decoy_peptides" value="false"/>
1793 <param name="add_decoy_proteins" value="true"/>
1794 <param name="conservative" value="true"/>
1795 </section>
1796 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1797 <output name="ctd_out" ftype="xml">
1798 <assert_contents>
1799 <is_valid_xml/>
1800 </assert_contents>
1801 </output>
1802 </test>
1803 <test expect_num_outputs="2">
1804 <conditional name="adv_opts_cond">
1805 <param name="adv_opts_selector" value="advanced"/>
1806 <param name="force" value="false"/>
1807 <param name="test" value="true"/>
1808 </conditional>
1809 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
1810 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1811 <param name="PSM" value="true"/>
1812 <param name="protein" value="false"/>
1813 <section name="FDR">
1814 <param name="PSM" value="0.05"/>
1815 <param name="protein" value="1.0"/>
1816 <section name="cleanup">
1817 <param name="remove_proteins_without_psms" value="true"/>
1818 <param name="remove_psms_without_proteins" value="true"/>
1819 <param name="remove_spectra_without_psms" value="true"/>
1820 </section>
1821 </section>
1822 <section name="algorithm">
1823 <param name="no_qvalues" value="false"/>
1824 <param name="use_all_hits" value="false"/>
1825 <param name="split_charge_variants" value="false"/>
1826 <param name="treat_runs_separately" value="false"/>
1827 <param name="add_decoy_peptides" value="false"/>
1828 <param name="add_decoy_proteins" value="false"/>
1829 <param name="conservative" value="true"/>
1830 </section>
1831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1832 <output name="ctd_out" ftype="xml">
1833 <assert_contents>
1834 <is_valid_xml/>
1835 </assert_contents>
1836 </output>
1837 </test>
1838 <test expect_num_outputs="2">
1839 <conditional name="adv_opts_cond">
1840 <param name="adv_opts_selector" value="advanced"/>
1841 <param name="force" value="true"/>
1842 <param name="test" value="true"/>
1843 </conditional>
1844 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
1845 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1846 <param name="PSM" value="false"/>
1847 <param name="protein" value="true"/>
1848 <section name="FDR">
1849 <param name="PSM" value="1.0"/>
1850 <param name="protein" value="0.3"/>
1851 <section name="cleanup">
1852 <param name="remove_proteins_without_psms" value="true"/>
1853 <param name="remove_psms_without_proteins" value="true"/>
1854 <param name="remove_spectra_without_psms" value="true"/>
1855 </section>
1856 </section>
1857 <section name="algorithm">
1858 <param name="no_qvalues" value="false"/>
1859 <param name="use_all_hits" value="false"/>
1860 <param name="split_charge_variants" value="false"/>
1861 <param name="treat_runs_separately" value="false"/>
1862 <param name="add_decoy_peptides" value="false"/>
1863 <param name="add_decoy_proteins" value="false"/>
1864 <param name="conservative" value="true"/>
1865 </section>
1866 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1867 <output name="ctd_out" ftype="xml">
1868 <assert_contents>
1869 <is_valid_xml/>
1870 </assert_contents>
1871 </output>
1872 </test>
1873 </xml>
1874 <xml name="autotest_FeatureFinderCentroided">
1875 <test expect_num_outputs="2">
1876 <conditional name="adv_opts_cond">
1877 <param name="adv_opts_selector" value="advanced"/>
1878 <param name="force" value="false"/>
1879 <param name="test" value="true"/>
1880 <param name="pseudo_rt_shift" value="500.0"/>
1881 </conditional>
1882 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
1883 <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1884 <section name="algorithm">
1885 <section name="intensity">
1886 <param name="bins" value="1"/>
1887 </section>
1888 <section name="mass_trace">
1889 <param name="mz_tolerance" value="0.02"/>
1890 <param name="min_spectra" value="14"/>
1891 <param name="max_missing" value="1"/>
1892 <param name="slope_bound" value="0.1"/>
1893 </section>
1894 <section name="isotopic_pattern">
1895 <param name="charge_low" value="2"/>
1896 <param name="charge_high" value="2"/>
1897 <param name="mz_tolerance" value="0.02"/>
1898 <param name="intensity_percentage" value="10.0"/>
1899 <param name="intensity_percentage_optional" value="0.1"/>
1900 <param name="optional_fit_improvement" value="2.0"/>
1901 <param name="mass_window_width" value="100.0"/>
1902 <param name="abundance_12C" value="98.93"/>
1903 <param name="abundance_14N" value="99.632"/>
1904 </section>
1905 <section name="seed">
1906 <param name="min_score" value="0.8"/>
1907 </section>
1908 <section name="fit">
1909 <param name="max_iterations" value="500"/>
1910 </section>
1911 <section name="feature">
1912 <param name="min_score" value="0.7"/>
1913 <param name="min_isotope_fit" value="0.8"/>
1914 <param name="min_trace_score" value="0.5"/>
1915 <param name="min_rt_span" value="0.333"/>
1916 <param name="max_rt_span" value="2.5"/>
1917 <param name="rt_shape" value="symmetric"/>
1918 <param name="max_intersection" value="0.35"/>
1919 <param name="reported_mz" value="monoisotopic"/>
1920 </section>
1921 <section name="user-seed">
1922 <param name="rt_tolerance" value="5.0"/>
1923 <param name="mz_tolerance" value="1.1"/>
1924 <param name="min_score" value="0.5"/>
1925 </section>
1926 </section>
1927 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1928 <output name="ctd_out" ftype="xml">
1929 <assert_contents>
1930 <is_valid_xml/>
1931 </assert_contents>
1932 </output>
1933 </test>
1934 </xml>
1935 <xml name="autotest_FeatureFinderIdentification">
1936 <test expect_num_outputs="2">
1937 <conditional name="adv_opts_cond">
1938 <param name="adv_opts_selector" value="advanced"/>
1939 <param name="force" value="false"/>
1940 <param name="test" value="true"/>
1941 </conditional>
1942 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
1943 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
1944 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1945 <section name="extract">
1946 <param name="batch_size" value="1000"/>
1947 <param name="mz_window" value="0.1"/>
1948 <param name="n_isotopes" value="2"/>
1949 <param name="isotope_pmin" value="0.0"/>
1950 <param name="rt_quantile" value="0.95"/>
1951 <param name="rt_window" value="0.0"/>
1952 </section>
1953 <section name="detect">
1954 <param name="peak_width" value="60.0"/>
1955 <param name="min_peak_width" value="0.2"/>
1956 <param name="signal_to_noise" value="0.8"/>
1957 <param name="mapping_tolerance" value="0.0"/>
1958 </section>
1959 <section name="svm">
1960 <param name="samples" value="0"/>
1961 <param name="no_selection" value="false"/>
1962 <param name="kernel" value="RBF"/>
1963 <param name="xval" value="5"/>
1964 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
1965 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
1966 <param name="epsilon" value="0.001"/>
1967 <param name="cache_size" value="100.0"/>
1968 <param name="no_shrinking" value="false"/>
1969 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
1970 <param name="min_prob" value="0.0"/>
1971 </section>
1972 <section name="model">
1973 <param name="type" value="none"/>
1974 <param name="add_zeros" value="0.2"/>
1975 <param name="unweighted_fit" value="false"/>
1976 <param name="no_imputation" value="false"/>
1977 <section name="check">
1978 <param name="min_area" value="1.0"/>
1979 <param name="boundaries" value="0.5"/>
1980 <param name="width" value="10.0"/>
1981 <param name="asymmetry" value="10.0"/>
1982 </section>
1983 </section>
1984 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1985 <output name="ctd_out" ftype="xml">
1986 <assert_contents>
1987 <is_valid_xml/>
1988 </assert_contents>
1989 </output>
1990 </test>
1991 <test expect_num_outputs="2">
1992 <conditional name="adv_opts_cond">
1993 <param name="adv_opts_selector" value="advanced"/>
1994 <param name="force" value="false"/>
1995 <param name="test" value="true"/>
1996 </conditional>
1997 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
1998 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
1999 <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2000 <section name="extract">
2001 <param name="batch_size" value="1000"/>
2002 <param name="mz_window" value="0.1"/>
2003 <param name="n_isotopes" value="2"/>
2004 <param name="isotope_pmin" value="0.0"/>
2005 <param name="rt_quantile" value="0.95"/>
2006 <param name="rt_window" value="0.0"/>
2007 </section>
2008 <section name="detect">
2009 <param name="peak_width" value="60.0"/>
2010 <param name="min_peak_width" value="0.2"/>
2011 <param name="signal_to_noise" value="0.8"/>
2012 <param name="mapping_tolerance" value="0.0"/>
2013 </section>
2014 <section name="svm">
2015 <param name="samples" value="0"/>
2016 <param name="no_selection" value="false"/>
2017 <param name="kernel" value="RBF"/>
2018 <param name="xval" value="5"/>
2019 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
2020 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
2021 <param name="epsilon" value="0.001"/>
2022 <param name="cache_size" value="100.0"/>
2023 <param name="no_shrinking" value="false"/>
2024 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
2025 <param name="min_prob" value="0.0"/>
2026 </section>
2027 <section name="model">
2028 <param name="type" value="symmetric"/>
2029 <param name="add_zeros" value="0.2"/>
2030 <param name="unweighted_fit" value="false"/>
2031 <param name="no_imputation" value="false"/>
2032 <section name="check">
2033 <param name="min_area" value="1.0"/>
2034 <param name="boundaries" value="0.5"/>
2035 <param name="width" value="10.0"/>
2036 <param name="asymmetry" value="10.0"/>
2037 </section>
2038 </section>
2039 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2040 <output name="ctd_out" ftype="xml">
2041 <assert_contents>
2042 <is_valid_xml/>
2043 </assert_contents>
2044 </output>
2045 </test>
2046 <test expect_num_outputs="2">
2047 <conditional name="adv_opts_cond">
2048 <param name="adv_opts_selector" value="advanced"/>
2049 <param name="force" value="false"/>
2050 <param name="test" value="true"/>
2051 </conditional>
2052 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2053 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2054 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2055 <section name="extract">
2056 <param name="batch_size" value="10"/>
2057 <param name="mz_window" value="0.1"/>
2058 <param name="n_isotopes" value="2"/>
2059 <param name="isotope_pmin" value="0.0"/>
2060 <param name="rt_quantile" value="0.95"/>
2061 <param name="rt_window" value="0.0"/>
2062 </section>
2063 <section name="detect">
2064 <param name="peak_width" value="60.0"/>
2065 <param name="min_peak_width" value="0.2"/>
2066 <param name="signal_to_noise" value="0.8"/>
2067 <param name="mapping_tolerance" value="0.0"/>
2068 </section>
2069 <section name="svm">
2070 <param name="samples" value="0"/>
2071 <param name="no_selection" value="false"/>
2072 <param name="kernel" value="RBF"/>
2073 <param name="xval" value="5"/>
2074 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
2075 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
2076 <param name="epsilon" value="0.001"/>
2077 <param name="cache_size" value="100.0"/>
2078 <param name="no_shrinking" value="false"/>
2079 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
2080 <param name="min_prob" value="0.0"/>
2081 </section>
2082 <section name="model">
2083 <param name="type" value="none"/>
2084 <param name="add_zeros" value="0.2"/>
2085 <param name="unweighted_fit" value="false"/>
2086 <param name="no_imputation" value="false"/>
2087 <section name="check">
2088 <param name="min_area" value="1.0"/>
2089 <param name="boundaries" value="0.5"/>
2090 <param name="width" value="10.0"/>
2091 <param name="asymmetry" value="10.0"/>
2092 </section>
2093 </section>
2094 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2095 <output name="ctd_out" ftype="xml">
2096 <assert_contents>
2097 <is_valid_xml/>
2098 </assert_contents>
2099 </output>
2100 </test>
2101 </xml>
2102 <xml name="autotest_FeatureFinderIsotopeWavelet">
2103 </xml>
2104 <xml name="autotest_FeatureFinderMetaboIdent">
2105 <test expect_num_outputs="2">
2106 <conditional name="adv_opts_cond">
2107 <param name="adv_opts_selector" value="advanced"/>
2108 <param name="force" value="false"/>
2109 <param name="test" value="true"/>
2110 </conditional>
2111 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
2112 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
2113 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2114 <section name="extract">
2115 <param name="mz_window" value="5.0"/>
2116 <param name="n_isotopes" value="2"/>
2117 <param name="isotope_pmin" value="0.0"/>
2118 <param name="rt_window" value="20.0"/>
2119 </section>
2120 <section name="detect">
2121 <param name="peak_width" value="3.0"/>
2122 <param name="min_peak_width" value="0.2"/>
2123 <param name="signal_to_noise" value="0.8"/>
2124 </section>
2125 <section name="model">
2126 <param name="type" value="symmetric"/>
2127 <param name="add_zeros" value="0.2"/>
2128 <param name="unweighted_fit" value="false"/>
2129 <param name="no_imputation" value="false"/>
2130 <section name="check">
2131 <param name="min_area" value="1.0"/>
2132 <param name="boundaries" value="0.5"/>
2133 <param name="width" value="10.0"/>
2134 <param name="asymmetry" value="10.0"/>
2135 </section>
2136 </section>
2137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2138 <output name="ctd_out" ftype="xml">
2139 <assert_contents>
2140 <is_valid_xml/>
2141 </assert_contents>
2142 </output>
2143 </test>
2144 </xml>
2145 <xml name="autotest_FeatureFinderMetabo">
2146 <test expect_num_outputs="2">
2147 <conditional name="adv_opts_cond">
2148 <param name="adv_opts_selector" value="advanced"/>
2149 <param name="force" value="false"/>
2150 <param name="test" value="true"/>
2151 </conditional>
2152 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2153 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2154 <section name="algorithm">
2155 <section name="common">
2156 <param name="noise_threshold_int" value="10.0"/>
2157 <param name="chrom_peak_snr" value="3.0"/>
2158 <param name="chrom_fwhm" value="5.0"/>
2159 </section>
2160 <section name="mtd">
2161 <param name="mass_error_ppm" value="20.0"/>
2162 <param name="reestimate_mt_sd" value="true"/>
2163 <param name="quant_method" value="area"/>
2164 <param name="trace_termination_criterion" value="outlier"/>
2165 <param name="trace_termination_outliers" value="5"/>
2166 <param name="min_sample_rate" value="0.5"/>
2167 <param name="min_trace_length" value="5.0"/>
2168 <param name="max_trace_length" value="300.0"/>
2169 </section>
2170 <section name="epd">
2171 <param name="enabled" value="true"/>
2172 <param name="width_filtering" value="off"/>
2173 <param name="min_fwhm" value="3.0"/>
2174 <param name="max_fwhm" value="60.0"/>
2175 <param name="masstrace_snr_filtering" value="false"/>
2176 </section>
2177 <section name="ffm">
2178 <param name="local_rt_range" value="10.0"/>
2179 <param name="local_mz_range" value="6.5"/>
2180 <param name="charge_lower_bound" value="1"/>
2181 <param name="charge_upper_bound" value="3"/>
2182 <param name="report_summed_ints" value="false"/>
2183 <param name="enable_RT_filtering" value="true"/>
2184 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2185 <param name="mz_scoring_13C" value="true"/>
2186 <param name="use_smoothed_intensities" value="true"/>
2187 <param name="report_convex_hulls" value="false"/>
2188 <param name="remove_single_traces" value="false"/>
2189 <param name="mz_scoring_by_elements" value="false"/>
2190 <param name="elements" value="CHNOPS"/>
2191 </section>
2192 </section>
2193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2194 <output name="ctd_out" ftype="xml">
2195 <assert_contents>
2196 <is_valid_xml/>
2197 </assert_contents>
2198 </output>
2199 </test>
2200 <test expect_num_outputs="2">
2201 <conditional name="adv_opts_cond">
2202 <param name="adv_opts_selector" value="advanced"/>
2203 <param name="force" value="false"/>
2204 <param name="test" value="true"/>
2205 </conditional>
2206 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
2207 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2208 <section name="algorithm">
2209 <section name="common">
2210 <param name="noise_threshold_int" value="100.0"/>
2211 <param name="chrom_peak_snr" value="0.0"/>
2212 <param name="chrom_fwhm" value="100.0"/>
2213 </section>
2214 <section name="mtd">
2215 <param name="mass_error_ppm" value="5.0"/>
2216 <param name="reestimate_mt_sd" value="true"/>
2217 <param name="quant_method" value="median"/>
2218 <param name="trace_termination_criterion" value="sample_rate"/>
2219 <param name="trace_termination_outliers" value="2"/>
2220 <param name="min_sample_rate" value="0.01"/>
2221 <param name="min_trace_length" value="30.0"/>
2222 <param name="max_trace_length" value="3000.0"/>
2223 </section>
2224 <section name="epd">
2225 <param name="enabled" value="false"/>
2226 <param name="width_filtering" value="off"/>
2227 <param name="min_fwhm" value="10.0"/>
2228 <param name="max_fwhm" value="80.0"/>
2229 <param name="masstrace_snr_filtering" value="false"/>
2230 </section>
2231 <section name="ffm">
2232 <param name="local_rt_range" value="10.0"/>
2233 <param name="local_mz_range" value="4.5"/>
2234 <param name="charge_lower_bound" value="1"/>
2235 <param name="charge_upper_bound" value="3"/>
2236 <param name="report_summed_ints" value="false"/>
2237 <param name="enable_RT_filtering" value="false"/>
2238 <param name="isotope_filtering_model" value="none"/>
2239 <param name="mz_scoring_13C" value="false"/>
2240 <param name="use_smoothed_intensities" value="false"/>
2241 <param name="report_convex_hulls" value="true"/>
2242 <param name="remove_single_traces" value="false"/>
2243 <param name="mz_scoring_by_elements" value="false"/>
2244 <param name="elements" value="CHNOPS"/>
2245 </section>
2246 </section>
2247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2248 <output name="ctd_out" ftype="xml">
2249 <assert_contents>
2250 <is_valid_xml/>
2251 </assert_contents>
2252 </output>
2253 </test>
2254 <test expect_num_outputs="3">
2255 <conditional name="adv_opts_cond">
2256 <param name="adv_opts_selector" value="advanced"/>
2257 <param name="force" value="false"/>
2258 <param name="test" value="true"/>
2259 </conditional>
2260 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2261 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
2262 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2263 <section name="algorithm">
2264 <section name="common">
2265 <param name="noise_threshold_int" value="10.0"/>
2266 <param name="chrom_peak_snr" value="3.0"/>
2267 <param name="chrom_fwhm" value="5.0"/>
2268 </section>
2269 <section name="mtd">
2270 <param name="mass_error_ppm" value="5.0"/>
2271 <param name="reestimate_mt_sd" value="true"/>
2272 <param name="quant_method" value="area"/>
2273 <param name="trace_termination_criterion" value="outlier"/>
2274 <param name="trace_termination_outliers" value="5"/>
2275 <param name="min_sample_rate" value="0.5"/>
2276 <param name="min_trace_length" value="5.0"/>
2277 <param name="max_trace_length" value="-1.0"/>
2278 </section>
2279 <section name="epd">
2280 <param name="enabled" value="true"/>
2281 <param name="width_filtering" value="fixed"/>
2282 <param name="min_fwhm" value="3.0"/>
2283 <param name="max_fwhm" value="60.0"/>
2284 <param name="masstrace_snr_filtering" value="false"/>
2285 </section>
2286 <section name="ffm">
2287 <param name="local_rt_range" value="10.0"/>
2288 <param name="local_mz_range" value="6.5"/>
2289 <param name="charge_lower_bound" value="1"/>
2290 <param name="charge_upper_bound" value="3"/>
2291 <param name="report_summed_ints" value="false"/>
2292 <param name="enable_RT_filtering" value="true"/>
2293 <param name="isotope_filtering_model" value="none"/>
2294 <param name="mz_scoring_13C" value="true"/>
2295 <param name="use_smoothed_intensities" value="true"/>
2296 <param name="report_convex_hulls" value="true"/>
2297 <param name="remove_single_traces" value="false"/>
2298 <param name="mz_scoring_by_elements" value="false"/>
2299 <param name="elements" value="CHNOPS"/>
2300 </section>
2301 </section>
2302 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2303 <output name="ctd_out" ftype="xml">
2304 <assert_contents>
2305 <is_valid_xml/>
2306 </assert_contents>
2307 </output>
2308 </test>
2309 <test expect_num_outputs="3">
2310 <conditional name="adv_opts_cond">
2311 <param name="adv_opts_selector" value="advanced"/>
2312 <param name="force" value="false"/>
2313 <param name="test" value="true"/>
2314 </conditional>
2315 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2316 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2317 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2318 <section name="algorithm">
2319 <section name="common">
2320 <param name="noise_threshold_int" value="10.0"/>
2321 <param name="chrom_peak_snr" value="3.0"/>
2322 <param name="chrom_fwhm" value="5.0"/>
2323 </section>
2324 <section name="mtd">
2325 <param name="mass_error_ppm" value="5.0"/>
2326 <param name="reestimate_mt_sd" value="true"/>
2327 <param name="quant_method" value="area"/>
2328 <param name="trace_termination_criterion" value="outlier"/>
2329 <param name="trace_termination_outliers" value="5"/>
2330 <param name="min_sample_rate" value="0.5"/>
2331 <param name="min_trace_length" value="5.0"/>
2332 <param name="max_trace_length" value="-1.0"/>
2333 </section>
2334 <section name="epd">
2335 <param name="enabled" value="true"/>
2336 <param name="width_filtering" value="fixed"/>
2337 <param name="min_fwhm" value="3.0"/>
2338 <param name="max_fwhm" value="60.0"/>
2339 <param name="masstrace_snr_filtering" value="false"/>
2340 </section>
2341 <section name="ffm">
2342 <param name="local_rt_range" value="10.0"/>
2343 <param name="local_mz_range" value="6.5"/>
2344 <param name="charge_lower_bound" value="1"/>
2345 <param name="charge_upper_bound" value="3"/>
2346 <param name="report_summed_ints" value="false"/>
2347 <param name="enable_RT_filtering" value="true"/>
2348 <param name="isotope_filtering_model" value="none"/>
2349 <param name="mz_scoring_13C" value="true"/>
2350 <param name="use_smoothed_intensities" value="true"/>
2351 <param name="report_convex_hulls" value="true"/>
2352 <param name="remove_single_traces" value="true"/>
2353 <param name="mz_scoring_by_elements" value="false"/>
2354 <param name="elements" value="CHNOPS"/>
2355 </section>
2356 </section>
2357 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2358 <output name="ctd_out" ftype="xml">
2359 <assert_contents>
2360 <is_valid_xml/>
2361 </assert_contents>
2362 </output>
2363 </test>
2364 <test expect_num_outputs="2">
2365 <conditional name="adv_opts_cond">
2366 <param name="adv_opts_selector" value="advanced"/>
2367 <param name="force" value="false"/>
2368 <param name="test" value="true"/>
2369 </conditional>
2370 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2371 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2372 <section name="algorithm">
2373 <section name="common">
2374 <param name="noise_threshold_int" value="10.0"/>
2375 <param name="chrom_peak_snr" value="3.0"/>
2376 <param name="chrom_fwhm" value="5.0"/>
2377 </section>
2378 <section name="mtd">
2379 <param name="mass_error_ppm" value="20.0"/>
2380 <param name="reestimate_mt_sd" value="true"/>
2381 <param name="quant_method" value="max_height"/>
2382 <param name="trace_termination_criterion" value="outlier"/>
2383 <param name="trace_termination_outliers" value="5"/>
2384 <param name="min_sample_rate" value="0.5"/>
2385 <param name="min_trace_length" value="5.0"/>
2386 <param name="max_trace_length" value="300.0"/>
2387 </section>
2388 <section name="epd">
2389 <param name="enabled" value="true"/>
2390 <param name="width_filtering" value="off"/>
2391 <param name="min_fwhm" value="3.0"/>
2392 <param name="max_fwhm" value="60.0"/>
2393 <param name="masstrace_snr_filtering" value="false"/>
2394 </section>
2395 <section name="ffm">
2396 <param name="local_rt_range" value="10.0"/>
2397 <param name="local_mz_range" value="6.5"/>
2398 <param name="charge_lower_bound" value="1"/>
2399 <param name="charge_upper_bound" value="3"/>
2400 <param name="report_summed_ints" value="false"/>
2401 <param name="enable_RT_filtering" value="true"/>
2402 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2403 <param name="mz_scoring_13C" value="true"/>
2404 <param name="use_smoothed_intensities" value="true"/>
2405 <param name="report_convex_hulls" value="false"/>
2406 <param name="remove_single_traces" value="false"/>
2407 <param name="mz_scoring_by_elements" value="false"/>
2408 <param name="elements" value="CHNOPS"/>
2409 </section>
2410 </section>
2411 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2412 <output name="ctd_out" ftype="xml">
2413 <assert_contents>
2414 <is_valid_xml/>
2415 </assert_contents>
2416 </output>
2417 </test>
2418 </xml>
2419 <xml name="autotest_FeatureFinderMRM">
2420 <test expect_num_outputs="2">
2421 <conditional name="adv_opts_cond">
2422 <param name="adv_opts_selector" value="advanced"/>
2423 <param name="force" value="false"/>
2424 <param name="test" value="true"/>
2425 </conditional>
2426 <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
2427 <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2428 <section name="algorithm">
2429 <param name="min_rt_distance" value="10.0"/>
2430 <param name="min_num_peaks_per_feature" value="5"/>
2431 <param name="min_signal_to_noise_ratio" value="2.0"/>
2432 <param name="write_debug_files" value="false"/>
2433 <param name="resample_traces" value="false"/>
2434 <param name="write_debuginfo" value="false"/>
2435 </section>
2436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2437 <output name="ctd_out" ftype="xml">
2438 <assert_contents>
2439 <is_valid_xml/>
2440 </assert_contents>
2441 </output>
2442 </test>
2443 </xml>
2444 <xml name="autotest_FeatureFinderMultiplex">
2445 <test expect_num_outputs="3">
2446 <conditional name="adv_opts_cond">
2447 <param name="adv_opts_selector" value="advanced"/>
2448 <param name="force" value="false"/>
2449 <param name="test" value="true"/>
2450 </conditional>
2451 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
2452 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2453 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2454 <section name="algorithm">
2455 <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
2456 <param name="charge" value="1:4"/>
2457 <param name="isotopes_per_peptide" value="3:6"/>
2458 <param name="rt_typical" value="90.0"/>
2459 <param name="rt_band" value="10.0"/>
2460 <param name="rt_min" value="5.0"/>
2461 <param name="mz_tolerance" value="40.0"/>
2462 <param name="mz_unit" value="ppm"/>
2463 <param name="intensity_cutoff" value="10.0"/>
2464 <param name="peptide_similarity" value="0.8"/>
2465 <param name="averagine_similarity" value="0.75"/>
2466 <param name="averagine_similarity_scaling" value="0.75"/>
2467 <param name="missed_cleavages" value="1"/>
2468 <param name="spectrum_type" value="automatic"/>
2469 <param name="averagine_type" value="peptide"/>
2470 <param name="knock_out" value="false"/>
2471 </section>
2472 <section name="labels">
2473 <param name="Arg6" value="6.0201290268"/>
2474 <param name="Arg10" value="10.0082686"/>
2475 <param name="Lys4" value="4.0251069836"/>
2476 <param name="Lys6" value="6.0201290268"/>
2477 <param name="Lys8" value="8.0141988132"/>
2478 <param name="Leu3" value="3.01883"/>
2479 <param name="Dimethyl0" value="28.0313"/>
2480 <param name="Dimethyl4" value="32.056407"/>
2481 <param name="Dimethyl6" value="34.063117"/>
2482 <param name="Dimethyl8" value="36.07567"/>
2483 <param name="ICPL0" value="105.021464"/>
2484 <param name="ICPL4" value="109.046571"/>
2485 <param name="ICPL6" value="111.041593"/>
2486 <param name="ICPL10" value="115.0667"/>
2487 </section>
2488 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2489 <output name="ctd_out" ftype="xml">
2490 <assert_contents>
2491 <is_valid_xml/>
2492 </assert_contents>
2493 </output>
2494 </test>
2495 <test expect_num_outputs="3">
2496 <conditional name="adv_opts_cond">
2497 <param name="adv_opts_selector" value="advanced"/>
2498 <param name="force" value="false"/>
2499 <param name="test" value="true"/>
2500 </conditional>
2501 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
2502 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2503 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2504 <section name="algorithm">
2505 <param name="labels" value="[][Lys8,Arg10]"/>
2506 <param name="charge" value="1:4"/>
2507 <param name="isotopes_per_peptide" value="3:6"/>
2508 <param name="rt_typical" value="40.0"/>
2509 <param name="rt_band" value="5.0"/>
2510 <param name="rt_min" value="2.0"/>
2511 <param name="mz_tolerance" value="6.0"/>
2512 <param name="mz_unit" value="ppm"/>
2513 <param name="intensity_cutoff" value="1000.0"/>
2514 <param name="peptide_similarity" value="0.5"/>
2515 <param name="averagine_similarity" value="0.4"/>
2516 <param name="averagine_similarity_scaling" value="0.75"/>
2517 <param name="missed_cleavages" value="0"/>
2518 <param name="spectrum_type" value="automatic"/>
2519 <param name="averagine_type" value="peptide"/>
2520 <param name="knock_out" value="false"/>
2521 </section>
2522 <section name="labels">
2523 <param name="Arg6" value="6.0201290268"/>
2524 <param name="Arg10" value="10.0082686"/>
2525 <param name="Lys4" value="4.0251069836"/>
2526 <param name="Lys6" value="6.0201290268"/>
2527 <param name="Lys8" value="8.0141988132"/>
2528 <param name="Leu3" value="3.01883"/>
2529 <param name="Dimethyl0" value="28.0313"/>
2530 <param name="Dimethyl4" value="32.056407"/>
2531 <param name="Dimethyl6" value="34.063117"/>
2532 <param name="Dimethyl8" value="36.07567"/>
2533 <param name="ICPL0" value="105.021464"/>
2534 <param name="ICPL4" value="109.046571"/>
2535 <param name="ICPL6" value="111.041593"/>
2536 <param name="ICPL10" value="115.0667"/>
2537 </section>
2538 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2539 <output name="ctd_out" ftype="xml">
2540 <assert_contents>
2541 <is_valid_xml/>
2542 </assert_contents>
2543 </output>
2544 </test>
2545 <test expect_num_outputs="3">
2546 <conditional name="adv_opts_cond">
2547 <param name="adv_opts_selector" value="advanced"/>
2548 <param name="force" value="false"/>
2549 <param name="test" value="true"/>
2550 </conditional>
2551 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
2552 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2553 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2554 <section name="algorithm">
2555 <param name="labels" value="[]"/>
2556 <param name="charge" value="5:15"/>
2557 <param name="isotopes_per_peptide" value="5:10"/>
2558 <param name="rt_typical" value="45.0"/>
2559 <param name="rt_band" value="5.0"/>
2560 <param name="rt_min" value="2.0"/>
2561 <param name="mz_tolerance" value="6.0"/>
2562 <param name="mz_unit" value="ppm"/>
2563 <param name="intensity_cutoff" value="200.0"/>
2564 <param name="peptide_similarity" value="0.5"/>
2565 <param name="averagine_similarity" value="0.4"/>
2566 <param name="averagine_similarity_scaling" value="0.75"/>
2567 <param name="missed_cleavages" value="0"/>
2568 <param name="spectrum_type" value="automatic"/>
2569 <param name="averagine_type" value="RNA"/>
2570 <param name="knock_out" value="false"/>
2571 </section>
2572 <section name="labels">
2573 <param name="Arg6" value="6.0201290268"/>
2574 <param name="Arg10" value="10.0082686"/>
2575 <param name="Lys4" value="4.0251069836"/>
2576 <param name="Lys6" value="6.0201290268"/>
2577 <param name="Lys8" value="8.0141988132"/>
2578 <param name="Leu3" value="3.01883"/>
2579 <param name="Dimethyl0" value="28.0313"/>
2580 <param name="Dimethyl4" value="32.056407"/>
2581 <param name="Dimethyl6" value="34.063117"/>
2582 <param name="Dimethyl8" value="36.07567"/>
2583 <param name="ICPL0" value="105.021464"/>
2584 <param name="ICPL4" value="109.046571"/>
2585 <param name="ICPL6" value="111.041593"/>
2586 <param name="ICPL10" value="115.0667"/>
2587 </section>
2588 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2589 <output name="ctd_out" ftype="xml">
2590 <assert_contents>
2591 <is_valid_xml/>
2592 </assert_contents>
2593 </output>
2594 </test>
2595 <test expect_num_outputs="3">
2596 <conditional name="adv_opts_cond">
2597 <param name="adv_opts_selector" value="advanced"/>
2598 <param name="force" value="false"/>
2599 <param name="test" value="true"/>
2600 </conditional>
2601 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
2602 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2603 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2604 <section name="algorithm">
2605 <param name="labels" value="[]"/>
2606 <param name="charge" value="5:15"/>
2607 <param name="isotopes_per_peptide" value="5:10"/>
2608 <param name="rt_typical" value="45.0"/>
2609 <param name="rt_band" value="5.0"/>
2610 <param name="rt_min" value="2.0"/>
2611 <param name="mz_tolerance" value="6.0"/>
2612 <param name="mz_unit" value="ppm"/>
2613 <param name="intensity_cutoff" value="200.0"/>
2614 <param name="peptide_similarity" value="0.5"/>
2615 <param name="averagine_similarity" value="0.4"/>
2616 <param name="averagine_similarity_scaling" value="0.75"/>
2617 <param name="missed_cleavages" value="0"/>
2618 <param name="spectrum_type" value="automatic"/>
2619 <param name="averagine_type" value="DNA"/>
2620 <param name="knock_out" value="false"/>
2621 </section>
2622 <section name="labels">
2623 <param name="Arg6" value="6.0201290268"/>
2624 <param name="Arg10" value="10.0082686"/>
2625 <param name="Lys4" value="4.0251069836"/>
2626 <param name="Lys6" value="6.0201290268"/>
2627 <param name="Lys8" value="8.0141988132"/>
2628 <param name="Leu3" value="3.01883"/>
2629 <param name="Dimethyl0" value="28.0313"/>
2630 <param name="Dimethyl4" value="32.056407"/>
2631 <param name="Dimethyl6" value="34.063117"/>
2632 <param name="Dimethyl8" value="36.07567"/>
2633 <param name="ICPL0" value="105.021464"/>
2634 <param name="ICPL4" value="109.046571"/>
2635 <param name="ICPL6" value="111.041593"/>
2636 <param name="ICPL10" value="115.0667"/>
2637 </section>
2638 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2639 <output name="ctd_out" ftype="xml">
2640 <assert_contents>
2641 <is_valid_xml/>
2642 </assert_contents>
2643 </output>
2644 </test>
2645 <test expect_num_outputs="3">
2646 <conditional name="adv_opts_cond">
2647 <param name="adv_opts_selector" value="advanced"/>
2648 <param name="force" value="false"/>
2649 <param name="test" value="true"/>
2650 </conditional>
2651 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
2652 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2653 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2654 <section name="algorithm">
2655 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2656 <param name="charge" value="1:5"/>
2657 <param name="isotopes_per_peptide" value="3:6"/>
2658 <param name="rt_typical" value="50.0"/>
2659 <param name="rt_band" value="3.0"/>
2660 <param name="rt_min" value="8.0"/>
2661 <param name="mz_tolerance" value="10.0"/>
2662 <param name="mz_unit" value="ppm"/>
2663 <param name="intensity_cutoff" value="10000000.0"/>
2664 <param name="peptide_similarity" value="0.95"/>
2665 <param name="averagine_similarity" value="0.8"/>
2666 <param name="averagine_similarity_scaling" value="0.95"/>
2667 <param name="missed_cleavages" value="3"/>
2668 <param name="spectrum_type" value="profile"/>
2669 <param name="averagine_type" value="peptide"/>
2670 <param name="knock_out" value="false"/>
2671 </section>
2672 <section name="labels">
2673 <param name="Arg6" value="6.0201290268"/>
2674 <param name="Arg10" value="10.0082686"/>
2675 <param name="Lys4" value="4.0251069836"/>
2676 <param name="Lys6" value="6.0201290268"/>
2677 <param name="Lys8" value="8.0141988132"/>
2678 <param name="Leu3" value="3.01883"/>
2679 <param name="Dimethyl0" value="28.0313"/>
2680 <param name="Dimethyl4" value="32.056407"/>
2681 <param name="Dimethyl6" value="34.063117"/>
2682 <param name="Dimethyl8" value="36.07567"/>
2683 <param name="ICPL0" value="105.021464"/>
2684 <param name="ICPL4" value="109.046571"/>
2685 <param name="ICPL6" value="111.041593"/>
2686 <param name="ICPL10" value="115.0667"/>
2687 </section>
2688 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2689 <output name="ctd_out" ftype="xml">
2690 <assert_contents>
2691 <is_valid_xml/>
2692 </assert_contents>
2693 </output>
2694 </test>
2695 <test expect_num_outputs="3">
2696 <conditional name="adv_opts_cond">
2697 <param name="adv_opts_selector" value="advanced"/>
2698 <param name="force" value="false"/>
2699 <param name="test" value="true"/>
2700 </conditional>
2701 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
2702 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2703 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2704 <section name="algorithm">
2705 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2706 <param name="charge" value="1:5"/>
2707 <param name="isotopes_per_peptide" value="3:6"/>
2708 <param name="rt_typical" value="50.0"/>
2709 <param name="rt_band" value="3.0"/>
2710 <param name="rt_min" value="8.0"/>
2711 <param name="mz_tolerance" value="10.0"/>
2712 <param name="mz_unit" value="ppm"/>
2713 <param name="intensity_cutoff" value="10000000.0"/>
2714 <param name="peptide_similarity" value="0.95"/>
2715 <param name="averagine_similarity" value="0.8"/>
2716 <param name="averagine_similarity_scaling" value="1.0"/>
2717 <param name="missed_cleavages" value="3"/>
2718 <param name="spectrum_type" value="profile"/>
2719 <param name="averagine_type" value="peptide"/>
2720 <param name="knock_out" value="false"/>
2721 </section>
2722 <section name="labels">
2723 <param name="Arg6" value="6.0201290268"/>
2724 <param name="Arg10" value="10.0082686"/>
2725 <param name="Lys4" value="4.0251069836"/>
2726 <param name="Lys6" value="6.0201290268"/>
2727 <param name="Lys8" value="8.0141988132"/>
2728 <param name="Leu3" value="3.01883"/>
2729 <param name="Dimethyl0" value="28.0313"/>
2730 <param name="Dimethyl4" value="32.056407"/>
2731 <param name="Dimethyl6" value="34.063117"/>
2732 <param name="Dimethyl8" value="36.07567"/>
2733 <param name="ICPL0" value="105.021464"/>
2734 <param name="ICPL4" value="109.046571"/>
2735 <param name="ICPL6" value="111.041593"/>
2736 <param name="ICPL10" value="115.0667"/>
2737 </section>
2738 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2739 <output name="ctd_out" ftype="xml">
2740 <assert_contents>
2741 <is_valid_xml/>
2742 </assert_contents>
2743 </output>
2744 </test>
2745 <test expect_num_outputs="3">
2746 <conditional name="adv_opts_cond">
2747 <param name="adv_opts_selector" value="advanced"/>
2748 <param name="force" value="false"/>
2749 <param name="test" value="true"/>
2750 </conditional>
2751 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
2752 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2753 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2754 <section name="algorithm">
2755 <param name="labels" value="[][Dimethyl4]"/>
2756 <param name="charge" value="1:4"/>
2757 <param name="isotopes_per_peptide" value="3:6"/>
2758 <param name="rt_typical" value="40.0"/>
2759 <param name="rt_band" value="5.0"/>
2760 <param name="rt_min" value="2.0"/>
2761 <param name="mz_tolerance" value="6.0"/>
2762 <param name="mz_unit" value="ppm"/>
2763 <param name="intensity_cutoff" value="1000.0"/>
2764 <param name="peptide_similarity" value="0.5"/>
2765 <param name="averagine_similarity" value="0.4"/>
2766 <param name="averagine_similarity_scaling" value="0.75"/>
2767 <param name="missed_cleavages" value="0"/>
2768 <param name="spectrum_type" value="automatic"/>
2769 <param name="averagine_type" value="peptide"/>
2770 <param name="knock_out" value="false"/>
2771 </section>
2772 <section name="labels">
2773 <param name="Arg6" value="6.0201290268"/>
2774 <param name="Arg10" value="10.0082686"/>
2775 <param name="Lys4" value="4.0251069836"/>
2776 <param name="Lys6" value="6.0201290268"/>
2777 <param name="Lys8" value="8.0141988132"/>
2778 <param name="Leu3" value="3.01883"/>
2779 <param name="Dimethyl0" value="28.0313"/>
2780 <param name="Dimethyl4" value="31.0094"/>
2781 <param name="Dimethyl6" value="34.063117"/>
2782 <param name="Dimethyl8" value="36.07567"/>
2783 <param name="ICPL0" value="105.021464"/>
2784 <param name="ICPL4" value="109.046571"/>
2785 <param name="ICPL6" value="111.041593"/>
2786 <param name="ICPL10" value="115.0667"/>
2787 </section>
2788 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2789 <output name="ctd_out" ftype="xml">
2790 <assert_contents>
2791 <is_valid_xml/>
2792 </assert_contents>
2793 </output>
2794 </test>
2795 <test expect_num_outputs="3">
2796 <conditional name="adv_opts_cond">
2797 <param name="adv_opts_selector" value="advanced"/>
2798 <param name="force" value="false"/>
2799 <param name="test" value="true"/>
2800 </conditional>
2801 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
2802 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2803 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2804 <section name="algorithm">
2805 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
2806 <param name="charge" value="1:7"/>
2807 <param name="isotopes_per_peptide" value="3:8"/>
2808 <param name="rt_typical" value="50.0"/>
2809 <param name="rt_band" value="3.0"/>
2810 <param name="rt_min" value="8.0"/>
2811 <param name="mz_tolerance" value="10.0"/>
2812 <param name="mz_unit" value="ppm"/>
2813 <param name="intensity_cutoff" value="10.0"/>
2814 <param name="peptide_similarity" value="0.2"/>
2815 <param name="averagine_similarity" value="0.25"/>
2816 <param name="averagine_similarity_scaling" value="0.95"/>
2817 <param name="missed_cleavages" value="4"/>
2818 <param name="spectrum_type" value="automatic"/>
2819 <param name="averagine_type" value="peptide"/>
2820 <param name="knock_out" value="true"/>
2821 </section>
2822 <section name="labels">
2823 <param name="Arg6" value="6.0201290268"/>
2824 <param name="Arg10" value="10.0082686"/>
2825 <param name="Lys4" value="4.0251069836"/>
2826 <param name="Lys6" value="6.0201290268"/>
2827 <param name="Lys8" value="8.0141988132"/>
2828 <param name="Leu3" value="3.01883"/>
2829 <param name="Dimethyl0" value="28.0313"/>
2830 <param name="Dimethyl4" value="32.056407"/>
2831 <param name="Dimethyl6" value="34.063117"/>
2832 <param name="Dimethyl8" value="36.07567"/>
2833 <param name="ICPL0" value="105.021464"/>
2834 <param name="ICPL4" value="109.046571"/>
2835 <param name="ICPL6" value="111.041593"/>
2836 <param name="ICPL10" value="115.0667"/>
2837 </section>
2838 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2839 <output name="ctd_out" ftype="xml">
2840 <assert_contents>
2841 <is_valid_xml/>
2842 </assert_contents>
2843 </output>
2844 </test>
2845 <test expect_num_outputs="3">
2846 <conditional name="adv_opts_cond">
2847 <param name="adv_opts_selector" value="advanced"/>
2848 <param name="force" value="false"/>
2849 <param name="test" value="true"/>
2850 </conditional>
2851 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
2852 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2853 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2854 <section name="algorithm">
2855 <param name="labels" value="[0][6.03705]"/>
2856 <param name="charge" value="2:8"/>
2857 <param name="isotopes_per_peptide" value="3:8"/>
2858 <param name="rt_typical" value="40.0"/>
2859 <param name="rt_band" value="0.0"/>
2860 <param name="rt_min" value="4.0"/>
2861 <param name="mz_tolerance" value="10.0"/>
2862 <param name="mz_unit" value="ppm"/>
2863 <param name="intensity_cutoff" value="1000.0"/>
2864 <param name="peptide_similarity" value="0.5"/>
2865 <param name="averagine_similarity" value="0.4"/>
2866 <param name="averagine_similarity_scaling" value="0.95"/>
2867 <param name="missed_cleavages" value="0"/>
2868 <param name="spectrum_type" value="centroid"/>
2869 <param name="averagine_type" value="peptide"/>
2870 <param name="knock_out" value="false"/>
2871 </section>
2872 <section name="labels">
2873 <param name="Arg6" value="6.0201290268"/>
2874 <param name="Arg10" value="10.0082686"/>
2875 <param name="Lys4" value="4.0251069836"/>
2876 <param name="Lys6" value="6.0201290268"/>
2877 <param name="Lys8" value="8.0141988132"/>
2878 <param name="Leu3" value="3.01883"/>
2879 <param name="Dimethyl0" value="28.0313"/>
2880 <param name="Dimethyl4" value="32.056407"/>
2881 <param name="Dimethyl6" value="34.063117"/>
2882 <param name="Dimethyl8" value="36.07567"/>
2883 <param name="ICPL0" value="105.021464"/>
2884 <param name="ICPL4" value="109.046571"/>
2885 <param name="ICPL6" value="111.041593"/>
2886 <param name="ICPL10" value="115.0667"/>
2887 </section>
2888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2889 <output name="ctd_out" ftype="xml">
2890 <assert_contents>
2891 <is_valid_xml/>
2892 </assert_contents>
2893 </output>
2894 </test>
2895 <test expect_num_outputs="3">
2896 <conditional name="adv_opts_cond">
2897 <param name="adv_opts_selector" value="advanced"/>
2898 <param name="force" value="false"/>
2899 <param name="test" value="true"/>
2900 </conditional>
2901 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
2902 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2903 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2904 <section name="algorithm">
2905 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2906 <param name="charge" value="1:7"/>
2907 <param name="isotopes_per_peptide" value="3:6"/>
2908 <param name="rt_typical" value="50.0"/>
2909 <param name="rt_band" value="5.0"/>
2910 <param name="rt_min" value="8.0"/>
2911 <param name="mz_tolerance" value="6.0"/>
2912 <param name="mz_unit" value="ppm"/>
2913 <param name="intensity_cutoff" value="10.0"/>
2914 <param name="peptide_similarity" value="0.4"/>
2915 <param name="averagine_similarity" value="0.5"/>
2916 <param name="averagine_similarity_scaling" value="0.95"/>
2917 <param name="missed_cleavages" value="3"/>
2918 <param name="spectrum_type" value="profile"/>
2919 <param name="averagine_type" value="peptide"/>
2920 <param name="knock_out" value="true"/>
2921 </section>
2922 <section name="labels">
2923 <param name="Arg6" value="6.0201290268"/>
2924 <param name="Arg10" value="10.0082686"/>
2925 <param name="Lys4" value="4.0251069836"/>
2926 <param name="Lys6" value="6.0201290268"/>
2927 <param name="Lys8" value="8.0141988132"/>
2928 <param name="Leu3" value="3.01883"/>
2929 <param name="Dimethyl0" value="28.0313"/>
2930 <param name="Dimethyl4" value="32.056407"/>
2931 <param name="Dimethyl6" value="34.063117"/>
2932 <param name="Dimethyl8" value="36.07567"/>
2933 <param name="ICPL0" value="105.021464"/>
2934 <param name="ICPL4" value="109.046571"/>
2935 <param name="ICPL6" value="111.041593"/>
2936 <param name="ICPL10" value="115.0667"/>
2937 </section>
2938 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2939 <output name="ctd_out" ftype="xml">
2940 <assert_contents>
2941 <is_valid_xml/>
2942 </assert_contents>
2943 </output>
2944 </test>
2945 <test expect_num_outputs="2">
2946 <conditional name="adv_opts_cond">
2947 <param name="adv_opts_selector" value="advanced"/>
2948 <param name="force" value="false"/>
2949 <param name="test" value="true"/>
2950 </conditional>
2951 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
2952 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2953 <section name="algorithm">
2954 <param name="labels" value="[]"/>
2955 <param name="charge" value="1:4"/>
2956 <param name="isotopes_per_peptide" value="3:6"/>
2957 <param name="rt_typical" value="1e-05"/>
2958 <param name="rt_band" value="0.0"/>
2959 <param name="rt_min" value="0.0"/>
2960 <param name="mz_tolerance" value="10.0"/>
2961 <param name="mz_unit" value="ppm"/>
2962 <param name="intensity_cutoff" value="1000.0"/>
2963 <param name="peptide_similarity" value="0.5"/>
2964 <param name="averagine_similarity" value="0.7"/>
2965 <param name="averagine_similarity_scaling" value="0.95"/>
2966 <param name="missed_cleavages" value="0"/>
2967 <param name="spectrum_type" value="automatic"/>
2968 <param name="averagine_type" value="peptide"/>
2969 <param name="knock_out" value="false"/>
2970 </section>
2971 <section name="labels">
2972 <param name="Arg6" value="6.0201290268"/>
2973 <param name="Arg10" value="10.0082686"/>
2974 <param name="Lys4" value="4.0251069836"/>
2975 <param name="Lys6" value="6.0201290268"/>
2976 <param name="Lys8" value="8.0141988132"/>
2977 <param name="Leu3" value="3.01883"/>
2978 <param name="Dimethyl0" value="28.0313"/>
2979 <param name="Dimethyl4" value="32.056407"/>
2980 <param name="Dimethyl6" value="34.063117"/>
2981 <param name="Dimethyl8" value="36.07567"/>
2982 <param name="ICPL0" value="105.021464"/>
2983 <param name="ICPL4" value="109.046571"/>
2984 <param name="ICPL6" value="111.041593"/>
2985 <param name="ICPL10" value="115.0667"/>
2986 </section>
2987 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
2988 <output name="ctd_out" ftype="xml">
2989 <assert_contents>
2990 <is_valid_xml/>
2991 </assert_contents>
2992 </output>
2993 </test>
2994 </xml>
2995 <xml name="autotest_FeatureFinderSuperHirn">
2996 <test expect_num_outputs="2">
2997 <conditional name="adv_opts_cond">
2998 <param name="adv_opts_selector" value="advanced"/>
2999 <param name="force" value="false"/>
3000 <param name="test" value="true"/>
3001 </conditional>
3002 <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/>
3003 <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3004 <section name="algorithm">
3005 <section name="centroiding">
3006 <param name="active" value="false"/>
3007 <param name="window_width" value="5"/>
3008 <param name="absolute_isotope_mass_precision" value="0.01"/>
3009 <param name="relative_isotope_mass_precision" value="10.0"/>
3010 <param name="minimal_peak_height" value="0.0"/>
3011 <param name="min_ms_signal_intensity" value="50.0"/>
3012 </section>
3013 <section name="ms1">
3014 <param name="precursor_detection_scan_levels" value="1"/>
3015 <param name="max_inter_scan_distance" value="0"/>
3016 <param name="tr_resolution" value="0.01"/>
3017 <param name="intensity_threshold" value="1000.0"/>
3018 <param name="max_inter_scan_rt_distance" value="0.1"/>
3019 <param name="min_nb_cluster_members" value="4"/>
3020 <param name="detectable_isotope_factor" value="0.05"/>
3021 <param name="intensity_cv" value="0.9"/>
3022 <param name="retention_time_tolerance" value="0.5"/>
3023 <param name="mz_tolerance" value="0.0"/>
3024 </section>
3025 <section name="ms1_feature_merger">
3026 <param name="active" value="true"/>
3027 <param name="tr_resolution" value="0.01"/>
3028 <param name="initial_apex_tr_tolerance" value="5.0"/>
3029 <param name="feature_merging_tr_tolerance" value="1.0"/>
3030 <param name="intensity_variation_percentage" value="25.0"/>
3031 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3032 </section>
3033 <section name="ms1_feature_selection_options">
3034 <param name="start_elution_window" value="0.0"/>
3035 <param name="end_elution_window" value="180.0"/>
3036 <param name="mz_range_min" value="0.0"/>
3037 <param name="mz_range_max" value="2000.0"/>
3038 <param name="chrg_range_min" value="1"/>
3039 <param name="chrg_range_max" value="5"/>
3040 </section>
3041 </section>
3042 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3043 <output name="ctd_out" ftype="xml">
3044 <assert_contents>
3045 <is_valid_xml/>
3046 </assert_contents>
3047 </output>
3048 </test>
3049 <test expect_num_outputs="2">
3050 <conditional name="adv_opts_cond">
3051 <param name="adv_opts_selector" value="advanced"/>
3052 <param name="force" value="false"/>
3053 <param name="test" value="true"/>
3054 </conditional>
3055 <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/>
3056 <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3057 <section name="algorithm">
3058 <section name="centroiding">
3059 <param name="active" value="true"/>
3060 <param name="window_width" value="5"/>
3061 <param name="absolute_isotope_mass_precision" value="0.01"/>
3062 <param name="relative_isotope_mass_precision" value="10.0"/>
3063 <param name="minimal_peak_height" value="0.0"/>
3064 <param name="min_ms_signal_intensity" value="50.0"/>
3065 </section>
3066 <section name="ms1">
3067 <param name="precursor_detection_scan_levels" value="1"/>
3068 <param name="max_inter_scan_distance" value="0"/>
3069 <param name="tr_resolution" value="0.01"/>
3070 <param name="intensity_threshold" value="1000.0"/>
3071 <param name="max_inter_scan_rt_distance" value="0.1"/>
3072 <param name="min_nb_cluster_members" value="4"/>
3073 <param name="detectable_isotope_factor" value="0.05"/>
3074 <param name="intensity_cv" value="0.9"/>
3075 <param name="retention_time_tolerance" value="0.5"/>
3076 <param name="mz_tolerance" value="0.0"/>
3077 </section>
3078 <section name="ms1_feature_merger">
3079 <param name="active" value="true"/>
3080 <param name="tr_resolution" value="0.01"/>
3081 <param name="initial_apex_tr_tolerance" value="5.0"/>
3082 <param name="feature_merging_tr_tolerance" value="1.0"/>
3083 <param name="intensity_variation_percentage" value="25.0"/>
3084 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3085 </section>
3086 <section name="ms1_feature_selection_options">
3087 <param name="start_elution_window" value="0.0"/>
3088 <param name="end_elution_window" value="180.0"/>
3089 <param name="mz_range_min" value="0.0"/>
3090 <param name="mz_range_max" value="2000.0"/>
3091 <param name="chrg_range_min" value="1"/>
3092 <param name="chrg_range_max" value="5"/>
3093 </section>
3094 </section>
3095 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3096 <output name="ctd_out" ftype="xml">
3097 <assert_contents>
3098 <is_valid_xml/>
3099 </assert_contents>
3100 </output>
3101 </test>
3102 </xml>
3103 <xml name="autotest_FeatureLinkerLabeled">
3104 <test expect_num_outputs="2">
3105 <conditional name="adv_opts_cond">
3106 <param name="adv_opts_selector" value="advanced"/>
3107 <param name="force" value="false"/>
3108 <param name="test" value="true"/>
3109 </conditional>
3110 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
3111 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3112 <section name="algorithm">
3113 <param name="rt_estimate" value="false"/>
3114 <param name="rt_pair_dist" value="-1.0"/>
3115 <param name="rt_dev_low" value="0.4"/>
3116 <param name="rt_dev_high" value="0.4"/>
3117 <param name="mz_pair_dists" value="8.0"/>
3118 <param name="mz_dev" value="0.1"/>
3119 <param name="mrm" value="false"/>
3120 </section>
3121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3122 <output name="ctd_out" ftype="xml">
3123 <assert_contents>
3124 <is_valid_xml/>
3125 </assert_contents>
3126 </output>
3127 </test>
3128 <test expect_num_outputs="2">
3129 <conditional name="adv_opts_cond">
3130 <param name="adv_opts_selector" value="advanced"/>
3131 <param name="force" value="false"/>
3132 <param name="test" value="true"/>
3133 </conditional>
3134 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
3135 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3136 <section name="algorithm">
3137 <param name="rt_estimate" value="true"/>
3138 <param name="rt_pair_dist" value="-121.0382"/>
3139 <param name="rt_dev_low" value="123.3965"/>
3140 <param name="rt_dev_high" value="123.3965"/>
3141 <param name="mz_pair_dists" value="4.0"/>
3142 <param name="mz_dev" value="0.1"/>
3143 <param name="mrm" value="false"/>
3144 </section>
3145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3146 <output name="ctd_out" ftype="xml">
3147 <assert_contents>
3148 <is_valid_xml/>
3149 </assert_contents>
3150 </output>
3151 </test>
3152 </xml>
3153 <xml name="autotest_FeatureLinkerUnlabeledKD">
3154 <test expect_num_outputs="2">
3155 <conditional name="adv_opts_cond">
3156 <param name="adv_opts_selector" value="advanced"/>
3157 <param name="force" value="false"/>
3158 <param name="test" value="true"/>
3159 </conditional>
3160 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3161 <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3162 <param name="keep_subelements" value="false"/>
3163 <section name="algorithm">
3164 <param name="mz_unit" value="Da"/>
3165 <param name="nr_partitions" value="1"/>
3166 <section name="warp">
3167 <param name="enabled" value="false"/>
3168 <param name="rt_tol" value="100.0"/>
3169 <param name="mz_tol" value="0.3"/>
3170 <param name="max_pairwise_log_fc" value="0.5"/>
3171 <param name="min_rel_cc_size" value="0.5"/>
3172 <param name="max_nr_conflicts" value="0"/>
3173 </section>
3174 <section name="link">
3175 <param name="rt_tol" value="100.0"/>
3176 <param name="mz_tol" value="0.3"/>
3177 <param name="charge_merging" value="With_charge_zero"/>
3178 <param name="adduct_merging" value="Any"/>
3179 </section>
3180 <section name="distance_RT">
3181 <param name="exponent" value="1.0"/>
3182 <param name="weight" value="1.0"/>
3183 </section>
3184 <section name="distance_MZ">
3185 <param name="exponent" value="2.0"/>
3186 <param name="weight" value="1.0"/>
3187 </section>
3188 <section name="distance_intensity">
3189 <param name="exponent" value="1.0"/>
3190 <param name="weight" value="1.0"/>
3191 <param name="log_transform" value="enabled"/>
3192 </section>
3193 <section name="LOWESS">
3194 <param name="span" value="0.666666666666667"/>
3195 <param name="num_iterations" value="3"/>
3196 <param name="delta" value="-1.0"/>
3197 <param name="interpolation_type" value="cspline"/>
3198 <param name="extrapolation_type" value="four-point-linear"/>
3199 </section>
3200 </section>
3201 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3202 <output name="ctd_out" ftype="xml">
3203 <assert_contents>
3204 <is_valid_xml/>
3205 </assert_contents>
3206 </output>
3207 </test>
3208 <test expect_num_outputs="2">
3209 <conditional name="adv_opts_cond">
3210 <param name="adv_opts_selector" value="advanced"/>
3211 <param name="force" value="false"/>
3212 <param name="test" value="true"/>
3213 </conditional>
3214 <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
3215 <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3216 <param name="keep_subelements" value="true"/>
3217 <section name="algorithm">
3218 <param name="mz_unit" value="Da"/>
3219 <param name="nr_partitions" value="99999"/>
3220 <section name="warp">
3221 <param name="enabled" value="false"/>
3222 <param name="rt_tol" value="100.0"/>
3223 <param name="mz_tol" value="0.3"/>
3224 <param name="max_pairwise_log_fc" value="0.5"/>
3225 <param name="min_rel_cc_size" value="0.5"/>
3226 <param name="max_nr_conflicts" value="0"/>
3227 </section>
3228 <section name="link">
3229 <param name="rt_tol" value="100.0"/>
3230 <param name="mz_tol" value="0.3"/>
3231 <param name="charge_merging" value="With_charge_zero"/>
3232 <param name="adduct_merging" value="Any"/>
3233 </section>
3234 <section name="distance_RT">
3235 <param name="exponent" value="1.0"/>
3236 <param name="weight" value="1.0"/>
3237 </section>
3238 <section name="distance_MZ">
3239 <param name="exponent" value="2.0"/>
3240 <param name="weight" value="1.0"/>
3241 </section>
3242 <section name="distance_intensity">
3243 <param name="exponent" value="1.0"/>
3244 <param name="weight" value="1.0"/>
3245 <param name="log_transform" value="enabled"/>
3246 </section>
3247 <section name="LOWESS">
3248 <param name="span" value="0.666666666666667"/>
3249 <param name="num_iterations" value="3"/>
3250 <param name="delta" value="-1.0"/>
3251 <param name="interpolation_type" value="cspline"/>
3252 <param name="extrapolation_type" value="four-point-linear"/>
3253 </section>
3254 </section>
3255 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3256 <output name="ctd_out" ftype="xml">
3257 <assert_contents>
3258 <is_valid_xml/>
3259 </assert_contents>
3260 </output>
3261 </test>
3262 <test expect_num_outputs="2">
3263 <conditional name="adv_opts_cond">
3264 <param name="adv_opts_selector" value="advanced"/>
3265 <param name="force" value="false"/>
3266 <param name="test" value="true"/>
3267 </conditional>
3268 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3269 <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3270 <param name="keep_subelements" value="false"/>
3271 <section name="algorithm">
3272 <param name="mz_unit" value="Da"/>
3273 <param name="nr_partitions" value="100"/>
3274 <section name="warp">
3275 <param name="enabled" value="false"/>
3276 <param name="rt_tol" value="100.0"/>
3277 <param name="mz_tol" value="0.3"/>
3278 <param name="max_pairwise_log_fc" value="0.5"/>
3279 <param name="min_rel_cc_size" value="0.5"/>
3280 <param name="max_nr_conflicts" value="0"/>
3281 </section>
3282 <section name="link">
3283 <param name="rt_tol" value="100.0"/>
3284 <param name="mz_tol" value="0.3"/>
3285 <param name="charge_merging" value="With_charge_zero"/>
3286 <param name="adduct_merging" value="Any"/>
3287 </section>
3288 <section name="distance_RT">
3289 <param name="exponent" value="1.0"/>
3290 <param name="weight" value="1.0"/>
3291 </section>
3292 <section name="distance_MZ">
3293 <param name="exponent" value="2.0"/>
3294 <param name="weight" value="1.0"/>
3295 </section>
3296 <section name="distance_intensity">
3297 <param name="exponent" value="1.0"/>
3298 <param name="weight" value="1.0"/>
3299 <param name="log_transform" value="enabled"/>
3300 </section>
3301 <section name="LOWESS">
3302 <param name="span" value="0.666666666666667"/>
3303 <param name="num_iterations" value="3"/>
3304 <param name="delta" value="-1.0"/>
3305 <param name="interpolation_type" value="cspline"/>
3306 <param name="extrapolation_type" value="four-point-linear"/>
3307 </section>
3308 </section>
3309 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3310 <output name="ctd_out" ftype="xml">
3311 <assert_contents>
3312 <is_valid_xml/>
3313 </assert_contents>
3314 </output>
3315 </test>
3316 <test expect_num_outputs="2">
3317 <conditional name="adv_opts_cond">
3318 <param name="adv_opts_selector" value="advanced"/>
3319 <param name="force" value="false"/>
3320 <param name="test" value="true"/>
3321 </conditional>
3322 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
3323 <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3324 <param name="keep_subelements" value="false"/>
3325 <section name="algorithm">
3326 <param name="mz_unit" value="ppm"/>
3327 <param name="nr_partitions" value="100"/>
3328 <section name="warp">
3329 <param name="enabled" value="true"/>
3330 <param name="rt_tol" value="100.0"/>
3331 <param name="mz_tol" value="5.0"/>
3332 <param name="max_pairwise_log_fc" value="0.5"/>
3333 <param name="min_rel_cc_size" value="0.5"/>
3334 <param name="max_nr_conflicts" value="0"/>
3335 </section>
3336 <section name="link">
3337 <param name="rt_tol" value="30.0"/>
3338 <param name="mz_tol" value="10.0"/>
3339 <param name="charge_merging" value="Identical"/>
3340 <param name="adduct_merging" value="Any"/>
3341 </section>
3342 <section name="distance_RT">
3343 <param name="exponent" value="1.0"/>
3344 <param name="weight" value="1.0"/>
3345 </section>
3346 <section name="distance_MZ">
3347 <param name="exponent" value="2.0"/>
3348 <param name="weight" value="1.0"/>
3349 </section>
3350 <section name="distance_intensity">
3351 <param name="exponent" value="1.0"/>
3352 <param name="weight" value="1.0"/>
3353 <param name="log_transform" value="enabled"/>
3354 </section>
3355 <section name="LOWESS">
3356 <param name="span" value="0.666666666666667"/>
3357 <param name="num_iterations" value="3"/>
3358 <param name="delta" value="-1.0"/>
3359 <param name="interpolation_type" value="cspline"/>
3360 <param name="extrapolation_type" value="four-point-linear"/>
3361 </section>
3362 </section>
3363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3364 <output name="ctd_out" ftype="xml">
3365 <assert_contents>
3366 <is_valid_xml/>
3367 </assert_contents>
3368 </output>
3369 </test>
3370 <test expect_num_outputs="2">
3371 <conditional name="adv_opts_cond">
3372 <param name="adv_opts_selector" value="advanced"/>
3373 <param name="force" value="false"/>
3374 <param name="test" value="true"/>
3375 </conditional>
3376 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
3377 <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3378 <param name="keep_subelements" value="false"/>
3379 <section name="algorithm">
3380 <param name="mz_unit" value="ppm"/>
3381 <param name="nr_partitions" value="100"/>
3382 <section name="warp">
3383 <param name="enabled" value="true"/>
3384 <param name="rt_tol" value="100.0"/>
3385 <param name="mz_tol" value="5.0"/>
3386 <param name="max_pairwise_log_fc" value="0.5"/>
3387 <param name="min_rel_cc_size" value="0.5"/>
3388 <param name="max_nr_conflicts" value="0"/>
3389 </section>
3390 <section name="link">
3391 <param name="rt_tol" value="30.0"/>
3392 <param name="mz_tol" value="10.0"/>
3393 <param name="charge_merging" value="With_charge_zero"/>
3394 <param name="adduct_merging" value="Any"/>
3395 </section>
3396 <section name="distance_RT">
3397 <param name="exponent" value="1.0"/>
3398 <param name="weight" value="1.0"/>
3399 </section>
3400 <section name="distance_MZ">
3401 <param name="exponent" value="2.0"/>
3402 <param name="weight" value="1.0"/>
3403 </section>
3404 <section name="distance_intensity">
3405 <param name="exponent" value="1.0"/>
3406 <param name="weight" value="1.0"/>
3407 <param name="log_transform" value="enabled"/>
3408 </section>
3409 <section name="LOWESS">
3410 <param name="span" value="0.666666666666667"/>
3411 <param name="num_iterations" value="3"/>
3412 <param name="delta" value="-1.0"/>
3413 <param name="interpolation_type" value="cspline"/>
3414 <param name="extrapolation_type" value="four-point-linear"/>
3415 </section>
3416 </section>
3417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3418 <output name="ctd_out" ftype="xml">
3419 <assert_contents>
3420 <is_valid_xml/>
3421 </assert_contents>
3422 </output>
3423 </test>
3424 <test expect_num_outputs="2">
3425 <conditional name="adv_opts_cond">
3426 <param name="adv_opts_selector" value="advanced"/>
3427 <param name="force" value="false"/>
3428 <param name="test" value="true"/>
3429 </conditional>
3430 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
3431 <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3432 <param name="keep_subelements" value="false"/>
3433 <section name="algorithm">
3434 <param name="mz_unit" value="ppm"/>
3435 <param name="nr_partitions" value="100"/>
3436 <section name="warp">
3437 <param name="enabled" value="true"/>
3438 <param name="rt_tol" value="100.0"/>
3439 <param name="mz_tol" value="5.0"/>
3440 <param name="max_pairwise_log_fc" value="0.5"/>
3441 <param name="min_rel_cc_size" value="0.5"/>
3442 <param name="max_nr_conflicts" value="0"/>
3443 </section>
3444 <section name="link">
3445 <param name="rt_tol" value="30.0"/>
3446 <param name="mz_tol" value="10.0"/>
3447 <param name="charge_merging" value="Any"/>
3448 <param name="adduct_merging" value="With_unknown_adducts"/>
3449 </section>
3450 <section name="distance_RT">
3451 <param name="exponent" value="1.0"/>
3452 <param name="weight" value="1.0"/>
3453 </section>
3454 <section name="distance_MZ">
3455 <param name="exponent" value="2.0"/>
3456 <param name="weight" value="1.0"/>
3457 </section>
3458 <section name="distance_intensity">
3459 <param name="exponent" value="1.0"/>
3460 <param name="weight" value="1.0"/>
3461 <param name="log_transform" value="enabled"/>
3462 </section>
3463 <section name="LOWESS">
3464 <param name="span" value="0.666666666666667"/>
3465 <param name="num_iterations" value="3"/>
3466 <param name="delta" value="-1.0"/>
3467 <param name="interpolation_type" value="cspline"/>
3468 <param name="extrapolation_type" value="four-point-linear"/>
3469 </section>
3470 </section>
3471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3472 <output name="ctd_out" ftype="xml">
3473 <assert_contents>
3474 <is_valid_xml/>
3475 </assert_contents>
3476 </output>
3477 </test>
3478 <test expect_num_outputs="2">
3479 <conditional name="adv_opts_cond">
3480 <param name="adv_opts_selector" value="advanced"/>
3481 <param name="force" value="false"/>
3482 <param name="test" value="true"/>
3483 </conditional>
3484 <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
3485 <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3486 <param name="keep_subelements" value="false"/>
3487 <section name="algorithm">
3488 <param name="mz_unit" value="ppm"/>
3489 <param name="nr_partitions" value="100"/>
3490 <section name="warp">
3491 <param name="enabled" value="true"/>
3492 <param name="rt_tol" value="100.0"/>
3493 <param name="mz_tol" value="5.0"/>
3494 <param name="max_pairwise_log_fc" value="0.5"/>
3495 <param name="min_rel_cc_size" value="0.5"/>
3496 <param name="max_nr_conflicts" value="0"/>
3497 </section>
3498 <section name="link">
3499 <param name="rt_tol" value="30.0"/>
3500 <param name="mz_tol" value="10.0"/>
3501 <param name="charge_merging" value="Any"/>
3502 <param name="adduct_merging" value="Identical"/>
3503 </section>
3504 <section name="distance_RT">
3505 <param name="exponent" value="1.0"/>
3506 <param name="weight" value="1.0"/>
3507 </section>
3508 <section name="distance_MZ">
3509 <param name="exponent" value="2.0"/>
3510 <param name="weight" value="1.0"/>
3511 </section>
3512 <section name="distance_intensity">
3513 <param name="exponent" value="1.0"/>
3514 <param name="weight" value="1.0"/>
3515 <param name="log_transform" value="enabled"/>
3516 </section>
3517 <section name="LOWESS">
3518 <param name="span" value="0.666666666666667"/>
3519 <param name="num_iterations" value="3"/>
3520 <param name="delta" value="-1.0"/>
3521 <param name="interpolation_type" value="cspline"/>
3522 <param name="extrapolation_type" value="four-point-linear"/>
3523 </section>
3524 </section>
3525 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3526 <output name="ctd_out" ftype="xml">
3527 <assert_contents>
3528 <is_valid_xml/>
3529 </assert_contents>
3530 </output>
3531 </test>
3532 </xml>
3533 <xml name="autotest_FeatureLinkerUnlabeledQT">
3534 <test expect_num_outputs="2">
3535 <conditional name="adv_opts_cond">
3536 <param name="adv_opts_selector" value="advanced"/>
3537 <param name="force" value="false"/>
3538 <param name="test" value="true"/>
3539 </conditional>
3540 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3541 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3542 <param name="keep_subelements" value="false"/>
3543 <section name="algorithm">
3544 <param name="use_identifications" value="false"/>
3545 <param name="nr_partitions" value="100"/>
3546 <param name="ignore_charge" value="false"/>
3547 <param name="ignore_adduct" value="true"/>
3548 <section name="distance_RT">
3549 <param name="max_difference" value="100.0"/>
3550 <param name="exponent" value="1.0"/>
3551 <param name="weight" value="1.0"/>
3552 </section>
3553 <section name="distance_MZ">
3554 <param name="max_difference" value="0.3"/>
3555 <param name="unit" value="Da"/>
3556 <param name="exponent" value="2.0"/>
3557 <param name="weight" value="1.0"/>
3558 </section>
3559 <section name="distance_intensity">
3560 <param name="exponent" value="1.0"/>
3561 <param name="weight" value="0.0"/>
3562 <param name="log_transform" value="disabled"/>
3563 </section>
3564 </section>
3565 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3566 <output name="ctd_out" ftype="xml">
3567 <assert_contents>
3568 <is_valid_xml/>
3569 </assert_contents>
3570 </output>
3571 </test>
3572 <test expect_num_outputs="2">
3573 <conditional name="adv_opts_cond">
3574 <param name="adv_opts_selector" value="advanced"/>
3575 <param name="force" value="false"/>
3576 <param name="test" value="true"/>
3577 </conditional>
3578 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
3579 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3580 <param name="keep_subelements" value="true"/>
3581 <section name="algorithm">
3582 <param name="use_identifications" value="false"/>
3583 <param name="nr_partitions" value="100"/>
3584 <param name="ignore_charge" value="false"/>
3585 <param name="ignore_adduct" value="true"/>
3586 <section name="distance_RT">
3587 <param name="max_difference" value="100.0"/>
3588 <param name="exponent" value="1.0"/>
3589 <param name="weight" value="1.0"/>
3590 </section>
3591 <section name="distance_MZ">
3592 <param name="max_difference" value="0.3"/>
3593 <param name="unit" value="Da"/>
3594 <param name="exponent" value="2.0"/>
3595 <param name="weight" value="1.0"/>
3596 </section>
3597 <section name="distance_intensity">
3598 <param name="exponent" value="1.0"/>
3599 <param name="weight" value="0.0"/>
3600 <param name="log_transform" value="disabled"/>
3601 </section>
3602 </section>
3603 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3604 <output name="ctd_out" ftype="xml">
3605 <assert_contents>
3606 <is_valid_xml/>
3607 </assert_contents>
3608 </output>
3609 </test>
3610 <test expect_num_outputs="2">
3611 <conditional name="adv_opts_cond">
3612 <param name="adv_opts_selector" value="advanced"/>
3613 <param name="force" value="false"/>
3614 <param name="test" value="true"/>
3615 </conditional>
3616 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3617 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3618 <param name="keep_subelements" value="false"/>
3619 <section name="algorithm">
3620 <param name="use_identifications" value="false"/>
3621 <param name="nr_partitions" value="99999"/>
3622 <param name="ignore_charge" value="false"/>
3623 <param name="ignore_adduct" value="true"/>
3624 <section name="distance_RT">
3625 <param name="max_difference" value="100.0"/>
3626 <param name="exponent" value="1.0"/>
3627 <param name="weight" value="1.0"/>
3628 </section>
3629 <section name="distance_MZ">
3630 <param name="max_difference" value="0.3"/>
3631 <param name="unit" value="Da"/>
3632 <param name="exponent" value="2.0"/>
3633 <param name="weight" value="1.0"/>
3634 </section>
3635 <section name="distance_intensity">
3636 <param name="exponent" value="1.0"/>
3637 <param name="weight" value="0.0"/>
3638 <param name="log_transform" value="disabled"/>
3639 </section>
3640 </section>
3641 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3642 <output name="ctd_out" ftype="xml">
3643 <assert_contents>
3644 <is_valid_xml/>
3645 </assert_contents>
3646 </output>
3647 </test>
3648 <test expect_num_outputs="2">
3649 <conditional name="adv_opts_cond">
3650 <param name="adv_opts_selector" value="advanced"/>
3651 <param name="force" value="false"/>
3652 <param name="test" value="true"/>
3653 </conditional>
3654 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3655 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3656 <param name="keep_subelements" value="false"/>
3657 <section name="algorithm">
3658 <param name="use_identifications" value="true"/>
3659 <param name="nr_partitions" value="100"/>
3660 <param name="ignore_charge" value="false"/>
3661 <param name="ignore_adduct" value="true"/>
3662 <section name="distance_RT">
3663 <param name="max_difference" value="100.0"/>
3664 <param name="exponent" value="1.0"/>
3665 <param name="weight" value="1.0"/>
3666 </section>
3667 <section name="distance_MZ">
3668 <param name="max_difference" value="0.3"/>
3669 <param name="unit" value="Da"/>
3670 <param name="exponent" value="2.0"/>
3671 <param name="weight" value="1.0"/>
3672 </section>
3673 <section name="distance_intensity">
3674 <param name="exponent" value="1.0"/>
3675 <param name="weight" value="0.0"/>
3676 <param name="log_transform" value="disabled"/>
3677 </section>
3678 </section>
3679 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3680 <output name="ctd_out" ftype="xml">
3681 <assert_contents>
3682 <is_valid_xml/>
3683 </assert_contents>
3684 </output>
3685 </test>
3686 <test expect_num_outputs="2">
3687 <conditional name="adv_opts_cond">
3688 <param name="adv_opts_selector" value="advanced"/>
3689 <param name="force" value="false"/>
3690 <param name="test" value="true"/>
3691 </conditional>
3692 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3693 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3694 <param name="keep_subelements" value="false"/>
3695 <section name="algorithm">
3696 <param name="use_identifications" value="false"/>
3697 <param name="nr_partitions" value="100"/>
3698 <param name="ignore_charge" value="false"/>
3699 <param name="ignore_adduct" value="true"/>
3700 <section name="distance_RT">
3701 <param name="max_difference" value="200.0"/>
3702 <param name="exponent" value="1.0"/>
3703 <param name="weight" value="1.0"/>
3704 </section>
3705 <section name="distance_MZ">
3706 <param name="max_difference" value="0.3"/>
3707 <param name="unit" value="Da"/>
3708 <param name="exponent" value="2.0"/>
3709 <param name="weight" value="1.0"/>
3710 </section>
3711 <section name="distance_intensity">
3712 <param name="exponent" value="1.0"/>
3713 <param name="weight" value="0.0"/>
3714 <param name="log_transform" value="disabled"/>
3715 </section>
3716 </section>
3717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3718 <output name="ctd_out" ftype="xml">
3719 <assert_contents>
3720 <is_valid_xml/>
3721 </assert_contents>
3722 </output>
3723 </test>
3724 <test expect_num_outputs="2">
3725 <conditional name="adv_opts_cond">
3726 <param name="adv_opts_selector" value="advanced"/>
3727 <param name="force" value="false"/>
3728 <param name="test" value="true"/>
3729 </conditional>
3730 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3731 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3732 <param name="keep_subelements" value="false"/>
3733 <section name="algorithm">
3734 <param name="use_identifications" value="true"/>
3735 <param name="nr_partitions" value="100"/>
3736 <param name="ignore_charge" value="false"/>
3737 <param name="ignore_adduct" value="true"/>
3738 <section name="distance_RT">
3739 <param name="max_difference" value="200.0"/>
3740 <param name="exponent" value="1.0"/>
3741 <param name="weight" value="1.0"/>
3742 </section>
3743 <section name="distance_MZ">
3744 <param name="max_difference" value="0.3"/>
3745 <param name="unit" value="Da"/>
3746 <param name="exponent" value="2.0"/>
3747 <param name="weight" value="1.0"/>
3748 </section>
3749 <section name="distance_intensity">
3750 <param name="exponent" value="1.0"/>
3751 <param name="weight" value="0.0"/>
3752 <param name="log_transform" value="disabled"/>
3753 </section>
3754 </section>
3755 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3756 <output name="ctd_out" ftype="xml">
3757 <assert_contents>
3758 <is_valid_xml/>
3759 </assert_contents>
3760 </output>
3761 </test>
3762 </xml>
3763 <xml name="autotest_FeatureLinkerUnlabeled">
3764 <test expect_num_outputs="2">
3765 <conditional name="adv_opts_cond">
3766 <param name="adv_opts_selector" value="advanced"/>
3767 <param name="force" value="false"/>
3768 <param name="test" value="true"/>
3769 </conditional>
3770 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3771 <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3772 <param name="keep_subelements" value="false"/>
3773 <section name="algorithm">
3774 <param name="second_nearest_gap" value="2.0"/>
3775 <param name="use_identifications" value="false"/>
3776 <param name="ignore_charge" value="true"/>
3777 <param name="ignore_adduct" value="true"/>
3778 <section name="distance_RT">
3779 <param name="max_difference" value="200.0"/>
3780 <param name="exponent" value="1.0"/>
3781 <param name="weight" value="1.0"/>
3782 </section>
3783 <section name="distance_MZ">
3784 <param name="max_difference" value="0.5"/>
3785 <param name="unit" value="Da"/>
3786 <param name="exponent" value="1.0"/>
3787 <param name="weight" value="1.0"/>
3788 </section>
3789 <section name="distance_intensity">
3790 <param name="exponent" value="1.0"/>
3791 <param name="weight" value="0.0"/>
3792 <param name="log_transform" value="disabled"/>
3793 </section>
3794 </section>
3795 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3796 <output name="ctd_out" ftype="xml">
3797 <assert_contents>
3798 <is_valid_xml/>
3799 </assert_contents>
3800 </output>
3801 </test>
3802 <test expect_num_outputs="2">
3803 <conditional name="adv_opts_cond">
3804 <param name="adv_opts_selector" value="advanced"/>
3805 <param name="force" value="false"/>
3806 <param name="test" value="true"/>
3807 </conditional>
3808 <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
3809 <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3810 <param name="keep_subelements" value="false"/>
3811 <section name="algorithm">
3812 <param name="second_nearest_gap" value="2.0"/>
3813 <param name="use_identifications" value="false"/>
3814 <param name="ignore_charge" value="false"/>
3815 <param name="ignore_adduct" value="true"/>
3816 <section name="distance_RT">
3817 <param name="max_difference" value="100.0"/>
3818 <param name="exponent" value="1.0"/>
3819 <param name="weight" value="1.0"/>
3820 </section>
3821 <section name="distance_MZ">
3822 <param name="max_difference" value="0.3"/>
3823 <param name="unit" value="Da"/>
3824 <param name="exponent" value="2.0"/>
3825 <param name="weight" value="1.0"/>
3826 </section>
3827 <section name="distance_intensity">
3828 <param name="exponent" value="1.0"/>
3829 <param name="weight" value="0.5"/>
3830 <param name="log_transform" value="disabled"/>
3831 </section>
3832 </section>
3833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3834 <output name="ctd_out" ftype="xml">
3835 <assert_contents>
3836 <is_valid_xml/>
3837 </assert_contents>
3838 </output>
3839 </test>
3840 <test expect_num_outputs="2">
3841 <conditional name="adv_opts_cond">
3842 <param name="adv_opts_selector" value="advanced"/>
3843 <param name="force" value="false"/>
3844 <param name="test" value="true"/>
3845 </conditional>
3846 <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
3847 <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3848 <param name="keep_subelements" value="false"/>
3849 <section name="algorithm">
3850 <param name="second_nearest_gap" value="1.5"/>
3851 <param name="use_identifications" value="false"/>
3852 <param name="ignore_charge" value="true"/>
3853 <param name="ignore_adduct" value="true"/>
3854 <section name="distance_RT">
3855 <param name="max_difference" value="30.0"/>
3856 <param name="exponent" value="1.0"/>
3857 <param name="weight" value="1.0"/>
3858 </section>
3859 <section name="distance_MZ">
3860 <param name="max_difference" value="0.3"/>
3861 <param name="unit" value="Da"/>
3862 <param name="exponent" value="2.0"/>
3863 <param name="weight" value="1.0"/>
3864 </section>
3865 <section name="distance_intensity">
3866 <param name="exponent" value="1.0"/>
3867 <param name="weight" value="0.0"/>
3868 <param name="log_transform" value="disabled"/>
3869 </section>
3870 </section>
3871 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3872 <output name="ctd_out" ftype="xml">
3873 <assert_contents>
3874 <is_valid_xml/>
3875 </assert_contents>
3876 </output>
3877 </test>
3878 <test expect_num_outputs="2">
3879 <conditional name="adv_opts_cond">
3880 <param name="adv_opts_selector" value="advanced"/>
3881 <param name="force" value="false"/>
3882 <param name="test" value="true"/>
3883 </conditional>
3884 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3885 <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3886 <param name="keep_subelements" value="false"/>
3887 <section name="algorithm">
3888 <param name="second_nearest_gap" value="2.0"/>
3889 <param name="use_identifications" value="true"/>
3890 <param name="ignore_charge" value="true"/>
3891 <param name="ignore_adduct" value="true"/>
3892 <section name="distance_RT">
3893 <param name="max_difference" value="200.0"/>
3894 <param name="exponent" value="2.0"/>
3895 <param name="weight" value="1.0"/>
3896 </section>
3897 <section name="distance_MZ">
3898 <param name="max_difference" value="0.5"/>
3899 <param name="unit" value="Da"/>
3900 <param name="exponent" value="2.0"/>
3901 <param name="weight" value="1.0"/>
3902 </section>
3903 <section name="distance_intensity">
3904 <param name="exponent" value="1.0"/>
3905 <param name="weight" value="0.0"/>
3906 <param name="log_transform" value="disabled"/>
3907 </section>
3908 </section>
3909 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3910 <output name="ctd_out" ftype="xml">
3911 <assert_contents>
3912 <is_valid_xml/>
3913 </assert_contents>
3914 </output>
3915 </test>
3916 </xml>
3917 <xml name="autotest_FFEval">
3918 </xml>
3919 <xml name="autotest_FidoAdapter">
3920 <test expect_num_outputs="2">
3921 <conditional name="adv_opts_cond">
3922 <param name="adv_opts_selector" value="advanced"/>
3923 <param name="keep_zero_group" value="false"/>
3924 <param name="accuracy" value=""/>
3925 <param name="log2_states_precalc" value="0"/>
3926 <param name="force" value="false"/>
3927 <param name="test" value="true"/>
3928 </conditional>
3929 <param name="in" value="FidoAdapter_1_input.idXML"/>
3930 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
3931 <param name="separate_runs" value="false"/>
3932 <param name="greedy_group_resolution" value="false"/>
3933 <param name="no_cleanup" value="false"/>
3934 <param name="all_PSMs" value="false"/>
3935 <param name="group_level" value="false"/>
3936 <param name="log2_states" value="0"/>
3937 <section name="prob">
3938 <param name="protein" value="0.0"/>
3939 <param name="peptide" value="0.0"/>
3940 <param name="spurious" value="0.0"/>
3941 </section>
3942 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3943 <output name="ctd_out" ftype="xml">
3944 <assert_contents>
3945 <is_valid_xml/>
3946 </assert_contents>
3947 </output>
3948 </test>
3949 <test expect_num_outputs="2">
3950 <conditional name="adv_opts_cond">
3951 <param name="adv_opts_selector" value="advanced"/>
3952 <param name="keep_zero_group" value="false"/>
3953 <param name="accuracy" value=""/>
3954 <param name="log2_states_precalc" value="0"/>
3955 <param name="force" value="false"/>
3956 <param name="test" value="true"/>
3957 </conditional>
3958 <param name="in" value="FidoAdapter_1_input.idXML"/>
3959 <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
3960 <param name="separate_runs" value="true"/>
3961 <param name="greedy_group_resolution" value="false"/>
3962 <param name="no_cleanup" value="false"/>
3963 <param name="all_PSMs" value="false"/>
3964 <param name="group_level" value="false"/>
3965 <param name="log2_states" value="0"/>
3966 <section name="prob">
3967 <param name="protein" value="0.0"/>
3968 <param name="peptide" value="0.0"/>
3969 <param name="spurious" value="0.0"/>
3970 </section>
3971 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3972 <output name="ctd_out" ftype="xml">
3973 <assert_contents>
3974 <is_valid_xml/>
3975 </assert_contents>
3976 </output>
3977 </test>
3978 <test expect_num_outputs="2">
3979 <conditional name="adv_opts_cond">
3980 <param name="adv_opts_selector" value="advanced"/>
3981 <param name="keep_zero_group" value="false"/>
3982 <param name="accuracy" value=""/>
3983 <param name="log2_states_precalc" value="0"/>
3984 <param name="force" value="false"/>
3985 <param name="test" value="true"/>
3986 </conditional>
3987 <param name="in" value="FidoAdapter_1_input.idXML"/>
3988 <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
3989 <param name="separate_runs" value="false"/>
3990 <param name="greedy_group_resolution" value="false"/>
3991 <param name="no_cleanup" value="false"/>
3992 <param name="all_PSMs" value="true"/>
3993 <param name="group_level" value="true"/>
3994 <param name="log2_states" value="0"/>
3995 <section name="prob">
3996 <param name="protein" value="0.0"/>
3997 <param name="peptide" value="0.0"/>
3998 <param name="spurious" value="0.0"/>
3999 </section>
4000 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4001 <output name="ctd_out" ftype="xml">
4002 <assert_contents>
4003 <is_valid_xml/>
4004 </assert_contents>
4005 </output>
4006 </test>
4007 <test expect_num_outputs="2">
4008 <conditional name="adv_opts_cond">
4009 <param name="adv_opts_selector" value="advanced"/>
4010 <param name="keep_zero_group" value="false"/>
4011 <param name="accuracy" value=""/>
4012 <param name="log2_states_precalc" value="0"/>
4013 <param name="force" value="false"/>
4014 <param name="test" value="true"/>
4015 </conditional>
4016 <param name="in" value="FidoAdapter_4_input.idXML"/>
4017 <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4018 <param name="separate_runs" value="false"/>
4019 <param name="greedy_group_resolution" value="false"/>
4020 <param name="no_cleanup" value="false"/>
4021 <param name="all_PSMs" value="false"/>
4022 <param name="group_level" value="false"/>
4023 <param name="log2_states" value="0"/>
4024 <section name="prob">
4025 <param name="protein" value="0.0"/>
4026 <param name="peptide" value="0.0"/>
4027 <param name="spurious" value="0.0"/>
4028 </section>
4029 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4030 <output name="ctd_out" ftype="xml">
4031 <assert_contents>
4032 <is_valid_xml/>
4033 </assert_contents>
4034 </output>
4035 </test>
4036 <test expect_num_outputs="2">
4037 <conditional name="adv_opts_cond">
4038 <param name="adv_opts_selector" value="advanced"/>
4039 <param name="keep_zero_group" value="false"/>
4040 <param name="accuracy" value=""/>
4041 <param name="log2_states_precalc" value="0"/>
4042 <param name="force" value="false"/>
4043 <param name="test" value="true"/>
4044 </conditional>
4045 <param name="in" value="FidoAdapter_5_input.idXML"/>
4046 <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4047 <param name="separate_runs" value="false"/>
4048 <param name="greedy_group_resolution" value="true"/>
4049 <param name="no_cleanup" value="false"/>
4050 <param name="all_PSMs" value="false"/>
4051 <param name="group_level" value="false"/>
4052 <param name="log2_states" value="0"/>
4053 <section name="prob">
4054 <param name="protein" value="0.0"/>
4055 <param name="peptide" value="0.0"/>
4056 <param name="spurious" value="0.0"/>
4057 </section>
4058 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4059 <output name="ctd_out" ftype="xml">
4060 <assert_contents>
4061 <is_valid_xml/>
4062 </assert_contents>
4063 </output>
4064 </test>
4065 <test expect_num_outputs="2">
4066 <conditional name="adv_opts_cond">
4067 <param name="adv_opts_selector" value="advanced"/>
4068 <param name="keep_zero_group" value="false"/>
4069 <param name="accuracy" value=""/>
4070 <param name="log2_states_precalc" value="0"/>
4071 <param name="force" value="false"/>
4072 <param name="test" value="true"/>
4073 </conditional>
4074 <param name="in" value="FidoAdapter_1_input.idXML"/>
4075 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4076 <param name="separate_runs" value="false"/>
4077 <param name="greedy_group_resolution" value="false"/>
4078 <param name="no_cleanup" value="false"/>
4079 <param name="all_PSMs" value="false"/>
4080 <param name="group_level" value="false"/>
4081 <param name="log2_states" value="0"/>
4082 <section name="prob">
4083 <param name="protein" value="0.9"/>
4084 <param name="peptide" value="0.01"/>
4085 <param name="spurious" value="0.0"/>
4086 </section>
4087 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4088 <output name="ctd_out" ftype="xml">
4089 <assert_contents>
4090 <is_valid_xml/>
4091 </assert_contents>
4092 </output>
4093 </test>
4094 </xml>
4095 <xml name="autotest_FileConverter">
4096 <test expect_num_outputs="2">
4097 <conditional name="adv_opts_cond">
4098 <param name="adv_opts_selector" value="advanced"/>
4099 <param name="UID_postprocessing" value="ensure"/>
4100 <param name="TIC_DTA2D" value="false"/>
4101 <param name="MGF_compact" value="false"/>
4102 <param name="force_MaxQuant_compatibility" value="false"/>
4103 <param name="convert_to_chromatograms" value="false"/>
4104 <param name="force_TPP_compatibility" value="false"/>
4105 <param name="change_im_format" value="none"/>
4106 <param name="write_scan_index" value="true"/>
4107 <param name="lossy_compression" value="false"/>
4108 <param name="lossy_mass_accuracy" value="-1.0"/>
4109 <param name="process_lowmemory" value="false"/>
4110 <param name="no_peak_picking" value="false"/>
4111 <param name="force" value="false"/>
4112 <param name="test" value="true"/>
4113 </conditional>
4114 <param name="in" value="FileConverter_1_input.mzData"/>
4115 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4116 <param name="out_type" value="mzML"/>
4117 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4118 <output name="ctd_out" ftype="xml">
4119 <assert_contents>
4120 <is_valid_xml/>
4121 </assert_contents>
4122 </output>
4123 </test>
4124 <test expect_num_outputs="2">
4125 <conditional name="adv_opts_cond">
4126 <param name="adv_opts_selector" value="advanced"/>
4127 <param name="UID_postprocessing" value="ensure"/>
4128 <param name="TIC_DTA2D" value="false"/>
4129 <param name="MGF_compact" value="false"/>
4130 <param name="force_MaxQuant_compatibility" value="false"/>
4131 <param name="convert_to_chromatograms" value="false"/>
4132 <param name="force_TPP_compatibility" value="false"/>
4133 <param name="change_im_format" value="none"/>
4134 <param name="write_scan_index" value="true"/>
4135 <param name="lossy_compression" value="false"/>
4136 <param name="lossy_mass_accuracy" value="-1.0"/>
4137 <param name="process_lowmemory" value="false"/>
4138 <param name="no_peak_picking" value="false"/>
4139 <param name="force" value="false"/>
4140 <param name="test" value="true"/>
4141 </conditional>
4142 <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
4143 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4144 <param name="out_type" value="mzML"/>
4145 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4146 <output name="ctd_out" ftype="xml">
4147 <assert_contents>
4148 <is_valid_xml/>
4149 </assert_contents>
4150 </output>
4151 </test>
4152 <test expect_num_outputs="2">
4153 <conditional name="adv_opts_cond">
4154 <param name="adv_opts_selector" value="advanced"/>
4155 <param name="UID_postprocessing" value="ensure"/>
4156 <param name="TIC_DTA2D" value="false"/>
4157 <param name="MGF_compact" value="false"/>
4158 <param name="force_MaxQuant_compatibility" value="false"/>
4159 <param name="convert_to_chromatograms" value="false"/>
4160 <param name="force_TPP_compatibility" value="false"/>
4161 <param name="change_im_format" value="none"/>
4162 <param name="write_scan_index" value="true"/>
4163 <param name="lossy_compression" value="false"/>
4164 <param name="lossy_mass_accuracy" value="-1.0"/>
4165 <param name="process_lowmemory" value="false"/>
4166 <param name="no_peak_picking" value="false"/>
4167 <param name="force" value="false"/>
4168 <param name="test" value="true"/>
4169 </conditional>
4170 <param name="in" value="FileConverter_3_input.featureXML"/>
4171 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4172 <param name="out_type" value="mzML"/>
4173 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4174 <output name="ctd_out" ftype="xml">
4175 <assert_contents>
4176 <is_valid_xml/>
4177 </assert_contents>
4178 </output>
4179 </test>
4180 <test expect_num_outputs="2">
4181 <conditional name="adv_opts_cond">
4182 <param name="adv_opts_selector" value="advanced"/>
4183 <param name="UID_postprocessing" value="ensure"/>
4184 <param name="TIC_DTA2D" value="false"/>
4185 <param name="MGF_compact" value="false"/>
4186 <param name="force_MaxQuant_compatibility" value="false"/>
4187 <param name="convert_to_chromatograms" value="false"/>
4188 <param name="force_TPP_compatibility" value="false"/>
4189 <param name="change_im_format" value="none"/>
4190 <param name="write_scan_index" value="true"/>
4191 <param name="lossy_compression" value="false"/>
4192 <param name="lossy_mass_accuracy" value="-1.0"/>
4193 <param name="process_lowmemory" value="false"/>
4194 <param name="no_peak_picking" value="false"/>
4195 <param name="force" value="false"/>
4196 <param name="test" value="true"/>
4197 </conditional>
4198 <param name="in" value="FileConverter_4_input.mzXML"/>
4199 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4200 <param name="out_type" value="mzML"/>
4201 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4202 <output name="ctd_out" ftype="xml">
4203 <assert_contents>
4204 <is_valid_xml/>
4205 </assert_contents>
4206 </output>
4207 </test>
4208 <test expect_num_outputs="2">
4209 <conditional name="adv_opts_cond">
4210 <param name="adv_opts_selector" value="advanced"/>
4211 <param name="UID_postprocessing" value="ensure"/>
4212 <param name="TIC_DTA2D" value="false"/>
4213 <param name="MGF_compact" value="false"/>
4214 <param name="force_MaxQuant_compatibility" value="false"/>
4215 <param name="convert_to_chromatograms" value="false"/>
4216 <param name="force_TPP_compatibility" value="false"/>
4217 <param name="change_im_format" value="none"/>
4218 <param name="write_scan_index" value="true"/>
4219 <param name="lossy_compression" value="false"/>
4220 <param name="lossy_mass_accuracy" value="-1.0"/>
4221 <param name="process_lowmemory" value="false"/>
4222 <param name="no_peak_picking" value="false"/>
4223 <param name="force" value="false"/>
4224 <param name="test" value="true"/>
4225 </conditional>
4226 <param name="in" value="FileConverter_5_input.mzML"/>
4227 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4228 <param name="out_type" value="mzXML"/>
4229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4230 <output name="ctd_out" ftype="xml">
4231 <assert_contents>
4232 <is_valid_xml/>
4233 </assert_contents>
4234 </output>
4235 </test>
4236 <test expect_num_outputs="2">
4237 <conditional name="adv_opts_cond">
4238 <param name="adv_opts_selector" value="advanced"/>
4239 <param name="UID_postprocessing" value="ensure"/>
4240 <param name="TIC_DTA2D" value="false"/>
4241 <param name="MGF_compact" value="false"/>
4242 <param name="force_MaxQuant_compatibility" value="false"/>
4243 <param name="convert_to_chromatograms" value="false"/>
4244 <param name="force_TPP_compatibility" value="false"/>
4245 <param name="change_im_format" value="none"/>
4246 <param name="write_scan_index" value="true"/>
4247 <param name="lossy_compression" value="false"/>
4248 <param name="lossy_mass_accuracy" value="-1.0"/>
4249 <param name="process_lowmemory" value="false"/>
4250 <param name="no_peak_picking" value="false"/>
4251 <param name="force" value="false"/>
4252 <param name="test" value="true"/>
4253 </conditional>
4254 <param name="in" value="FileConverter_6_input.mzML"/>
4255 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4256 <param name="out_type" value="mzXML"/>
4257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4258 <output name="ctd_out" ftype="xml">
4259 <assert_contents>
4260 <is_valid_xml/>
4261 </assert_contents>
4262 </output>
4263 </test>
4264 <test expect_num_outputs="2">
4265 <conditional name="adv_opts_cond">
4266 <param name="adv_opts_selector" value="advanced"/>
4267 <param name="UID_postprocessing" value="ensure"/>
4268 <param name="TIC_DTA2D" value="false"/>
4269 <param name="MGF_compact" value="false"/>
4270 <param name="force_MaxQuant_compatibility" value="false"/>
4271 <param name="convert_to_chromatograms" value="false"/>
4272 <param name="force_TPP_compatibility" value="false"/>
4273 <param name="change_im_format" value="none"/>
4274 <param name="write_scan_index" value="true"/>
4275 <param name="lossy_compression" value="false"/>
4276 <param name="lossy_mass_accuracy" value="-1.0"/>
4277 <param name="process_lowmemory" value="false"/>
4278 <param name="no_peak_picking" value="false"/>
4279 <param name="force" value="false"/>
4280 <param name="test" value="true"/>
4281 </conditional>
4282 <param name="in" value="FileConverter_7_input.consensusXML"/>
4283 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4284 <param name="out_type" value="featureXML"/>
4285 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4286 <output name="ctd_out" ftype="xml">
4287 <assert_contents>
4288 <is_valid_xml/>
4289 </assert_contents>
4290 </output>
4291 </test>
4292 <test expect_num_outputs="2">
4293 <conditional name="adv_opts_cond">
4294 <param name="adv_opts_selector" value="advanced"/>
4295 <param name="UID_postprocessing" value="ensure"/>
4296 <param name="TIC_DTA2D" value="false"/>
4297 <param name="MGF_compact" value="false"/>
4298 <param name="force_MaxQuant_compatibility" value="false"/>
4299 <param name="convert_to_chromatograms" value="false"/>
4300 <param name="force_TPP_compatibility" value="false"/>
4301 <param name="change_im_format" value="none"/>
4302 <param name="write_scan_index" value="true"/>
4303 <param name="lossy_compression" value="false"/>
4304 <param name="lossy_mass_accuracy" value="-1.0"/>
4305 <param name="process_lowmemory" value="false"/>
4306 <param name="no_peak_picking" value="false"/>
4307 <param name="force" value="false"/>
4308 <param name="test" value="true"/>
4309 </conditional>
4310 <param name="in" value="FileConverter_8_input.mzML"/>
4311 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
4312 <param name="out_type" value="mzData"/>
4313 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4314 <output name="ctd_out" ftype="xml">
4315 <assert_contents>
4316 <is_valid_xml/>
4317 </assert_contents>
4318 </output>
4319 </test>
4320 <test expect_num_outputs="2">
4321 <conditional name="adv_opts_cond">
4322 <param name="adv_opts_selector" value="advanced"/>
4323 <param name="UID_postprocessing" value="ensure"/>
4324 <param name="TIC_DTA2D" value="false"/>
4325 <param name="MGF_compact" value="false"/>
4326 <param name="force_MaxQuant_compatibility" value="false"/>
4327 <param name="convert_to_chromatograms" value="false"/>
4328 <param name="force_TPP_compatibility" value="false"/>
4329 <param name="change_im_format" value="none"/>
4330 <param name="write_scan_index" value="true"/>
4331 <param name="lossy_compression" value="false"/>
4332 <param name="lossy_mass_accuracy" value="-1.0"/>
4333 <param name="process_lowmemory" value="false"/>
4334 <param name="no_peak_picking" value="false"/>
4335 <param name="force" value="false"/>
4336 <param name="test" value="true"/>
4337 </conditional>
4338 <param name="in" value="FileConverter_9_input.consensusXML"/>
4339 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4340 <param name="out_type" value="featureXML"/>
4341 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4342 <output name="ctd_out" ftype="xml">
4343 <assert_contents>
4344 <is_valid_xml/>
4345 </assert_contents>
4346 </output>
4347 </test>
4348 <test expect_num_outputs="2">
4349 <conditional name="adv_opts_cond">
4350 <param name="adv_opts_selector" value="advanced"/>
4351 <param name="UID_postprocessing" value="ensure"/>
4352 <param name="TIC_DTA2D" value="false"/>
4353 <param name="MGF_compact" value="false"/>
4354 <param name="force_MaxQuant_compatibility" value="false"/>
4355 <param name="convert_to_chromatograms" value="false"/>
4356 <param name="force_TPP_compatibility" value="false"/>
4357 <param name="change_im_format" value="none"/>
4358 <param name="write_scan_index" value="true"/>
4359 <param name="lossy_compression" value="false"/>
4360 <param name="lossy_mass_accuracy" value="-1.0"/>
4361 <param name="process_lowmemory" value="false"/>
4362 <param name="no_peak_picking" value="false"/>
4363 <param name="force" value="false"/>
4364 <param name="test" value="true"/>
4365 </conditional>
4366 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4367 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4368 <param name="out_type" value="featureXML"/>
4369 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4370 <output name="ctd_out" ftype="xml">
4371 <assert_contents>
4372 <is_valid_xml/>
4373 </assert_contents>
4374 </output>
4375 </test>
4376 <test expect_num_outputs="2">
4377 <conditional name="adv_opts_cond">
4378 <param name="adv_opts_selector" value="advanced"/>
4379 <param name="UID_postprocessing" value="ensure"/>
4380 <param name="TIC_DTA2D" value="false"/>
4381 <param name="MGF_compact" value="false"/>
4382 <param name="force_MaxQuant_compatibility" value="false"/>
4383 <param name="convert_to_chromatograms" value="false"/>
4384 <param name="force_TPP_compatibility" value="false"/>
4385 <param name="change_im_format" value="none"/>
4386 <param name="write_scan_index" value="true"/>
4387 <param name="lossy_compression" value="false"/>
4388 <param name="lossy_mass_accuracy" value="-1.0"/>
4389 <param name="process_lowmemory" value="false"/>
4390 <param name="no_peak_picking" value="false"/>
4391 <param name="force" value="false"/>
4392 <param name="test" value="true"/>
4393 </conditional>
4394 <param name="in" value="FileConverter_11_input.peplist"/>
4395 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4396 <param name="out_type" value="featureXML"/>
4397 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4398 <output name="ctd_out" ftype="xml">
4399 <assert_contents>
4400 <is_valid_xml/>
4401 </assert_contents>
4402 </output>
4403 </test>
4404 <test expect_num_outputs="2">
4405 <conditional name="adv_opts_cond">
4406 <param name="adv_opts_selector" value="advanced"/>
4407 <param name="UID_postprocessing" value="ensure"/>
4408 <param name="TIC_DTA2D" value="false"/>
4409 <param name="MGF_compact" value="false"/>
4410 <param name="force_MaxQuant_compatibility" value="false"/>
4411 <param name="convert_to_chromatograms" value="false"/>
4412 <param name="force_TPP_compatibility" value="false"/>
4413 <param name="change_im_format" value="none"/>
4414 <param name="write_scan_index" value="true"/>
4415 <param name="lossy_compression" value="false"/>
4416 <param name="lossy_mass_accuracy" value="-1.0"/>
4417 <param name="process_lowmemory" value="false"/>
4418 <param name="no_peak_picking" value="false"/>
4419 <param name="force" value="false"/>
4420 <param name="test" value="true"/>
4421 </conditional>
4422 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
4423 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4424 <param name="out_type" value="featureXML"/>
4425 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4426 <output name="ctd_out" ftype="xml">
4427 <assert_contents>
4428 <is_valid_xml/>
4429 </assert_contents>
4430 </output>
4431 </test>
4432 <test expect_num_outputs="2">
4433 <conditional name="adv_opts_cond">
4434 <param name="adv_opts_selector" value="advanced"/>
4435 <param name="UID_postprocessing" value="ensure"/>
4436 <param name="TIC_DTA2D" value="false"/>
4437 <param name="MGF_compact" value="false"/>
4438 <param name="force_MaxQuant_compatibility" value="false"/>
4439 <param name="convert_to_chromatograms" value="false"/>
4440 <param name="force_TPP_compatibility" value="false"/>
4441 <param name="change_im_format" value="none"/>
4442 <param name="write_scan_index" value="true"/>
4443 <param name="lossy_compression" value="false"/>
4444 <param name="lossy_mass_accuracy" value="-1.0"/>
4445 <param name="process_lowmemory" value="false"/>
4446 <param name="no_peak_picking" value="false"/>
4447 <param name="force" value="false"/>
4448 <param name="test" value="true"/>
4449 </conditional>
4450 <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
4451 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4452 <param name="out_type" value="featureXML"/>
4453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4454 <output name="ctd_out" ftype="xml">
4455 <assert_contents>
4456 <is_valid_xml/>
4457 </assert_contents>
4458 </output>
4459 </test>
4460 <test expect_num_outputs="2">
4461 <conditional name="adv_opts_cond">
4462 <param name="adv_opts_selector" value="advanced"/>
4463 <param name="UID_postprocessing" value="ensure"/>
4464 <param name="TIC_DTA2D" value="false"/>
4465 <param name="MGF_compact" value="false"/>
4466 <param name="force_MaxQuant_compatibility" value="false"/>
4467 <param name="convert_to_chromatograms" value="false"/>
4468 <param name="force_TPP_compatibility" value="false"/>
4469 <param name="change_im_format" value="none"/>
4470 <param name="write_scan_index" value="true"/>
4471 <param name="lossy_compression" value="false"/>
4472 <param name="lossy_mass_accuracy" value="-1.0"/>
4473 <param name="process_lowmemory" value="false"/>
4474 <param name="no_peak_picking" value="false"/>
4475 <param name="force" value="false"/>
4476 <param name="test" value="true"/>
4477 </conditional>
4478 <param name="in" value="FileConverter_9_output.featureXML"/>
4479 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4480 <param name="out_type" value="consensusXML"/>
4481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4482 <output name="ctd_out" ftype="xml">
4483 <assert_contents>
4484 <is_valid_xml/>
4485 </assert_contents>
4486 </output>
4487 </test>
4488 <test expect_num_outputs="2">
4489 <conditional name="adv_opts_cond">
4490 <param name="adv_opts_selector" value="advanced"/>
4491 <param name="UID_postprocessing" value="ensure"/>
4492 <param name="TIC_DTA2D" value="false"/>
4493 <param name="MGF_compact" value="false"/>
4494 <param name="force_MaxQuant_compatibility" value="false"/>
4495 <param name="convert_to_chromatograms" value="false"/>
4496 <param name="force_TPP_compatibility" value="false"/>
4497 <param name="change_im_format" value="none"/>
4498 <param name="write_scan_index" value="true"/>
4499 <param name="lossy_compression" value="false"/>
4500 <param name="lossy_mass_accuracy" value="-1.0"/>
4501 <param name="process_lowmemory" value="false"/>
4502 <param name="no_peak_picking" value="false"/>
4503 <param name="force" value="false"/>
4504 <param name="test" value="true"/>
4505 </conditional>
4506 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4507 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4508 <param name="out_type" value="consensusXML"/>
4509 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4510 <output name="ctd_out" ftype="xml">
4511 <assert_contents>
4512 <is_valid_xml/>
4513 </assert_contents>
4514 </output>
4515 </test>
4516 <test expect_num_outputs="2">
4517 <conditional name="adv_opts_cond">
4518 <param name="adv_opts_selector" value="advanced"/>
4519 <param name="UID_postprocessing" value="ensure"/>
4520 <param name="TIC_DTA2D" value="false"/>
4521 <param name="MGF_compact" value="false"/>
4522 <param name="force_MaxQuant_compatibility" value="false"/>
4523 <param name="convert_to_chromatograms" value="false"/>
4524 <param name="force_TPP_compatibility" value="false"/>
4525 <param name="change_im_format" value="none"/>
4526 <param name="write_scan_index" value="true"/>
4527 <param name="lossy_compression" value="false"/>
4528 <param name="lossy_mass_accuracy" value="-1.0"/>
4529 <param name="process_lowmemory" value="false"/>
4530 <param name="no_peak_picking" value="false"/>
4531 <param name="force" value="false"/>
4532 <param name="test" value="true"/>
4533 </conditional>
4534 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
4535 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4536 <param name="out_type" value="consensusXML"/>
4537 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4538 <output name="ctd_out" ftype="xml">
4539 <assert_contents>
4540 <is_valid_xml/>
4541 </assert_contents>
4542 </output>
4543 </test>
4544 <test expect_num_outputs="2">
4545 <conditional name="adv_opts_cond">
4546 <param name="adv_opts_selector" value="advanced"/>
4547 <param name="UID_postprocessing" value="ensure"/>
4548 <param name="TIC_DTA2D" value="false"/>
4549 <param name="MGF_compact" value="false"/>
4550 <param name="force_MaxQuant_compatibility" value="false"/>
4551 <param name="convert_to_chromatograms" value="false"/>
4552 <param name="force_TPP_compatibility" value="false"/>
4553 <param name="change_im_format" value="none"/>
4554 <param name="write_scan_index" value="true"/>
4555 <param name="lossy_compression" value="false"/>
4556 <param name="lossy_mass_accuracy" value="-1.0"/>
4557 <param name="process_lowmemory" value="false"/>
4558 <param name="no_peak_picking" value="false"/>
4559 <param name="force" value="false"/>
4560 <param name="test" value="true"/>
4561 </conditional>
4562 <param name="in" value="FileConverter_17_input.consensusXML"/>
4563 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
4564 <param name="out_type" value="csv"/>
4565 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4566 <output name="ctd_out" ftype="xml">
4567 <assert_contents>
4568 <is_valid_xml/>
4569 </assert_contents>
4570 </output>
4571 </test>
4572 <test expect_num_outputs="2">
4573 <conditional name="adv_opts_cond">
4574 <param name="adv_opts_selector" value="advanced"/>
4575 <param name="UID_postprocessing" value="ensure"/>
4576 <param name="TIC_DTA2D" value="false"/>
4577 <param name="MGF_compact" value="false"/>
4578 <param name="force_MaxQuant_compatibility" value="false"/>
4579 <param name="convert_to_chromatograms" value="false"/>
4580 <param name="force_TPP_compatibility" value="false"/>
4581 <param name="change_im_format" value="none"/>
4582 <param name="write_scan_index" value="true"/>
4583 <param name="lossy_compression" value="false"/>
4584 <param name="lossy_mass_accuracy" value="-1.0"/>
4585 <param name="process_lowmemory" value="false"/>
4586 <param name="no_peak_picking" value="false"/>
4587 <param name="force" value="false"/>
4588 <param name="test" value="true"/>
4589 </conditional>
4590 <param name="in" value="FileConverter_17_input.consensusXML"/>
4591 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
4592 <param name="out_type" value="csv"/>
4593 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4594 <output name="ctd_out" ftype="xml">
4595 <assert_contents>
4596 <is_valid_xml/>
4597 </assert_contents>
4598 </output>
4599 </test>
4600 <test expect_num_outputs="2">
4601 <conditional name="adv_opts_cond">
4602 <param name="adv_opts_selector" value="advanced"/>
4603 <param name="UID_postprocessing" value="ensure"/>
4604 <param name="TIC_DTA2D" value="false"/>
4605 <param name="MGF_compact" value="false"/>
4606 <param name="force_MaxQuant_compatibility" value="false"/>
4607 <param name="convert_to_chromatograms" value="false"/>
4608 <param name="force_TPP_compatibility" value="false"/>
4609 <param name="change_im_format" value="none"/>
4610 <param name="write_scan_index" value="true"/>
4611 <param name="lossy_compression" value="false"/>
4612 <param name="lossy_mass_accuracy" value="-1.0"/>
4613 <param name="process_lowmemory" value="true"/>
4614 <param name="no_peak_picking" value="false"/>
4615 <param name="force" value="false"/>
4616 <param name="test" value="true"/>
4617 </conditional>
4618 <param name="in" value="FileFilter_1_input.mzML"/>
4619 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4620 <param name="out_type" value="mzML"/>
4621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4622 <output name="ctd_out" ftype="xml">
4623 <assert_contents>
4624 <is_valid_xml/>
4625 </assert_contents>
4626 </output>
4627 </test>
4628 <test expect_num_outputs="2">
4629 <conditional name="adv_opts_cond">
4630 <param name="adv_opts_selector" value="advanced"/>
4631 <param name="UID_postprocessing" value="ensure"/>
4632 <param name="TIC_DTA2D" value="false"/>
4633 <param name="MGF_compact" value="false"/>
4634 <param name="force_MaxQuant_compatibility" value="false"/>
4635 <param name="convert_to_chromatograms" value="false"/>
4636 <param name="force_TPP_compatibility" value="false"/>
4637 <param name="change_im_format" value="none"/>
4638 <param name="write_scan_index" value="true"/>
4639 <param name="lossy_compression" value="false"/>
4640 <param name="lossy_mass_accuracy" value="-1.0"/>
4641 <param name="process_lowmemory" value="false"/>
4642 <param name="no_peak_picking" value="false"/>
4643 <param name="force" value="false"/>
4644 <param name="test" value="true"/>
4645 </conditional>
4646 <param name="in" value="FileConverter_20_input.featureXML"/>
4647 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4648 <param name="out_type" value="featureXML"/>
4649 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4650 <output name="ctd_out" ftype="xml">
4651 <assert_contents>
4652 <is_valid_xml/>
4653 </assert_contents>
4654 </output>
4655 </test>
4656 <test expect_num_outputs="2">
4657 <conditional name="adv_opts_cond">
4658 <param name="adv_opts_selector" value="advanced"/>
4659 <param name="UID_postprocessing" value="ensure"/>
4660 <param name="TIC_DTA2D" value="false"/>
4661 <param name="MGF_compact" value="false"/>
4662 <param name="force_MaxQuant_compatibility" value="false"/>
4663 <param name="convert_to_chromatograms" value="false"/>
4664 <param name="force_TPP_compatibility" value="false"/>
4665 <param name="change_im_format" value="none"/>
4666 <param name="write_scan_index" value="true"/>
4667 <param name="lossy_compression" value="false"/>
4668 <param name="lossy_mass_accuracy" value="-1.0"/>
4669 <param name="process_lowmemory" value="true"/>
4670 <param name="no_peak_picking" value="false"/>
4671 <param name="force" value="false"/>
4672 <param name="test" value="true"/>
4673 </conditional>
4674 <param name="in" value="FileConverter_4_input.mzXML"/>
4675 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4676 <param name="out_type" value="mzML"/>
4677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4678 <output name="ctd_out" ftype="xml">
4679 <assert_contents>
4680 <is_valid_xml/>
4681 </assert_contents>
4682 </output>
4683 </test>
4684 <test expect_num_outputs="2">
4685 <conditional name="adv_opts_cond">
4686 <param name="adv_opts_selector" value="advanced"/>
4687 <param name="UID_postprocessing" value="ensure"/>
4688 <param name="TIC_DTA2D" value="false"/>
4689 <param name="MGF_compact" value="false"/>
4690 <param name="force_MaxQuant_compatibility" value="false"/>
4691 <param name="convert_to_chromatograms" value="false"/>
4692 <param name="force_TPP_compatibility" value="false"/>
4693 <param name="change_im_format" value="none"/>
4694 <param name="write_scan_index" value="true"/>
4695 <param name="lossy_compression" value="false"/>
4696 <param name="lossy_mass_accuracy" value="-1.0"/>
4697 <param name="process_lowmemory" value="false"/>
4698 <param name="no_peak_picking" value="false"/>
4699 <param name="force" value="false"/>
4700 <param name="test" value="true"/>
4701 </conditional>
4702 <param name="in" value="FileConverter_23_input.mzML"/>
4703 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4704 <param name="out_type" value="mzML"/>
4705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4706 <output name="ctd_out" ftype="xml">
4707 <assert_contents>
4708 <is_valid_xml/>
4709 </assert_contents>
4710 </output>
4711 </test>
4712 <test expect_num_outputs="2">
4713 <conditional name="adv_opts_cond">
4714 <param name="adv_opts_selector" value="advanced"/>
4715 <param name="UID_postprocessing" value="ensure"/>
4716 <param name="TIC_DTA2D" value="false"/>
4717 <param name="MGF_compact" value="false"/>
4718 <param name="force_MaxQuant_compatibility" value="false"/>
4719 <param name="convert_to_chromatograms" value="false"/>
4720 <param name="force_TPP_compatibility" value="false"/>
4721 <param name="change_im_format" value="none"/>
4722 <param name="write_scan_index" value="true"/>
4723 <param name="lossy_compression" value="true"/>
4724 <param name="lossy_mass_accuracy" value="0.0001"/>
4725 <param name="process_lowmemory" value="true"/>
4726 <param name="no_peak_picking" value="false"/>
4727 <param name="force" value="false"/>
4728 <param name="test" value="true"/>
4729 </conditional>
4730 <param name="in" value="FileFilter_1_input.mzML"/>
4731 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4732 <param name="out_type" value="mzML"/>
4733 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4734 <output name="ctd_out" ftype="xml">
4735 <assert_contents>
4736 <is_valid_xml/>
4737 </assert_contents>
4738 </output>
4739 </test>
4740 <test expect_num_outputs="2">
4741 <conditional name="adv_opts_cond">
4742 <param name="adv_opts_selector" value="advanced"/>
4743 <param name="UID_postprocessing" value="ensure"/>
4744 <param name="TIC_DTA2D" value="false"/>
4745 <param name="MGF_compact" value="false"/>
4746 <param name="force_MaxQuant_compatibility" value="false"/>
4747 <param name="convert_to_chromatograms" value="false"/>
4748 <param name="force_TPP_compatibility" value="false"/>
4749 <param name="change_im_format" value="none"/>
4750 <param name="write_scan_index" value="true"/>
4751 <param name="lossy_compression" value="true"/>
4752 <param name="lossy_mass_accuracy" value="-1.0"/>
4753 <param name="process_lowmemory" value="true"/>
4754 <param name="no_peak_picking" value="false"/>
4755 <param name="force" value="false"/>
4756 <param name="test" value="true"/>
4757 </conditional>
4758 <param name="in" value="FileFilter_1_input.mzML"/>
4759 <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4760 <param name="out_type" value="mzML"/>
4761 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4762 <output name="ctd_out" ftype="xml">
4763 <assert_contents>
4764 <is_valid_xml/>
4765 </assert_contents>
4766 </output>
4767 </test>
4768 <test expect_num_outputs="2">
4769 <conditional name="adv_opts_cond">
4770 <param name="adv_opts_selector" value="advanced"/>
4771 <param name="UID_postprocessing" value="ensure"/>
4772 <param name="TIC_DTA2D" value="false"/>
4773 <param name="MGF_compact" value="false"/>
4774 <param name="force_MaxQuant_compatibility" value="true"/>
4775 <param name="convert_to_chromatograms" value="false"/>
4776 <param name="force_TPP_compatibility" value="false"/>
4777 <param name="change_im_format" value="none"/>
4778 <param name="write_scan_index" value="true"/>
4779 <param name="lossy_compression" value="false"/>
4780 <param name="lossy_mass_accuracy" value="-1.0"/>
4781 <param name="process_lowmemory" value="false"/>
4782 <param name="no_peak_picking" value="false"/>
4783 <param name="force" value="false"/>
4784 <param name="test" value="true"/>
4785 </conditional>
4786 <param name="in" value="FileFilter_1_input.mzML"/>
4787 <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4788 <param name="out_type" value="mzXML"/>
4789 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4790 <output name="ctd_out" ftype="xml">
4791 <assert_contents>
4792 <is_valid_xml/>
4793 </assert_contents>
4794 </output>
4795 </test>
4796 <test expect_num_outputs="2">
4797 <conditional name="adv_opts_cond">
4798 <param name="adv_opts_selector" value="advanced"/>
4799 <param name="UID_postprocessing" value="ensure"/>
4800 <param name="TIC_DTA2D" value="false"/>
4801 <param name="MGF_compact" value="false"/>
4802 <param name="force_MaxQuant_compatibility" value="true"/>
4803 <param name="convert_to_chromatograms" value="false"/>
4804 <param name="force_TPP_compatibility" value="false"/>
4805 <param name="change_im_format" value="none"/>
4806 <param name="write_scan_index" value="true"/>
4807 <param name="lossy_compression" value="false"/>
4808 <param name="lossy_mass_accuracy" value="-1.0"/>
4809 <param name="process_lowmemory" value="false"/>
4810 <param name="no_peak_picking" value="false"/>
4811 <param name="force" value="false"/>
4812 <param name="test" value="true"/>
4813 </conditional>
4814 <param name="in" value="FileConverter_26_output.mzXML"/>
4815 <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4816 <param name="out_type" value="mzXML"/>
4817 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4818 <output name="ctd_out" ftype="xml">
4819 <assert_contents>
4820 <is_valid_xml/>
4821 </assert_contents>
4822 </output>
4823 </test>
4824 <test expect_num_outputs="2">
4825 <conditional name="adv_opts_cond">
4826 <param name="adv_opts_selector" value="advanced"/>
4827 <param name="UID_postprocessing" value="ensure"/>
4828 <param name="TIC_DTA2D" value="false"/>
4829 <param name="MGF_compact" value="false"/>
4830 <param name="force_MaxQuant_compatibility" value="false"/>
4831 <param name="convert_to_chromatograms" value="true"/>
4832 <param name="force_TPP_compatibility" value="false"/>
4833 <param name="change_im_format" value="none"/>
4834 <param name="write_scan_index" value="true"/>
4835 <param name="lossy_compression" value="false"/>
4836 <param name="lossy_mass_accuracy" value="-1.0"/>
4837 <param name="process_lowmemory" value="false"/>
4838 <param name="no_peak_picking" value="false"/>
4839 <param name="force" value="false"/>
4840 <param name="test" value="true"/>
4841 </conditional>
4842 <param name="in" value="FileConverter_27_input.mzML"/>
4843 <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4844 <param name="out_type" value="mzML"/>
4845 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4846 <output name="ctd_out" ftype="xml">
4847 <assert_contents>
4848 <is_valid_xml/>
4849 </assert_contents>
4850 </output>
4851 </test>
4852 <test expect_num_outputs="2">
4853 <conditional name="adv_opts_cond">
4854 <param name="adv_opts_selector" value="advanced"/>
4855 <param name="UID_postprocessing" value="ensure"/>
4856 <param name="TIC_DTA2D" value="false"/>
4857 <param name="MGF_compact" value="false"/>
4858 <param name="force_MaxQuant_compatibility" value="false"/>
4859 <param name="convert_to_chromatograms" value="true"/>
4860 <param name="force_TPP_compatibility" value="false"/>
4861 <param name="change_im_format" value="none"/>
4862 <param name="write_scan_index" value="true"/>
4863 <param name="lossy_compression" value="false"/>
4864 <param name="lossy_mass_accuracy" value="-1.0"/>
4865 <param name="process_lowmemory" value="false"/>
4866 <param name="no_peak_picking" value="false"/>
4867 <param name="force" value="false"/>
4868 <param name="test" value="true"/>
4869 </conditional>
4870 <param name="in" value="FileConverter_28_input.mzML"/>
4871 <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4872 <param name="out_type" value="mzML"/>
4873 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4874 <output name="ctd_out" ftype="xml">
4875 <assert_contents>
4876 <is_valid_xml/>
4877 </assert_contents>
4878 </output>
4879 </test>
4880 <test expect_num_outputs="2">
4881 <conditional name="adv_opts_cond">
4882 <param name="adv_opts_selector" value="advanced"/>
4883 <param name="UID_postprocessing" value="ensure"/>
4884 <param name="TIC_DTA2D" value="false"/>
4885 <param name="MGF_compact" value="false"/>
4886 <param name="force_MaxQuant_compatibility" value="false"/>
4887 <param name="convert_to_chromatograms" value="false"/>
4888 <param name="force_TPP_compatibility" value="false"/>
4889 <param name="change_im_format" value="none"/>
4890 <param name="write_scan_index" value="true"/>
4891 <param name="lossy_compression" value="true"/>
4892 <param name="lossy_mass_accuracy" value="1e-05"/>
4893 <param name="process_lowmemory" value="true"/>
4894 <param name="no_peak_picking" value="false"/>
4895 <param name="force" value="false"/>
4896 <param name="test" value="true"/>
4897 </conditional>
4898 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
4899 <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4900 <param name="out_type" value="mzML"/>
4901 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4902 <output name="ctd_out" ftype="xml">
4903 <assert_contents>
4904 <is_valid_xml/>
4905 </assert_contents>
4906 </output>
4907 </test>
4908 <test expect_num_outputs="2">
4909 <conditional name="adv_opts_cond">
4910 <param name="adv_opts_selector" value="advanced"/>
4911 <param name="UID_postprocessing" value="ensure"/>
4912 <param name="TIC_DTA2D" value="false"/>
4913 <param name="MGF_compact" value="false"/>
4914 <param name="force_MaxQuant_compatibility" value="false"/>
4915 <param name="convert_to_chromatograms" value="false"/>
4916 <param name="force_TPP_compatibility" value="false"/>
4917 <param name="change_im_format" value="none"/>
4918 <param name="write_scan_index" value="true"/>
4919 <param name="lossy_compression" value="false"/>
4920 <param name="lossy_mass_accuracy" value="-1.0"/>
4921 <param name="process_lowmemory" value="false"/>
4922 <param name="no_peak_picking" value="false"/>
4923 <param name="force" value="false"/>
4924 <param name="test" value="true"/>
4925 </conditional>
4926 <param name="in" value="FileConverter_29_output.mzML"/>
4927 <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/>
4928 <param name="out_type" value="mzML"/>
4929 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4930 <output name="ctd_out" ftype="xml">
4931 <assert_contents>
4932 <is_valid_xml/>
4933 </assert_contents>
4934 </output>
4935 </test>
4936 <test expect_num_outputs="2">
4937 <conditional name="adv_opts_cond">
4938 <param name="adv_opts_selector" value="advanced"/>
4939 <param name="UID_postprocessing" value="ensure"/>
4940 <param name="TIC_DTA2D" value="false"/>
4941 <param name="MGF_compact" value="false"/>
4942 <param name="force_MaxQuant_compatibility" value="false"/>
4943 <param name="convert_to_chromatograms" value="false"/>
4944 <param name="force_TPP_compatibility" value="false"/>
4945 <param name="change_im_format" value="multiple"/>
4946 <param name="write_scan_index" value="true"/>
4947 <param name="lossy_compression" value="false"/>
4948 <param name="lossy_mass_accuracy" value="-1.0"/>
4949 <param name="process_lowmemory" value="false"/>
4950 <param name="no_peak_picking" value="false"/>
4951 <param name="force" value="false"/>
4952 <param name="test" value="true"/>
4953 </conditional>
4954 <param name="in" value="FileConverter_30_input.mzML"/>
4955 <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4956 <param name="out_type" value="mzML"/>
4957 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4958 <output name="ctd_out" ftype="xml">
4959 <assert_contents>
4960 <is_valid_xml/>
4961 </assert_contents>
4962 </output>
4963 </test>
4964 <test expect_num_outputs="2">
4965 <conditional name="adv_opts_cond">
4966 <param name="adv_opts_selector" value="advanced"/>
4967 <param name="UID_postprocessing" value="ensure"/>
4968 <param name="TIC_DTA2D" value="false"/>
4969 <param name="MGF_compact" value="false"/>
4970 <param name="force_MaxQuant_compatibility" value="false"/>
4971 <param name="convert_to_chromatograms" value="false"/>
4972 <param name="force_TPP_compatibility" value="false"/>
4973 <param name="change_im_format" value="single"/>
4974 <param name="write_scan_index" value="true"/>
4975 <param name="lossy_compression" value="false"/>
4976 <param name="lossy_mass_accuracy" value="-1.0"/>
4977 <param name="process_lowmemory" value="false"/>
4978 <param name="no_peak_picking" value="false"/>
4979 <param name="force" value="false"/>
4980 <param name="test" value="true"/>
4981 </conditional>
4982 <param name="in" value="FileConverter_30_output.mzML"/>
4983 <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4984 <param name="out_type" value="mzML"/>
4985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4986 <output name="ctd_out" ftype="xml">
4987 <assert_contents>
4988 <is_valid_xml/>
4989 </assert_contents>
4990 </output>
4991 </test>
4992 <test expect_num_outputs="2">
4993 <conditional name="adv_opts_cond">
4994 <param name="adv_opts_selector" value="advanced"/>
4995 <param name="UID_postprocessing" value="ensure"/>
4996 <param name="TIC_DTA2D" value="false"/>
4997 <param name="MGF_compact" value="false"/>
4998 <param name="force_MaxQuant_compatibility" value="false"/>
4999 <param name="convert_to_chromatograms" value="false"/>
5000 <param name="force_TPP_compatibility" value="false"/>
5001 <param name="change_im_format" value="none"/>
5002 <param name="write_scan_index" value="true"/>
5003 <param name="lossy_compression" value="false"/>
5004 <param name="lossy_mass_accuracy" value="-1.0"/>
5005 <param name="process_lowmemory" value="false"/>
5006 <param name="no_peak_picking" value="false"/>
5007 <param name="force" value="false"/>
5008 <param name="test" value="true"/>
5009 </conditional>
5010 <param name="in" value="ginkgotoxin-ms-switching.raw"/>
5011 <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5012 <param name="out_type" value="mzml"/>
5013 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5014 <output name="ctd_out" ftype="xml">
5015 <assert_contents>
5016 <is_valid_xml/>
5017 </assert_contents>
5018 </output>
5019 </test>
5020 </xml>
5021 <xml name="autotest_FileFilter">
5022 <test expect_num_outputs="2">
5023 <conditional name="adv_opts_cond">
5024 <param name="adv_opts_selector" value="advanced"/>
5025 <param name="force" value="false"/>
5026 <param name="test" value="true"/>
5027 </conditional>
5028 <param name="in" value="FileFilter_1_input.mzML"/>
5029 <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5030 <param name="out_type" value="mzML"/>
5031 <param name="rt" value=":30"/>
5032 <param name="mz" value=":1000"/>
5033 <param name="int" value=":20000"/>
5034 <param name="sort" value="false"/>
5035 <section name="peak_options">
5036 <param name="sn" value="0.0"/>
5037 <param name="rm_pc_charge" value=""/>
5038 <param name="pc_mz_range" value=":"/>
5039 <param name="pc_mz_list" value=""/>
5040 <param name="level" value="1 2 3"/>
5041 <param name="sort_peaks" value="false"/>
5042 <param name="no_chromatograms" value="false"/>
5043 <param name="remove_chromatograms" value="false"/>
5044 <param name="remove_empty" value="false"/>
5045 <param name="mz_precision" value="64"/>
5046 <param name="int_precision" value="32"/>
5047 <param name="indexed_file" value="true"/>
5048 <param name="zlib_compression" value="false"/>
5049 <section name="numpress">
5050 <param name="masstime" value="none"/>
5051 <param name="lossy_mass_accuracy" value="-1.0"/>
5052 <param name="intensity" value="none"/>
5053 <param name="float_da" value="none"/>
5054 </section>
5055 </section>
5056 <section name="spectra">
5057 <param name="remove_zoom" value="false"/>
5058 <param name="remove_mode" value=""/>
5059 <param name="remove_activation" value=""/>
5060 <param name="remove_collision_energy" value=":"/>
5061 <param name="remove_isolation_window_width" value=":"/>
5062 <param name="select_zoom" value="false"/>
5063 <param name="select_mode" value=""/>
5064 <param name="select_activation" value=""/>
5065 <param name="select_collision_energy" value=":"/>
5066 <param name="select_isolation_window_width" value=":"/>
5067 <param name="select_polarity" value=""/>
5068 <section name="blackorwhitelist">
5069 <param name="similarity_threshold" value="-1.0"/>
5070 <param name="rt" value="0.01"/>
5071 <param name="mz" value="0.01"/>
5072 <param name="use_ppm_tolerance" value="false"/>
5073 <param name="blacklist" value="true"/>
5074 </section>
5075 </section>
5076 <section name="feature">
5077 <param name="q" value=":"/>
5078 </section>
5079 <section name="consensus">
5080 <param name="map" value=""/>
5081 <param name="map_and" value="false"/>
5082 <section name="blackorwhitelist">
5083 <param name="blacklist" value="true"/>
5084 <param name="maps" value=""/>
5085 <param name="rt" value="60.0"/>
5086 <param name="mz" value="0.01"/>
5087 <param name="use_ppm_tolerance" value="false"/>
5088 </section>
5089 </section>
5090 <section name="f_and_c">
5091 <param name="charge" value=":"/>
5092 <param name="size" value=":"/>
5093 <param name="remove_meta" value=""/>
5094 </section>
5095 <section name="id">
5096 <param name="remove_clashes" value="false"/>
5097 <param name="keep_best_score_id" value="false"/>
5098 <param name="sequences_whitelist" value=""/>
5099 <param name="sequence_comparison_method" value="substring"/>
5100 <param name="accessions_whitelist" value=""/>
5101 <param name="remove_annotated_features" value="false"/>
5102 <param name="remove_unannotated_features" value="false"/>
5103 <param name="remove_unassigned_ids" value="false"/>
5104 <param name="rt" value="0.1"/>
5105 <param name="mz" value="0.001"/>
5106 <param name="blacklist_imperfect" value="false"/>
5107 </section>
5108 <section name="algorithm">
5109 <section name="SignalToNoise">
5110 <param name="max_intensity" value="-1"/>
5111 <param name="auto_max_stdev_factor" value="3.0"/>
5112 <param name="auto_max_percentile" value="95"/>
5113 <param name="auto_mode" value="0"/>
5114 <param name="win_len" value="200.0"/>
5115 <param name="bin_count" value="30"/>
5116 <param name="min_required_elements" value="10"/>
5117 <param name="noise_for_empty_window" value="1e+20"/>
5118 <param name="write_log_messages" value="true"/>
5119 </section>
5120 </section>
5121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5122 <output name="ctd_out" ftype="xml">
5123 <assert_contents>
5124 <is_valid_xml/>
5125 </assert_contents>
5126 </output>
5127 </test>
5128 <test expect_num_outputs="2">
5129 <conditional name="adv_opts_cond">
5130 <param name="adv_opts_selector" value="advanced"/>
5131 <param name="force" value="false"/>
5132 <param name="test" value="true"/>
5133 </conditional>
5134 <param name="in" value="FileFilter_1_input.mzML"/>
5135 <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5136 <param name="out_type" value="mzML"/>
5137 <param name="rt" value="30:"/>
5138 <param name="mz" value="1000:"/>
5139 <param name="int" value="100:"/>
5140 <param name="sort" value="false"/>
5141 <section name="peak_options">
5142 <param name="sn" value="0.0"/>
5143 <param name="rm_pc_charge" value=""/>
5144 <param name="pc_mz_range" value=":"/>
5145 <param name="pc_mz_list" value=""/>
5146 <param name="level" value="1 2 3"/>
5147 <param name="sort_peaks" value="false"/>
5148 <param name="no_chromatograms" value="false"/>
5149 <param name="remove_chromatograms" value="false"/>
5150 <param name="remove_empty" value="false"/>
5151 <param name="mz_precision" value="64"/>
5152 <param name="int_precision" value="32"/>
5153 <param name="indexed_file" value="true"/>
5154 <param name="zlib_compression" value="false"/>
5155 <section name="numpress">
5156 <param name="masstime" value="none"/>
5157 <param name="lossy_mass_accuracy" value="-1.0"/>
5158 <param name="intensity" value="none"/>
5159 <param name="float_da" value="none"/>
5160 </section>
5161 </section>
5162 <section name="spectra">
5163 <param name="remove_zoom" value="false"/>
5164 <param name="remove_mode" value=""/>
5165 <param name="remove_activation" value=""/>
5166 <param name="remove_collision_energy" value=":"/>
5167 <param name="remove_isolation_window_width" value=":"/>
5168 <param name="select_zoom" value="false"/>
5169 <param name="select_mode" value=""/>
5170 <param name="select_activation" value=""/>
5171 <param name="select_collision_energy" value=":"/>
5172 <param name="select_isolation_window_width" value=":"/>
5173 <param name="select_polarity" value=""/>
5174 <section name="blackorwhitelist">
5175 <param name="similarity_threshold" value="-1.0"/>
5176 <param name="rt" value="0.01"/>
5177 <param name="mz" value="0.01"/>
5178 <param name="use_ppm_tolerance" value="false"/>
5179 <param name="blacklist" value="true"/>
5180 </section>
5181 </section>
5182 <section name="feature">
5183 <param name="q" value=":"/>
5184 </section>
5185 <section name="consensus">
5186 <param name="map" value=""/>
5187 <param name="map_and" value="false"/>
5188 <section name="blackorwhitelist">
5189 <param name="blacklist" value="true"/>
5190 <param name="maps" value=""/>
5191 <param name="rt" value="60.0"/>
5192 <param name="mz" value="0.01"/>
5193 <param name="use_ppm_tolerance" value="false"/>
5194 </section>
5195 </section>
5196 <section name="f_and_c">
5197 <param name="charge" value=":"/>
5198 <param name="size" value=":"/>
5199 <param name="remove_meta" value=""/>
5200 </section>
5201 <section name="id">
5202 <param name="remove_clashes" value="false"/>
5203 <param name="keep_best_score_id" value="false"/>
5204 <param name="sequences_whitelist" value=""/>
5205 <param name="sequence_comparison_method" value="substring"/>
5206 <param name="accessions_whitelist" value=""/>
5207 <param name="remove_annotated_features" value="false"/>
5208 <param name="remove_unannotated_features" value="false"/>
5209 <param name="remove_unassigned_ids" value="false"/>
5210 <param name="rt" value="0.1"/>
5211 <param name="mz" value="0.001"/>
5212 <param name="blacklist_imperfect" value="false"/>
5213 </section>
5214 <section name="algorithm">
5215 <section name="SignalToNoise">
5216 <param name="max_intensity" value="-1"/>
5217 <param name="auto_max_stdev_factor" value="3.0"/>
5218 <param name="auto_max_percentile" value="95"/>
5219 <param name="auto_mode" value="0"/>
5220 <param name="win_len" value="200.0"/>
5221 <param name="bin_count" value="30"/>
5222 <param name="min_required_elements" value="10"/>
5223 <param name="noise_for_empty_window" value="1e+20"/>
5224 <param name="write_log_messages" value="true"/>
5225 </section>
5226 </section>
5227 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5228 <output name="ctd_out" ftype="xml">
5229 <assert_contents>
5230 <is_valid_xml/>
5231 </assert_contents>
5232 </output>
5233 </test>
5234 <test expect_num_outputs="2">
5235 <conditional name="adv_opts_cond">
5236 <param name="adv_opts_selector" value="advanced"/>
5237 <param name="force" value="false"/>
5238 <param name="test" value="true"/>
5239 </conditional>
5240 <param name="in" value="FileFilter_1_input.mzML"/>
5241 <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5242 <param name="out_type" value="mzML"/>
5243 <param name="rt" value=":"/>
5244 <param name="mz" value=":"/>
5245 <param name="int" value=":"/>
5246 <param name="sort" value="false"/>
5247 <section name="peak_options">
5248 <param name="sn" value="0.0"/>
5249 <param name="rm_pc_charge" value=""/>
5250 <param name="pc_mz_range" value=":"/>
5251 <param name="pc_mz_list" value=""/>
5252 <param name="level" value="2"/>
5253 <param name="sort_peaks" value="false"/>
5254 <param name="no_chromatograms" value="false"/>
5255 <param name="remove_chromatograms" value="false"/>
5256 <param name="remove_empty" value="false"/>
5257 <param name="mz_precision" value="64"/>
5258 <param name="int_precision" value="32"/>
5259 <param name="indexed_file" value="true"/>
5260 <param name="zlib_compression" value="false"/>
5261 <section name="numpress">
5262 <param name="masstime" value="none"/>
5263 <param name="lossy_mass_accuracy" value="-1.0"/>
5264 <param name="intensity" value="none"/>
5265 <param name="float_da" value="none"/>
5266 </section>
5267 </section>
5268 <section name="spectra">
5269 <param name="remove_zoom" value="false"/>
5270 <param name="remove_mode" value=""/>
5271 <param name="remove_activation" value=""/>
5272 <param name="remove_collision_energy" value=":"/>
5273 <param name="remove_isolation_window_width" value=":"/>
5274 <param name="select_zoom" value="false"/>
5275 <param name="select_mode" value=""/>
5276 <param name="select_activation" value=""/>
5277 <param name="select_collision_energy" value=":"/>
5278 <param name="select_isolation_window_width" value=":"/>
5279 <param name="select_polarity" value=""/>
5280 <section name="blackorwhitelist">
5281 <param name="similarity_threshold" value="-1.0"/>
5282 <param name="rt" value="0.01"/>
5283 <param name="mz" value="0.01"/>
5284 <param name="use_ppm_tolerance" value="false"/>
5285 <param name="blacklist" value="true"/>
5286 </section>
5287 </section>
5288 <section name="feature">
5289 <param name="q" value=":"/>
5290 </section>
5291 <section name="consensus">
5292 <param name="map" value=""/>
5293 <param name="map_and" value="false"/>
5294 <section name="blackorwhitelist">
5295 <param name="blacklist" value="true"/>
5296 <param name="maps" value=""/>
5297 <param name="rt" value="60.0"/>
5298 <param name="mz" value="0.01"/>
5299 <param name="use_ppm_tolerance" value="false"/>
5300 </section>
5301 </section>
5302 <section name="f_and_c">
5303 <param name="charge" value=":"/>
5304 <param name="size" value=":"/>
5305 <param name="remove_meta" value=""/>
5306 </section>
5307 <section name="id">
5308 <param name="remove_clashes" value="false"/>
5309 <param name="keep_best_score_id" value="false"/>
5310 <param name="sequences_whitelist" value=""/>
5311 <param name="sequence_comparison_method" value="substring"/>
5312 <param name="accessions_whitelist" value=""/>
5313 <param name="remove_annotated_features" value="false"/>
5314 <param name="remove_unannotated_features" value="false"/>
5315 <param name="remove_unassigned_ids" value="false"/>
5316 <param name="rt" value="0.1"/>
5317 <param name="mz" value="0.001"/>
5318 <param name="blacklist_imperfect" value="false"/>
5319 </section>
5320 <section name="algorithm">
5321 <section name="SignalToNoise">
5322 <param name="max_intensity" value="-1"/>
5323 <param name="auto_max_stdev_factor" value="3.0"/>
5324 <param name="auto_max_percentile" value="95"/>
5325 <param name="auto_mode" value="0"/>
5326 <param name="win_len" value="200.0"/>
5327 <param name="bin_count" value="30"/>
5328 <param name="min_required_elements" value="10"/>
5329 <param name="noise_for_empty_window" value="1e+20"/>
5330 <param name="write_log_messages" value="true"/>
5331 </section>
5332 </section>
5333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5334 <output name="ctd_out" ftype="xml">
5335 <assert_contents>
5336 <is_valid_xml/>
5337 </assert_contents>
5338 </output>
5339 </test>
5340 <test expect_num_outputs="2">
5341 <conditional name="adv_opts_cond">
5342 <param name="adv_opts_selector" value="advanced"/>
5343 <param name="force" value="false"/>
5344 <param name="test" value="true"/>
5345 </conditional>
5346 <param name="in" value="FileFilter_4_input.mzML"/>
5347 <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5348 <param name="out_type" value="mzML"/>
5349 <param name="rt" value=":"/>
5350 <param name="mz" value=":"/>
5351 <param name="int" value=":"/>
5352 <param name="sort" value="false"/>
5353 <section name="peak_options">
5354 <param name="sn" value="0.0"/>
5355 <param name="rm_pc_charge" value=""/>
5356 <param name="pc_mz_range" value=":"/>
5357 <param name="pc_mz_list" value=""/>
5358 <param name="level" value="1 2 3"/>
5359 <param name="sort_peaks" value="false"/>
5360 <param name="no_chromatograms" value="false"/>
5361 <param name="remove_chromatograms" value="false"/>
5362 <param name="remove_empty" value="false"/>
5363 <param name="mz_precision" value="64"/>
5364 <param name="int_precision" value="32"/>
5365 <param name="indexed_file" value="true"/>
5366 <param name="zlib_compression" value="false"/>
5367 <section name="numpress">
5368 <param name="masstime" value="none"/>
5369 <param name="lossy_mass_accuracy" value="-1.0"/>
5370 <param name="intensity" value="none"/>
5371 <param name="float_da" value="none"/>
5372 </section>
5373 </section>
5374 <section name="spectra">
5375 <param name="remove_zoom" value="true"/>
5376 <param name="remove_mode" value=""/>
5377 <param name="remove_activation" value=""/>
5378 <param name="remove_collision_energy" value=":"/>
5379 <param name="remove_isolation_window_width" value=":"/>
5380 <param name="select_zoom" value="false"/>
5381 <param name="select_mode" value=""/>
5382 <param name="select_activation" value=""/>
5383 <param name="select_collision_energy" value=":"/>
5384 <param name="select_isolation_window_width" value=":"/>
5385 <param name="select_polarity" value=""/>
5386 <section name="blackorwhitelist">
5387 <param name="similarity_threshold" value="-1.0"/>
5388 <param name="rt" value="0.01"/>
5389 <param name="mz" value="0.01"/>
5390 <param name="use_ppm_tolerance" value="false"/>
5391 <param name="blacklist" value="true"/>
5392 </section>
5393 </section>
5394 <section name="feature">
5395 <param name="q" value=":"/>
5396 </section>
5397 <section name="consensus">
5398 <param name="map" value=""/>
5399 <param name="map_and" value="false"/>
5400 <section name="blackorwhitelist">
5401 <param name="blacklist" value="true"/>
5402 <param name="maps" value=""/>
5403 <param name="rt" value="60.0"/>
5404 <param name="mz" value="0.01"/>
5405 <param name="use_ppm_tolerance" value="false"/>
5406 </section>
5407 </section>
5408 <section name="f_and_c">
5409 <param name="charge" value=":"/>
5410 <param name="size" value=":"/>
5411 <param name="remove_meta" value=""/>
5412 </section>
5413 <section name="id">
5414 <param name="remove_clashes" value="false"/>
5415 <param name="keep_best_score_id" value="false"/>
5416 <param name="sequences_whitelist" value=""/>
5417 <param name="sequence_comparison_method" value="substring"/>
5418 <param name="accessions_whitelist" value=""/>
5419 <param name="remove_annotated_features" value="false"/>
5420 <param name="remove_unannotated_features" value="false"/>
5421 <param name="remove_unassigned_ids" value="false"/>
5422 <param name="rt" value="0.1"/>
5423 <param name="mz" value="0.001"/>
5424 <param name="blacklist_imperfect" value="false"/>
5425 </section>
5426 <section name="algorithm">
5427 <section name="SignalToNoise">
5428 <param name="max_intensity" value="-1"/>
5429 <param name="auto_max_stdev_factor" value="3.0"/>
5430 <param name="auto_max_percentile" value="95"/>
5431 <param name="auto_mode" value="0"/>
5432 <param name="win_len" value="200.0"/>
5433 <param name="bin_count" value="30"/>
5434 <param name="min_required_elements" value="10"/>
5435 <param name="noise_for_empty_window" value="1e+20"/>
5436 <param name="write_log_messages" value="true"/>
5437 </section>
5438 </section>
5439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5440 <output name="ctd_out" ftype="xml">
5441 <assert_contents>
5442 <is_valid_xml/>
5443 </assert_contents>
5444 </output>
5445 </test>
5446 <test expect_num_outputs="2">
5447 <conditional name="adv_opts_cond">
5448 <param name="adv_opts_selector" value="advanced"/>
5449 <param name="force" value="false"/>
5450 <param name="test" value="true"/>
5451 </conditional>
5452 <param name="in" value="FileFilter_5_input.featureXML"/>
5453 <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
5454 <param name="out_type" value="featureXML"/>
5455 <param name="rt" value=":1000"/>
5456 <param name="mz" value=":480"/>
5457 <param name="int" value=":79000"/>
5458 <param name="sort" value="false"/>
5459 <section name="peak_options">
5460 <param name="sn" value="0.0"/>
5461 <param name="rm_pc_charge" value=""/>
5462 <param name="pc_mz_range" value=":"/>
5463 <param name="pc_mz_list" value=""/>
5464 <param name="level" value="1 2 3"/>
5465 <param name="sort_peaks" value="false"/>
5466 <param name="no_chromatograms" value="false"/>
5467 <param name="remove_chromatograms" value="false"/>
5468 <param name="remove_empty" value="false"/>
5469 <param name="mz_precision" value="64"/>
5470 <param name="int_precision" value="32"/>
5471 <param name="indexed_file" value="true"/>
5472 <param name="zlib_compression" value="false"/>
5473 <section name="numpress">
5474 <param name="masstime" value="none"/>
5475 <param name="lossy_mass_accuracy" value="-1.0"/>
5476 <param name="intensity" value="none"/>
5477 <param name="float_da" value="none"/>
5478 </section>
5479 </section>
5480 <section name="spectra">
5481 <param name="remove_zoom" value="false"/>
5482 <param name="remove_mode" value=""/>
5483 <param name="remove_activation" value=""/>
5484 <param name="remove_collision_energy" value=":"/>
5485 <param name="remove_isolation_window_width" value=":"/>
5486 <param name="select_zoom" value="false"/>
5487 <param name="select_mode" value=""/>
5488 <param name="select_activation" value=""/>
5489 <param name="select_collision_energy" value=":"/>
5490 <param name="select_isolation_window_width" value=":"/>
5491 <param name="select_polarity" value=""/>
5492 <section name="blackorwhitelist">
5493 <param name="similarity_threshold" value="-1.0"/>
5494 <param name="rt" value="0.01"/>
5495 <param name="mz" value="0.01"/>
5496 <param name="use_ppm_tolerance" value="false"/>
5497 <param name="blacklist" value="true"/>
5498 </section>
5499 </section>
5500 <section name="feature">
5501 <param name="q" value=":0.6"/>
5502 </section>
5503 <section name="consensus">
5504 <param name="map" value=""/>
5505 <param name="map_and" value="false"/>
5506 <section name="blackorwhitelist">
5507 <param name="blacklist" value="true"/>
5508 <param name="maps" value=""/>
5509 <param name="rt" value="60.0"/>
5510 <param name="mz" value="0.01"/>
5511 <param name="use_ppm_tolerance" value="false"/>
5512 </section>
5513 </section>
5514 <section name="f_and_c">
5515 <param name="charge" value=":3"/>
5516 <param name="size" value=":"/>
5517 <param name="remove_meta" value=""/>
5518 </section>
5519 <section name="id">
5520 <param name="remove_clashes" value="false"/>
5521 <param name="keep_best_score_id" value="false"/>
5522 <param name="sequences_whitelist" value=""/>
5523 <param name="sequence_comparison_method" value="substring"/>
5524 <param name="accessions_whitelist" value=""/>
5525 <param name="remove_annotated_features" value="false"/>
5526 <param name="remove_unannotated_features" value="false"/>
5527 <param name="remove_unassigned_ids" value="false"/>
5528 <param name="rt" value="0.1"/>
5529 <param name="mz" value="0.001"/>
5530 <param name="blacklist_imperfect" value="false"/>
5531 </section>
5532 <section name="algorithm">
5533 <section name="SignalToNoise">
5534 <param name="max_intensity" value="-1"/>
5535 <param name="auto_max_stdev_factor" value="3.0"/>
5536 <param name="auto_max_percentile" value="95"/>
5537 <param name="auto_mode" value="0"/>
5538 <param name="win_len" value="200.0"/>
5539 <param name="bin_count" value="30"/>
5540 <param name="min_required_elements" value="10"/>
5541 <param name="noise_for_empty_window" value="1e+20"/>
5542 <param name="write_log_messages" value="true"/>
5543 </section>
5544 </section>
5545 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5546 <output name="ctd_out" ftype="xml">
5547 <assert_contents>
5548 <is_valid_xml/>
5549 </assert_contents>
5550 </output>
5551 </test>
5552 <test expect_num_outputs="2">
5553 <conditional name="adv_opts_cond">
5554 <param name="adv_opts_selector" value="advanced"/>
5555 <param name="force" value="false"/>
5556 <param name="test" value="true"/>
5557 </conditional>
5558 <param name="in" value="FileFilter_5_input.featureXML"/>
5559 <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
5560 <param name="out_type" value="featureXML"/>
5561 <param name="rt" value="1000:"/>
5562 <param name="mz" value="440:"/>
5563 <param name="int" value="70000:"/>
5564 <param name="sort" value="false"/>
5565 <section name="peak_options">
5566 <param name="sn" value="0.0"/>
5567 <param name="rm_pc_charge" value=""/>
5568 <param name="pc_mz_range" value=":"/>
5569 <param name="pc_mz_list" value=""/>
5570 <param name="level" value="1 2 3"/>
5571 <param name="sort_peaks" value="false"/>
5572 <param name="no_chromatograms" value="false"/>
5573 <param name="remove_chromatograms" value="false"/>
5574 <param name="remove_empty" value="false"/>
5575 <param name="mz_precision" value="64"/>
5576 <param name="int_precision" value="32"/>
5577 <param name="indexed_file" value="true"/>
5578 <param name="zlib_compression" value="false"/>
5579 <section name="numpress">
5580 <param name="masstime" value="none"/>
5581 <param name="lossy_mass_accuracy" value="-1.0"/>
5582 <param name="intensity" value="none"/>
5583 <param name="float_da" value="none"/>
5584 </section>
5585 </section>
5586 <section name="spectra">
5587 <param name="remove_zoom" value="false"/>
5588 <param name="remove_mode" value=""/>
5589 <param name="remove_activation" value=""/>
5590 <param name="remove_collision_energy" value=":"/>
5591 <param name="remove_isolation_window_width" value=":"/>
5592 <param name="select_zoom" value="false"/>
5593 <param name="select_mode" value=""/>
5594 <param name="select_activation" value=""/>
5595 <param name="select_collision_energy" value=":"/>
5596 <param name="select_isolation_window_width" value=":"/>
5597 <param name="select_polarity" value=""/>
5598 <section name="blackorwhitelist">
5599 <param name="similarity_threshold" value="-1.0"/>
5600 <param name="rt" value="0.01"/>
5601 <param name="mz" value="0.01"/>
5602 <param name="use_ppm_tolerance" value="false"/>
5603 <param name="blacklist" value="true"/>
5604 </section>
5605 </section>
5606 <section name="feature">
5607 <param name="q" value="0.51:"/>
5608 </section>
5609 <section name="consensus">
5610 <param name="map" value=""/>
5611 <param name="map_and" value="false"/>
5612 <section name="blackorwhitelist">
5613 <param name="blacklist" value="true"/>
5614 <param name="maps" value=""/>
5615 <param name="rt" value="60.0"/>
5616 <param name="mz" value="0.01"/>
5617 <param name="use_ppm_tolerance" value="false"/>
5618 </section>
5619 </section>
5620 <section name="f_and_c">
5621 <param name="charge" value="3:"/>
5622 <param name="size" value=":"/>
5623 <param name="remove_meta" value=""/>
5624 </section>
5625 <section name="id">
5626 <param name="remove_clashes" value="false"/>
5627 <param name="keep_best_score_id" value="false"/>
5628 <param name="sequences_whitelist" value=""/>
5629 <param name="sequence_comparison_method" value="substring"/>
5630 <param name="accessions_whitelist" value=""/>
5631 <param name="remove_annotated_features" value="false"/>
5632 <param name="remove_unannotated_features" value="false"/>
5633 <param name="remove_unassigned_ids" value="false"/>
5634 <param name="rt" value="0.1"/>
5635 <param name="mz" value="0.001"/>
5636 <param name="blacklist_imperfect" value="false"/>
5637 </section>
5638 <section name="algorithm">
5639 <section name="SignalToNoise">
5640 <param name="max_intensity" value="-1"/>
5641 <param name="auto_max_stdev_factor" value="3.0"/>
5642 <param name="auto_max_percentile" value="95"/>
5643 <param name="auto_mode" value="0"/>
5644 <param name="win_len" value="200.0"/>
5645 <param name="bin_count" value="30"/>
5646 <param name="min_required_elements" value="10"/>
5647 <param name="noise_for_empty_window" value="1e+20"/>
5648 <param name="write_log_messages" value="true"/>
5649 </section>
5650 </section>
5651 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5652 <output name="ctd_out" ftype="xml">
5653 <assert_contents>
5654 <is_valid_xml/>
5655 </assert_contents>
5656 </output>
5657 </test>
5658 <test expect_num_outputs="2">
5659 <conditional name="adv_opts_cond">
5660 <param name="adv_opts_selector" value="advanced"/>
5661 <param name="force" value="false"/>
5662 <param name="test" value="true"/>
5663 </conditional>
5664 <param name="in" value="FileFilter_7_input.mzML"/>
5665 <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5666 <param name="out_type" value="mzML"/>
5667 <param name="rt" value=":"/>
5668 <param name="mz" value=":"/>
5669 <param name="int" value="7000:"/>
5670 <param name="sort" value="false"/>
5671 <section name="peak_options">
5672 <param name="sn" value="0.0"/>
5673 <param name="rm_pc_charge" value=""/>
5674 <param name="pc_mz_range" value=":"/>
5675 <param name="pc_mz_list" value=""/>
5676 <param name="level" value="1 2 3"/>
5677 <param name="sort_peaks" value="false"/>
5678 <param name="no_chromatograms" value="false"/>
5679 <param name="remove_chromatograms" value="false"/>
5680 <param name="remove_empty" value="false"/>
5681 <param name="mz_precision" value="64"/>
5682 <param name="int_precision" value="32"/>
5683 <param name="indexed_file" value="true"/>
5684 <param name="zlib_compression" value="false"/>
5685 <section name="numpress">
5686 <param name="masstime" value="none"/>
5687 <param name="lossy_mass_accuracy" value="-1.0"/>
5688 <param name="intensity" value="none"/>
5689 <param name="float_da" value="none"/>
5690 </section>
5691 </section>
5692 <section name="spectra">
5693 <param name="remove_zoom" value="false"/>
5694 <param name="remove_mode" value=""/>
5695 <param name="remove_activation" value=""/>
5696 <param name="remove_collision_energy" value=":"/>
5697 <param name="remove_isolation_window_width" value=":"/>
5698 <param name="select_zoom" value="false"/>
5699 <param name="select_mode" value=""/>
5700 <param name="select_activation" value=""/>
5701 <param name="select_collision_energy" value=":"/>
5702 <param name="select_isolation_window_width" value=":"/>
5703 <param name="select_polarity" value=""/>
5704 <section name="blackorwhitelist">
5705 <param name="similarity_threshold" value="-1.0"/>
5706 <param name="rt" value="0.01"/>
5707 <param name="mz" value="0.01"/>
5708 <param name="use_ppm_tolerance" value="false"/>
5709 <param name="blacklist" value="true"/>
5710 </section>
5711 </section>
5712 <section name="feature">
5713 <param name="q" value=":"/>
5714 </section>
5715 <section name="consensus">
5716 <param name="map" value=""/>
5717 <param name="map_and" value="false"/>
5718 <section name="blackorwhitelist">
5719 <param name="blacklist" value="true"/>
5720 <param name="maps" value=""/>
5721 <param name="rt" value="60.0"/>
5722 <param name="mz" value="0.01"/>
5723 <param name="use_ppm_tolerance" value="false"/>
5724 </section>
5725 </section>
5726 <section name="f_and_c">
5727 <param name="charge" value=":"/>
5728 <param name="size" value=":"/>
5729 <param name="remove_meta" value=""/>
5730 </section>
5731 <section name="id">
5732 <param name="remove_clashes" value="false"/>
5733 <param name="keep_best_score_id" value="false"/>
5734 <param name="sequences_whitelist" value=""/>
5735 <param name="sequence_comparison_method" value="substring"/>
5736 <param name="accessions_whitelist" value=""/>
5737 <param name="remove_annotated_features" value="false"/>
5738 <param name="remove_unannotated_features" value="false"/>
5739 <param name="remove_unassigned_ids" value="false"/>
5740 <param name="rt" value="0.1"/>
5741 <param name="mz" value="0.001"/>
5742 <param name="blacklist_imperfect" value="false"/>
5743 </section>
5744 <section name="algorithm">
5745 <section name="SignalToNoise">
5746 <param name="max_intensity" value="-1"/>
5747 <param name="auto_max_stdev_factor" value="3.0"/>
5748 <param name="auto_max_percentile" value="95"/>
5749 <param name="auto_mode" value="0"/>
5750 <param name="win_len" value="200.0"/>
5751 <param name="bin_count" value="30"/>
5752 <param name="min_required_elements" value="10"/>
5753 <param name="noise_for_empty_window" value="1e+20"/>
5754 <param name="write_log_messages" value="true"/>
5755 </section>
5756 </section>
5757 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5758 <output name="ctd_out" ftype="xml">
5759 <assert_contents>
5760 <is_valid_xml/>
5761 </assert_contents>
5762 </output>
5763 </test>
5764 <test expect_num_outputs="2">
5765 <conditional name="adv_opts_cond">
5766 <param name="adv_opts_selector" value="advanced"/>
5767 <param name="force" value="false"/>
5768 <param name="test" value="true"/>
5769 </conditional>
5770 <param name="in" value="FileFilter_8_input.consensusXML"/>
5771 <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
5772 <param name="out_type" value="consensusXML"/>
5773 <param name="rt" value="600:1400"/>
5774 <param name="mz" value="700:2300"/>
5775 <param name="int" value="1100:6000"/>
5776 <param name="sort" value="false"/>
5777 <section name="peak_options">
5778 <param name="sn" value="0.0"/>
5779 <param name="rm_pc_charge" value=""/>
5780 <param name="pc_mz_range" value=":"/>
5781 <param name="pc_mz_list" value=""/>
5782 <param name="level" value="1 2 3"/>
5783 <param name="sort_peaks" value="false"/>
5784 <param name="no_chromatograms" value="false"/>
5785 <param name="remove_chromatograms" value="false"/>
5786 <param name="remove_empty" value="false"/>
5787 <param name="mz_precision" value="64"/>
5788 <param name="int_precision" value="32"/>
5789 <param name="indexed_file" value="true"/>
5790 <param name="zlib_compression" value="false"/>
5791 <section name="numpress">
5792 <param name="masstime" value="none"/>
5793 <param name="lossy_mass_accuracy" value="-1.0"/>
5794 <param name="intensity" value="none"/>
5795 <param name="float_da" value="none"/>
5796 </section>
5797 </section>
5798 <section name="spectra">
5799 <param name="remove_zoom" value="false"/>
5800 <param name="remove_mode" value=""/>
5801 <param name="remove_activation" value=""/>
5802 <param name="remove_collision_energy" value=":"/>
5803 <param name="remove_isolation_window_width" value=":"/>
5804 <param name="select_zoom" value="false"/>
5805 <param name="select_mode" value=""/>
5806 <param name="select_activation" value=""/>
5807 <param name="select_collision_energy" value=":"/>
5808 <param name="select_isolation_window_width" value=":"/>
5809 <param name="select_polarity" value=""/>
5810 <section name="blackorwhitelist">
5811 <param name="similarity_threshold" value="-1.0"/>
5812 <param name="rt" value="0.01"/>
5813 <param name="mz" value="0.01"/>
5814 <param name="use_ppm_tolerance" value="false"/>
5815 <param name="blacklist" value="true"/>
5816 </section>
5817 </section>
5818 <section name="feature">
5819 <param name="q" value=":"/>
5820 </section>
5821 <section name="consensus">
5822 <param name="map" value=""/>
5823 <param name="map_and" value="false"/>
5824 <section name="blackorwhitelist">
5825 <param name="blacklist" value="true"/>
5826 <param name="maps" value=""/>
5827 <param name="rt" value="60.0"/>
5828 <param name="mz" value="0.01"/>
5829 <param name="use_ppm_tolerance" value="false"/>
5830 </section>
5831 </section>
5832 <section name="f_and_c">
5833 <param name="charge" value=":"/>
5834 <param name="size" value=":"/>
5835 <param name="remove_meta" value=""/>
5836 </section>
5837 <section name="id">
5838 <param name="remove_clashes" value="false"/>
5839 <param name="keep_best_score_id" value="false"/>
5840 <param name="sequences_whitelist" value=""/>
5841 <param name="sequence_comparison_method" value="substring"/>
5842 <param name="accessions_whitelist" value=""/>
5843 <param name="remove_annotated_features" value="false"/>
5844 <param name="remove_unannotated_features" value="false"/>
5845 <param name="remove_unassigned_ids" value="false"/>
5846 <param name="rt" value="0.1"/>
5847 <param name="mz" value="0.001"/>
5848 <param name="blacklist_imperfect" value="false"/>
5849 </section>
5850 <section name="algorithm">
5851 <section name="SignalToNoise">
5852 <param name="max_intensity" value="-1"/>
5853 <param name="auto_max_stdev_factor" value="3.0"/>
5854 <param name="auto_max_percentile" value="95"/>
5855 <param name="auto_mode" value="0"/>
5856 <param name="win_len" value="200.0"/>
5857 <param name="bin_count" value="30"/>
5858 <param name="min_required_elements" value="10"/>
5859 <param name="noise_for_empty_window" value="1e+20"/>
5860 <param name="write_log_messages" value="true"/>
5861 </section>
5862 </section>
5863 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5864 <output name="ctd_out" ftype="xml">
5865 <assert_contents>
5866 <is_valid_xml/>
5867 </assert_contents>
5868 </output>
5869 </test>
5870 <test expect_num_outputs="2">
5871 <conditional name="adv_opts_cond">
5872 <param name="adv_opts_selector" value="advanced"/>
5873 <param name="force" value="false"/>
5874 <param name="test" value="true"/>
5875 </conditional>
5876 <param name="in" value="FileFilter_9_input.mzML"/>
5877 <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5878 <param name="out_type" value="mzML"/>
5879 <param name="rt" value=":"/>
5880 <param name="mz" value=":"/>
5881 <param name="int" value=":"/>
5882 <param name="sort" value="false"/>
5883 <section name="peak_options">
5884 <param name="sn" value="0.0"/>
5885 <param name="rm_pc_charge" value=""/>
5886 <param name="pc_mz_range" value=":"/>
5887 <param name="pc_mz_list" value=""/>
5888 <param name="level" value="1 2 3"/>
5889 <param name="sort_peaks" value="false"/>
5890 <param name="no_chromatograms" value="false"/>
5891 <param name="remove_chromatograms" value="false"/>
5892 <param name="remove_empty" value="false"/>
5893 <param name="mz_precision" value="64"/>
5894 <param name="int_precision" value="32"/>
5895 <param name="indexed_file" value="true"/>
5896 <param name="zlib_compression" value="false"/>
5897 <section name="numpress">
5898 <param name="masstime" value="none"/>
5899 <param name="lossy_mass_accuracy" value="-1.0"/>
5900 <param name="intensity" value="none"/>
5901 <param name="float_da" value="none"/>
5902 </section>
5903 </section>
5904 <section name="spectra">
5905 <param name="remove_zoom" value="false"/>
5906 <param name="remove_mode" value="SelectedIonMonitoring"/>
5907 <param name="remove_activation" value=""/>
5908 <param name="remove_collision_energy" value=":"/>
5909 <param name="remove_isolation_window_width" value=":"/>
5910 <param name="select_zoom" value="false"/>
5911 <param name="select_mode" value=""/>
5912 <param name="select_activation" value=""/>
5913 <param name="select_collision_energy" value=":"/>
5914 <param name="select_isolation_window_width" value=":"/>
5915 <param name="select_polarity" value=""/>
5916 <section name="blackorwhitelist">
5917 <param name="similarity_threshold" value="-1.0"/>
5918 <param name="rt" value="0.01"/>
5919 <param name="mz" value="0.01"/>
5920 <param name="use_ppm_tolerance" value="false"/>
5921 <param name="blacklist" value="true"/>
5922 </section>
5923 </section>
5924 <section name="feature">
5925 <param name="q" value=":"/>
5926 </section>
5927 <section name="consensus">
5928 <param name="map" value=""/>
5929 <param name="map_and" value="false"/>
5930 <section name="blackorwhitelist">
5931 <param name="blacklist" value="true"/>
5932 <param name="maps" value=""/>
5933 <param name="rt" value="60.0"/>
5934 <param name="mz" value="0.01"/>
5935 <param name="use_ppm_tolerance" value="false"/>
5936 </section>
5937 </section>
5938 <section name="f_and_c">
5939 <param name="charge" value=":"/>
5940 <param name="size" value=":"/>
5941 <param name="remove_meta" value=""/>
5942 </section>
5943 <section name="id">
5944 <param name="remove_clashes" value="false"/>
5945 <param name="keep_best_score_id" value="false"/>
5946 <param name="sequences_whitelist" value=""/>
5947 <param name="sequence_comparison_method" value="substring"/>
5948 <param name="accessions_whitelist" value=""/>
5949 <param name="remove_annotated_features" value="false"/>
5950 <param name="remove_unannotated_features" value="false"/>
5951 <param name="remove_unassigned_ids" value="false"/>
5952 <param name="rt" value="0.1"/>
5953 <param name="mz" value="0.001"/>
5954 <param name="blacklist_imperfect" value="false"/>
5955 </section>
5956 <section name="algorithm">
5957 <section name="SignalToNoise">
5958 <param name="max_intensity" value="-1"/>
5959 <param name="auto_max_stdev_factor" value="3.0"/>
5960 <param name="auto_max_percentile" value="95"/>
5961 <param name="auto_mode" value="0"/>
5962 <param name="win_len" value="200.0"/>
5963 <param name="bin_count" value="30"/>
5964 <param name="min_required_elements" value="10"/>
5965 <param name="noise_for_empty_window" value="1e+20"/>
5966 <param name="write_log_messages" value="true"/>
5967 </section>
5968 </section>
5969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5970 <output name="ctd_out" ftype="xml">
5971 <assert_contents>
5972 <is_valid_xml/>
5973 </assert_contents>
5974 </output>
5975 </test>
5976 <test expect_num_outputs="2">
5977 <conditional name="adv_opts_cond">
5978 <param name="adv_opts_selector" value="advanced"/>
5979 <param name="force" value="false"/>
5980 <param name="test" value="true"/>
5981 </conditional>
5982 <param name="in" value="FileFilter_10_input.mzML"/>
5983 <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
5984 <param name="out_type" value="mzML"/>
5985 <param name="rt" value=":"/>
5986 <param name="mz" value=":"/>
5987 <param name="int" value=":"/>
5988 <param name="sort" value="false"/>
5989 <section name="peak_options">
5990 <param name="sn" value="0.0"/>
5991 <param name="rm_pc_charge" value=""/>
5992 <param name="pc_mz_range" value=":"/>
5993 <param name="pc_mz_list" value=""/>
5994 <param name="level" value="1 2 3"/>
5995 <param name="sort_peaks" value="false"/>
5996 <param name="no_chromatograms" value="false"/>
5997 <param name="remove_chromatograms" value="false"/>
5998 <param name="remove_empty" value="false"/>
5999 <param name="mz_precision" value="64"/>
6000 <param name="int_precision" value="32"/>
6001 <param name="indexed_file" value="true"/>
6002 <param name="zlib_compression" value="false"/>
6003 <section name="numpress">
6004 <param name="masstime" value="none"/>
6005 <param name="lossy_mass_accuracy" value="-1.0"/>
6006 <param name="intensity" value="none"/>
6007 <param name="float_da" value="none"/>
6008 </section>
6009 </section>
6010 <section name="spectra">
6011 <param name="remove_zoom" value="false"/>
6012 <param name="remove_mode" value=""/>
6013 <param name="remove_activation" value="Collision-induced dissociation"/>
6014 <param name="remove_collision_energy" value=":"/>
6015 <param name="remove_isolation_window_width" value=":"/>
6016 <param name="select_zoom" value="false"/>
6017 <param name="select_mode" value=""/>
6018 <param name="select_activation" value=""/>
6019 <param name="select_collision_energy" value=":"/>
6020 <param name="select_isolation_window_width" value=":"/>
6021 <param name="select_polarity" value=""/>
6022 <section name="blackorwhitelist">
6023 <param name="similarity_threshold" value="-1.0"/>
6024 <param name="rt" value="0.01"/>
6025 <param name="mz" value="0.01"/>
6026 <param name="use_ppm_tolerance" value="false"/>
6027 <param name="blacklist" value="true"/>
6028 </section>
6029 </section>
6030 <section name="feature">
6031 <param name="q" value=":"/>
6032 </section>
6033 <section name="consensus">
6034 <param name="map" value=""/>
6035 <param name="map_and" value="false"/>
6036 <section name="blackorwhitelist">
6037 <param name="blacklist" value="true"/>
6038 <param name="maps" value=""/>
6039 <param name="rt" value="60.0"/>
6040 <param name="mz" value="0.01"/>
6041 <param name="use_ppm_tolerance" value="false"/>
6042 </section>
6043 </section>
6044 <section name="f_and_c">
6045 <param name="charge" value=":"/>
6046 <param name="size" value=":"/>
6047 <param name="remove_meta" value=""/>
6048 </section>
6049 <section name="id">
6050 <param name="remove_clashes" value="false"/>
6051 <param name="keep_best_score_id" value="false"/>
6052 <param name="sequences_whitelist" value=""/>
6053 <param name="sequence_comparison_method" value="substring"/>
6054 <param name="accessions_whitelist" value=""/>
6055 <param name="remove_annotated_features" value="false"/>
6056 <param name="remove_unannotated_features" value="false"/>
6057 <param name="remove_unassigned_ids" value="false"/>
6058 <param name="rt" value="0.1"/>
6059 <param name="mz" value="0.001"/>
6060 <param name="blacklist_imperfect" value="false"/>
6061 </section>
6062 <section name="algorithm">
6063 <section name="SignalToNoise">
6064 <param name="max_intensity" value="-1"/>
6065 <param name="auto_max_stdev_factor" value="3.0"/>
6066 <param name="auto_max_percentile" value="95"/>
6067 <param name="auto_mode" value="0"/>
6068 <param name="win_len" value="200.0"/>
6069 <param name="bin_count" value="30"/>
6070 <param name="min_required_elements" value="10"/>
6071 <param name="noise_for_empty_window" value="1e+20"/>
6072 <param name="write_log_messages" value="true"/>
6073 </section>
6074 </section>
6075 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6076 <output name="ctd_out" ftype="xml">
6077 <assert_contents>
6078 <is_valid_xml/>
6079 </assert_contents>
6080 </output>
6081 </test>
6082 <test expect_num_outputs="2">
6083 <conditional name="adv_opts_cond">
6084 <param name="adv_opts_selector" value="advanced"/>
6085 <param name="force" value="false"/>
6086 <param name="test" value="true"/>
6087 </conditional>
6088 <param name="in" value="FileFilter_11_input.mzML"/>
6089 <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6090 <param name="out_type" value="mzML"/>
6091 <param name="rt" value=":"/>
6092 <param name="mz" value=":"/>
6093 <param name="int" value=":"/>
6094 <param name="sort" value="false"/>
6095 <section name="peak_options">
6096 <param name="sn" value="0.0"/>
6097 <param name="rm_pc_charge" value=""/>
6098 <param name="pc_mz_range" value=":"/>
6099 <param name="pc_mz_list" value=""/>
6100 <param name="level" value="1 2 3"/>
6101 <param name="sort_peaks" value="false"/>
6102 <param name="no_chromatograms" value="false"/>
6103 <param name="remove_chromatograms" value="false"/>
6104 <param name="remove_empty" value="false"/>
6105 <param name="mz_precision" value="64"/>
6106 <param name="int_precision" value="32"/>
6107 <param name="indexed_file" value="true"/>
6108 <param name="zlib_compression" value="false"/>
6109 <section name="numpress">
6110 <param name="masstime" value="none"/>
6111 <param name="lossy_mass_accuracy" value="-1.0"/>
6112 <param name="intensity" value="none"/>
6113 <param name="float_da" value="none"/>
6114 </section>
6115 </section>
6116 <section name="spectra">
6117 <param name="remove_zoom" value="false"/>
6118 <param name="remove_mode" value=""/>
6119 <param name="remove_activation" value="Plasma desorption"/>
6120 <param name="remove_collision_energy" value=":"/>
6121 <param name="remove_isolation_window_width" value=":"/>
6122 <param name="select_zoom" value="false"/>
6123 <param name="select_mode" value=""/>
6124 <param name="select_activation" value=""/>
6125 <param name="select_collision_energy" value=":"/>
6126 <param name="select_isolation_window_width" value=":"/>
6127 <param name="select_polarity" value=""/>
6128 <section name="blackorwhitelist">
6129 <param name="similarity_threshold" value="-1.0"/>
6130 <param name="rt" value="0.01"/>
6131 <param name="mz" value="0.01"/>
6132 <param name="use_ppm_tolerance" value="false"/>
6133 <param name="blacklist" value="true"/>
6134 </section>
6135 </section>
6136 <section name="feature">
6137 <param name="q" value=":"/>
6138 </section>
6139 <section name="consensus">
6140 <param name="map" value=""/>
6141 <param name="map_and" value="false"/>
6142 <section name="blackorwhitelist">
6143 <param name="blacklist" value="true"/>
6144 <param name="maps" value=""/>
6145 <param name="rt" value="60.0"/>
6146 <param name="mz" value="0.01"/>
6147 <param name="use_ppm_tolerance" value="false"/>
6148 </section>
6149 </section>
6150 <section name="f_and_c">
6151 <param name="charge" value=":"/>
6152 <param name="size" value=":"/>
6153 <param name="remove_meta" value=""/>
6154 </section>
6155 <section name="id">
6156 <param name="remove_clashes" value="false"/>
6157 <param name="keep_best_score_id" value="false"/>
6158 <param name="sequences_whitelist" value=""/>
6159 <param name="sequence_comparison_method" value="substring"/>
6160 <param name="accessions_whitelist" value=""/>
6161 <param name="remove_annotated_features" value="false"/>
6162 <param name="remove_unannotated_features" value="false"/>
6163 <param name="remove_unassigned_ids" value="false"/>
6164 <param name="rt" value="0.1"/>
6165 <param name="mz" value="0.001"/>
6166 <param name="blacklist_imperfect" value="false"/>
6167 </section>
6168 <section name="algorithm">
6169 <section name="SignalToNoise">
6170 <param name="max_intensity" value="-1"/>
6171 <param name="auto_max_stdev_factor" value="3.0"/>
6172 <param name="auto_max_percentile" value="95"/>
6173 <param name="auto_mode" value="0"/>
6174 <param name="win_len" value="200.0"/>
6175 <param name="bin_count" value="30"/>
6176 <param name="min_required_elements" value="10"/>
6177 <param name="noise_for_empty_window" value="1e+20"/>
6178 <param name="write_log_messages" value="true"/>
6179 </section>
6180 </section>
6181 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6182 <output name="ctd_out" ftype="xml">
6183 <assert_contents>
6184 <is_valid_xml/>
6185 </assert_contents>
6186 </output>
6187 </test>
6188 <test expect_num_outputs="2">
6189 <conditional name="adv_opts_cond">
6190 <param name="adv_opts_selector" value="advanced"/>
6191 <param name="force" value="false"/>
6192 <param name="test" value="true"/>
6193 </conditional>
6194 <param name="in" value="FileFilter_12_input.mzML"/>
6195 <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
6196 <param name="out_type" value="mzML"/>
6197 <param name="rt" value=":"/>
6198 <param name="mz" value=":"/>
6199 <param name="int" value=":"/>
6200 <param name="sort" value="false"/>
6201 <section name="peak_options">
6202 <param name="sn" value="0.0"/>
6203 <param name="rm_pc_charge" value=""/>
6204 <param name="pc_mz_range" value=":"/>
6205 <param name="pc_mz_list" value=""/>
6206 <param name="level" value="1 2 3"/>
6207 <param name="sort_peaks" value="false"/>
6208 <param name="no_chromatograms" value="false"/>
6209 <param name="remove_chromatograms" value="true"/>
6210 <param name="remove_empty" value="false"/>
6211 <param name="mz_precision" value="64"/>
6212 <param name="int_precision" value="32"/>
6213 <param name="indexed_file" value="true"/>
6214 <param name="zlib_compression" value="false"/>
6215 <section name="numpress">
6216 <param name="masstime" value="none"/>
6217 <param name="lossy_mass_accuracy" value="-1.0"/>
6218 <param name="intensity" value="none"/>
6219 <param name="float_da" value="none"/>
6220 </section>
6221 </section>
6222 <section name="spectra">
6223 <param name="remove_zoom" value="false"/>
6224 <param name="remove_mode" value=""/>
6225 <param name="remove_activation" value=""/>
6226 <param name="remove_collision_energy" value=":"/>
6227 <param name="remove_isolation_window_width" value=":"/>
6228 <param name="select_zoom" value="false"/>
6229 <param name="select_mode" value=""/>
6230 <param name="select_activation" value=""/>
6231 <param name="select_collision_energy" value=":"/>
6232 <param name="select_isolation_window_width" value=":"/>
6233 <param name="select_polarity" value=""/>
6234 <section name="blackorwhitelist">
6235 <param name="similarity_threshold" value="-1.0"/>
6236 <param name="rt" value="0.01"/>
6237 <param name="mz" value="0.01"/>
6238 <param name="use_ppm_tolerance" value="false"/>
6239 <param name="blacklist" value="true"/>
6240 </section>
6241 </section>
6242 <section name="feature">
6243 <param name="q" value=":"/>
6244 </section>
6245 <section name="consensus">
6246 <param name="map" value=""/>
6247 <param name="map_and" value="false"/>
6248 <section name="blackorwhitelist">
6249 <param name="blacklist" value="true"/>
6250 <param name="maps" value=""/>
6251 <param name="rt" value="60.0"/>
6252 <param name="mz" value="0.01"/>
6253 <param name="use_ppm_tolerance" value="false"/>
6254 </section>
6255 </section>
6256 <section name="f_and_c">
6257 <param name="charge" value=":"/>
6258 <param name="size" value=":"/>
6259 <param name="remove_meta" value=""/>
6260 </section>
6261 <section name="id">
6262 <param name="remove_clashes" value="false"/>
6263 <param name="keep_best_score_id" value="false"/>
6264 <param name="sequences_whitelist" value=""/>
6265 <param name="sequence_comparison_method" value="substring"/>
6266 <param name="accessions_whitelist" value=""/>
6267 <param name="remove_annotated_features" value="false"/>
6268 <param name="remove_unannotated_features" value="false"/>
6269 <param name="remove_unassigned_ids" value="false"/>
6270 <param name="rt" value="0.1"/>
6271 <param name="mz" value="0.001"/>
6272 <param name="blacklist_imperfect" value="false"/>
6273 </section>
6274 <section name="algorithm">
6275 <section name="SignalToNoise">
6276 <param name="max_intensity" value="-1"/>
6277 <param name="auto_max_stdev_factor" value="3.0"/>
6278 <param name="auto_max_percentile" value="95"/>
6279 <param name="auto_mode" value="0"/>
6280 <param name="win_len" value="200.0"/>
6281 <param name="bin_count" value="30"/>
6282 <param name="min_required_elements" value="10"/>
6283 <param name="noise_for_empty_window" value="1e+20"/>
6284 <param name="write_log_messages" value="true"/>
6285 </section>
6286 </section>
6287 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6288 <output name="ctd_out" ftype="xml">
6289 <assert_contents>
6290 <is_valid_xml/>
6291 </assert_contents>
6292 </output>
6293 </test>
6294 <test expect_num_outputs="2">
6295 <conditional name="adv_opts_cond">
6296 <param name="adv_opts_selector" value="advanced"/>
6297 <param name="force" value="false"/>
6298 <param name="test" value="true"/>
6299 </conditional>
6300 <param name="in" value="FileFilter_13_input.consensusXML"/>
6301 <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6302 <param name="out_type" value="featureXML"/>
6303 <param name="rt" value=":"/>
6304 <param name="mz" value=":"/>
6305 <param name="int" value=":"/>
6306 <param name="sort" value="false"/>
6307 <section name="peak_options">
6308 <param name="sn" value="0.0"/>
6309 <param name="rm_pc_charge" value=""/>
6310 <param name="pc_mz_range" value=":"/>
6311 <param name="pc_mz_list" value=""/>
6312 <param name="level" value="1 2 3"/>
6313 <param name="sort_peaks" value="false"/>
6314 <param name="no_chromatograms" value="false"/>
6315 <param name="remove_chromatograms" value="false"/>
6316 <param name="remove_empty" value="false"/>
6317 <param name="mz_precision" value="64"/>
6318 <param name="int_precision" value="32"/>
6319 <param name="indexed_file" value="true"/>
6320 <param name="zlib_compression" value="false"/>
6321 <section name="numpress">
6322 <param name="masstime" value="none"/>
6323 <param name="lossy_mass_accuracy" value="-1.0"/>
6324 <param name="intensity" value="none"/>
6325 <param name="float_da" value="none"/>
6326 </section>
6327 </section>
6328 <section name="spectra">
6329 <param name="remove_zoom" value="false"/>
6330 <param name="remove_mode" value=""/>
6331 <param name="remove_activation" value=""/>
6332 <param name="remove_collision_energy" value=":"/>
6333 <param name="remove_isolation_window_width" value=":"/>
6334 <param name="select_zoom" value="false"/>
6335 <param name="select_mode" value=""/>
6336 <param name="select_activation" value=""/>
6337 <param name="select_collision_energy" value=":"/>
6338 <param name="select_isolation_window_width" value=":"/>
6339 <param name="select_polarity" value=""/>
6340 <section name="blackorwhitelist">
6341 <param name="similarity_threshold" value="-1.0"/>
6342 <param name="rt" value="0.01"/>
6343 <param name="mz" value="0.01"/>
6344 <param name="use_ppm_tolerance" value="false"/>
6345 <param name="blacklist" value="true"/>
6346 </section>
6347 </section>
6348 <section name="feature">
6349 <param name="q" value=":"/>
6350 </section>
6351 <section name="consensus">
6352 <param name="map" value="2"/>
6353 <param name="map_and" value="false"/>
6354 <section name="blackorwhitelist">
6355 <param name="blacklist" value="true"/>
6356 <param name="maps" value=""/>
6357 <param name="rt" value="60.0"/>
6358 <param name="mz" value="0.01"/>
6359 <param name="use_ppm_tolerance" value="false"/>
6360 </section>
6361 </section>
6362 <section name="f_and_c">
6363 <param name="charge" value=":"/>
6364 <param name="size" value=":"/>
6365 <param name="remove_meta" value=""/>
6366 </section>
6367 <section name="id">
6368 <param name="remove_clashes" value="false"/>
6369 <param name="keep_best_score_id" value="false"/>
6370 <param name="sequences_whitelist" value=""/>
6371 <param name="sequence_comparison_method" value="substring"/>
6372 <param name="accessions_whitelist" value=""/>
6373 <param name="remove_annotated_features" value="false"/>
6374 <param name="remove_unannotated_features" value="false"/>
6375 <param name="remove_unassigned_ids" value="false"/>
6376 <param name="rt" value="0.1"/>
6377 <param name="mz" value="0.001"/>
6378 <param name="blacklist_imperfect" value="false"/>
6379 </section>
6380 <section name="algorithm">
6381 <section name="SignalToNoise">
6382 <param name="max_intensity" value="-1"/>
6383 <param name="auto_max_stdev_factor" value="3.0"/>
6384 <param name="auto_max_percentile" value="95"/>
6385 <param name="auto_mode" value="0"/>
6386 <param name="win_len" value="200.0"/>
6387 <param name="bin_count" value="30"/>
6388 <param name="min_required_elements" value="10"/>
6389 <param name="noise_for_empty_window" value="1e+20"/>
6390 <param name="write_log_messages" value="true"/>
6391 </section>
6392 </section>
6393 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6394 <output name="ctd_out" ftype="xml">
6395 <assert_contents>
6396 <is_valid_xml/>
6397 </assert_contents>
6398 </output>
6399 </test>
6400 <test expect_num_outputs="2">
6401 <conditional name="adv_opts_cond">
6402 <param name="adv_opts_selector" value="advanced"/>
6403 <param name="force" value="false"/>
6404 <param name="test" value="true"/>
6405 </conditional>
6406 <param name="in" value="FileFilter_14_input.consensusXML"/>
6407 <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
6408 <param name="out_type" value="consensusXML"/>
6409 <param name="rt" value=":"/>
6410 <param name="mz" value=":"/>
6411 <param name="int" value=":"/>
6412 <param name="sort" value="false"/>
6413 <section name="peak_options">
6414 <param name="sn" value="0.0"/>
6415 <param name="rm_pc_charge" value=""/>
6416 <param name="pc_mz_range" value=":"/>
6417 <param name="pc_mz_list" value=""/>
6418 <param name="level" value="1 2 3"/>
6419 <param name="sort_peaks" value="false"/>
6420 <param name="no_chromatograms" value="false"/>
6421 <param name="remove_chromatograms" value="false"/>
6422 <param name="remove_empty" value="false"/>
6423 <param name="mz_precision" value="64"/>
6424 <param name="int_precision" value="32"/>
6425 <param name="indexed_file" value="true"/>
6426 <param name="zlib_compression" value="false"/>
6427 <section name="numpress">
6428 <param name="masstime" value="none"/>
6429 <param name="lossy_mass_accuracy" value="-1.0"/>
6430 <param name="intensity" value="none"/>
6431 <param name="float_da" value="none"/>
6432 </section>
6433 </section>
6434 <section name="spectra">
6435 <param name="remove_zoom" value="false"/>
6436 <param name="remove_mode" value=""/>
6437 <param name="remove_activation" value=""/>
6438 <param name="remove_collision_energy" value=":"/>
6439 <param name="remove_isolation_window_width" value=":"/>
6440 <param name="select_zoom" value="false"/>
6441 <param name="select_mode" value=""/>
6442 <param name="select_activation" value=""/>
6443 <param name="select_collision_energy" value=":"/>
6444 <param name="select_isolation_window_width" value=":"/>
6445 <param name="select_polarity" value=""/>
6446 <section name="blackorwhitelist">
6447 <param name="similarity_threshold" value="-1.0"/>
6448 <param name="rt" value="0.01"/>
6449 <param name="mz" value="0.01"/>
6450 <param name="use_ppm_tolerance" value="false"/>
6451 <param name="blacklist" value="true"/>
6452 </section>
6453 </section>
6454 <section name="feature">
6455 <param name="q" value=":"/>
6456 </section>
6457 <section name="consensus">
6458 <param name="map" value="0 2"/>
6459 <param name="map_and" value="false"/>
6460 <section name="blackorwhitelist">
6461 <param name="blacklist" value="true"/>
6462 <param name="maps" value=""/>
6463 <param name="rt" value="60.0"/>
6464 <param name="mz" value="0.01"/>
6465 <param name="use_ppm_tolerance" value="false"/>
6466 </section>
6467 </section>
6468 <section name="f_and_c">
6469 <param name="charge" value=":"/>
6470 <param name="size" value=":"/>
6471 <param name="remove_meta" value=""/>
6472 </section>
6473 <section name="id">
6474 <param name="remove_clashes" value="false"/>
6475 <param name="keep_best_score_id" value="false"/>
6476 <param name="sequences_whitelist" value=""/>
6477 <param name="sequence_comparison_method" value="substring"/>
6478 <param name="accessions_whitelist" value=""/>
6479 <param name="remove_annotated_features" value="false"/>
6480 <param name="remove_unannotated_features" value="false"/>
6481 <param name="remove_unassigned_ids" value="false"/>
6482 <param name="rt" value="0.1"/>
6483 <param name="mz" value="0.001"/>
6484 <param name="blacklist_imperfect" value="false"/>
6485 </section>
6486 <section name="algorithm">
6487 <section name="SignalToNoise">
6488 <param name="max_intensity" value="-1"/>
6489 <param name="auto_max_stdev_factor" value="3.0"/>
6490 <param name="auto_max_percentile" value="95"/>
6491 <param name="auto_mode" value="0"/>
6492 <param name="win_len" value="200.0"/>
6493 <param name="bin_count" value="30"/>
6494 <param name="min_required_elements" value="10"/>
6495 <param name="noise_for_empty_window" value="1e+20"/>
6496 <param name="write_log_messages" value="true"/>
6497 </section>
6498 </section>
6499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6500 <output name="ctd_out" ftype="xml">
6501 <assert_contents>
6502 <is_valid_xml/>
6503 </assert_contents>
6504 </output>
6505 </test>
6506 <test expect_num_outputs="2">
6507 <conditional name="adv_opts_cond">
6508 <param name="adv_opts_selector" value="advanced"/>
6509 <param name="force" value="false"/>
6510 <param name="test" value="true"/>
6511 </conditional>
6512 <param name="in" value="FileFilter_15_input.featureXML"/>
6513 <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6514 <param name="out_type" value="featurexml"/>
6515 <param name="rt" value=":"/>
6516 <param name="mz" value=":"/>
6517 <param name="int" value=":"/>
6518 <param name="sort" value="false"/>
6519 <section name="peak_options">
6520 <param name="sn" value="0.0"/>
6521 <param name="rm_pc_charge" value=""/>
6522 <param name="pc_mz_range" value=":"/>
6523 <param name="pc_mz_list" value=""/>
6524 <param name="level" value="1 2 3"/>
6525 <param name="sort_peaks" value="false"/>
6526 <param name="no_chromatograms" value="false"/>
6527 <param name="remove_chromatograms" value="false"/>
6528 <param name="remove_empty" value="false"/>
6529 <param name="mz_precision" value="64"/>
6530 <param name="int_precision" value="32"/>
6531 <param name="indexed_file" value="true"/>
6532 <param name="zlib_compression" value="false"/>
6533 <section name="numpress">
6534 <param name="masstime" value="none"/>
6535 <param name="lossy_mass_accuracy" value="-1.0"/>
6536 <param name="intensity" value="none"/>
6537 <param name="float_da" value="none"/>
6538 </section>
6539 </section>
6540 <section name="spectra">
6541 <param name="remove_zoom" value="false"/>
6542 <param name="remove_mode" value=""/>
6543 <param name="remove_activation" value=""/>
6544 <param name="remove_collision_energy" value=":"/>
6545 <param name="remove_isolation_window_width" value=":"/>
6546 <param name="select_zoom" value="false"/>
6547 <param name="select_mode" value=""/>
6548 <param name="select_activation" value=""/>
6549 <param name="select_collision_energy" value=":"/>
6550 <param name="select_isolation_window_width" value=":"/>
6551 <param name="select_polarity" value=""/>
6552 <section name="blackorwhitelist">
6553 <param name="similarity_threshold" value="-1.0"/>
6554 <param name="rt" value="0.01"/>
6555 <param name="mz" value="0.01"/>
6556 <param name="use_ppm_tolerance" value="false"/>
6557 <param name="blacklist" value="true"/>
6558 </section>
6559 </section>
6560 <section name="feature">
6561 <param name="q" value=":"/>
6562 </section>
6563 <section name="consensus">
6564 <param name="map" value=""/>
6565 <param name="map_and" value="false"/>
6566 <section name="blackorwhitelist">
6567 <param name="blacklist" value="true"/>
6568 <param name="maps" value=""/>
6569 <param name="rt" value="60.0"/>
6570 <param name="mz" value="0.01"/>
6571 <param name="use_ppm_tolerance" value="false"/>
6572 </section>
6573 </section>
6574 <section name="f_and_c">
6575 <param name="charge" value=":"/>
6576 <param name="size" value=":"/>
6577 <param name="remove_meta" value=""/>
6578 </section>
6579 <section name="id">
6580 <param name="remove_clashes" value="false"/>
6581 <param name="keep_best_score_id" value="false"/>
6582 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
6583 <param name="sequence_comparison_method" value="substring"/>
6584 <param name="accessions_whitelist" value=""/>
6585 <param name="remove_annotated_features" value="false"/>
6586 <param name="remove_unannotated_features" value="false"/>
6587 <param name="remove_unassigned_ids" value="true"/>
6588 <param name="rt" value="0.1"/>
6589 <param name="mz" value="0.001"/>
6590 <param name="blacklist_imperfect" value="false"/>
6591 </section>
6592 <section name="algorithm">
6593 <section name="SignalToNoise">
6594 <param name="max_intensity" value="-1"/>
6595 <param name="auto_max_stdev_factor" value="3.0"/>
6596 <param name="auto_max_percentile" value="95"/>
6597 <param name="auto_mode" value="0"/>
6598 <param name="win_len" value="200.0"/>
6599 <param name="bin_count" value="30"/>
6600 <param name="min_required_elements" value="10"/>
6601 <param name="noise_for_empty_window" value="1e+20"/>
6602 <param name="write_log_messages" value="true"/>
6603 </section>
6604 </section>
6605 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6606 <output name="ctd_out" ftype="xml">
6607 <assert_contents>
6608 <is_valid_xml/>
6609 </assert_contents>
6610 </output>
6611 </test>
6612 <test expect_num_outputs="2">
6613 <conditional name="adv_opts_cond">
6614 <param name="adv_opts_selector" value="advanced"/>
6615 <param name="force" value="false"/>
6616 <param name="test" value="true"/>
6617 </conditional>
6618 <param name="in" value="FileFilter_15_input.featureXML"/>
6619 <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6620 <param name="out_type" value="featurexml"/>
6621 <param name="rt" value="3000:4000"/>
6622 <param name="mz" value="400:600"/>
6623 <param name="int" value=":"/>
6624 <param name="sort" value="false"/>
6625 <section name="peak_options">
6626 <param name="sn" value="0.0"/>
6627 <param name="rm_pc_charge" value=""/>
6628 <param name="pc_mz_range" value=":"/>
6629 <param name="pc_mz_list" value=""/>
6630 <param name="level" value="1 2 3"/>
6631 <param name="sort_peaks" value="false"/>
6632 <param name="no_chromatograms" value="false"/>
6633 <param name="remove_chromatograms" value="false"/>
6634 <param name="remove_empty" value="false"/>
6635 <param name="mz_precision" value="64"/>
6636 <param name="int_precision" value="32"/>
6637 <param name="indexed_file" value="true"/>
6638 <param name="zlib_compression" value="false"/>
6639 <section name="numpress">
6640 <param name="masstime" value="none"/>
6641 <param name="lossy_mass_accuracy" value="-1.0"/>
6642 <param name="intensity" value="none"/>
6643 <param name="float_da" value="none"/>
6644 </section>
6645 </section>
6646 <section name="spectra">
6647 <param name="remove_zoom" value="false"/>
6648 <param name="remove_mode" value=""/>
6649 <param name="remove_activation" value=""/>
6650 <param name="remove_collision_energy" value=":"/>
6651 <param name="remove_isolation_window_width" value=":"/>
6652 <param name="select_zoom" value="false"/>
6653 <param name="select_mode" value=""/>
6654 <param name="select_activation" value=""/>
6655 <param name="select_collision_energy" value=":"/>
6656 <param name="select_isolation_window_width" value=":"/>
6657 <param name="select_polarity" value=""/>
6658 <section name="blackorwhitelist">
6659 <param name="similarity_threshold" value="-1.0"/>
6660 <param name="rt" value="0.01"/>
6661 <param name="mz" value="0.01"/>
6662 <param name="use_ppm_tolerance" value="false"/>
6663 <param name="blacklist" value="true"/>
6664 </section>
6665 </section>
6666 <section name="feature">
6667 <param name="q" value=":"/>
6668 </section>
6669 <section name="consensus">
6670 <param name="map" value=""/>
6671 <param name="map_and" value="false"/>
6672 <section name="blackorwhitelist">
6673 <param name="blacklist" value="true"/>
6674 <param name="maps" value=""/>
6675 <param name="rt" value="60.0"/>
6676 <param name="mz" value="0.01"/>
6677 <param name="use_ppm_tolerance" value="false"/>
6678 </section>
6679 </section>
6680 <section name="f_and_c">
6681 <param name="charge" value=":"/>
6682 <param name="size" value=":"/>
6683 <param name="remove_meta" value=""/>
6684 </section>
6685 <section name="id">
6686 <param name="remove_clashes" value="false"/>
6687 <param name="keep_best_score_id" value="false"/>
6688 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
6689 <param name="sequence_comparison_method" value="substring"/>
6690 <param name="accessions_whitelist" value=""/>
6691 <param name="remove_annotated_features" value="false"/>
6692 <param name="remove_unannotated_features" value="false"/>
6693 <param name="remove_unassigned_ids" value="true"/>
6694 <param name="rt" value="0.1"/>
6695 <param name="mz" value="0.001"/>
6696 <param name="blacklist_imperfect" value="false"/>
6697 </section>
6698 <section name="algorithm">
6699 <section name="SignalToNoise">
6700 <param name="max_intensity" value="-1"/>
6701 <param name="auto_max_stdev_factor" value="3.0"/>
6702 <param name="auto_max_percentile" value="95"/>
6703 <param name="auto_mode" value="0"/>
6704 <param name="win_len" value="200.0"/>
6705 <param name="bin_count" value="30"/>
6706 <param name="min_required_elements" value="10"/>
6707 <param name="noise_for_empty_window" value="1e+20"/>
6708 <param name="write_log_messages" value="true"/>
6709 </section>
6710 </section>
6711 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6712 <output name="ctd_out" ftype="xml">
6713 <assert_contents>
6714 <is_valid_xml/>
6715 </assert_contents>
6716 </output>
6717 </test>
6718 <test expect_num_outputs="2">
6719 <conditional name="adv_opts_cond">
6720 <param name="adv_opts_selector" value="advanced"/>
6721 <param name="force" value="false"/>
6722 <param name="test" value="true"/>
6723 </conditional>
6724 <param name="in" value="FileFilter_15_input.featureXML"/>
6725 <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
6726 <param name="out_type" value="featurexml"/>
6727 <param name="rt" value="3000:4000"/>
6728 <param name="mz" value="400:600"/>
6729 <param name="int" value=":"/>
6730 <param name="sort" value="false"/>
6731 <section name="peak_options">
6732 <param name="sn" value="0.0"/>
6733 <param name="rm_pc_charge" value=""/>
6734 <param name="pc_mz_range" value=":"/>
6735 <param name="pc_mz_list" value=""/>
6736 <param name="level" value="1 2 3"/>
6737 <param name="sort_peaks" value="false"/>
6738 <param name="no_chromatograms" value="false"/>
6739 <param name="remove_chromatograms" value="false"/>
6740 <param name="remove_empty" value="false"/>
6741 <param name="mz_precision" value="64"/>
6742 <param name="int_precision" value="32"/>
6743 <param name="indexed_file" value="true"/>
6744 <param name="zlib_compression" value="false"/>
6745 <section name="numpress">
6746 <param name="masstime" value="none"/>
6747 <param name="lossy_mass_accuracy" value="-1.0"/>
6748 <param name="intensity" value="none"/>
6749 <param name="float_da" value="none"/>
6750 </section>
6751 </section>
6752 <section name="spectra">
6753 <param name="remove_zoom" value="false"/>
6754 <param name="remove_mode" value=""/>
6755 <param name="remove_activation" value=""/>
6756 <param name="remove_collision_energy" value=":"/>
6757 <param name="remove_isolation_window_width" value=":"/>
6758 <param name="select_zoom" value="false"/>
6759 <param name="select_mode" value=""/>
6760 <param name="select_activation" value=""/>
6761 <param name="select_collision_energy" value=":"/>
6762 <param name="select_isolation_window_width" value=":"/>
6763 <param name="select_polarity" value=""/>
6764 <section name="blackorwhitelist">
6765 <param name="similarity_threshold" value="-1.0"/>
6766 <param name="rt" value="0.01"/>
6767 <param name="mz" value="0.01"/>
6768 <param name="use_ppm_tolerance" value="false"/>
6769 <param name="blacklist" value="true"/>
6770 </section>
6771 </section>
6772 <section name="feature">
6773 <param name="q" value=":"/>
6774 </section>
6775 <section name="consensus">
6776 <param name="map" value=""/>
6777 <param name="map_and" value="false"/>
6778 <section name="blackorwhitelist">
6779 <param name="blacklist" value="true"/>
6780 <param name="maps" value=""/>
6781 <param name="rt" value="60.0"/>
6782 <param name="mz" value="0.01"/>
6783 <param name="use_ppm_tolerance" value="false"/>
6784 </section>
6785 </section>
6786 <section name="f_and_c">
6787 <param name="charge" value=":"/>
6788 <param name="size" value=":"/>
6789 <param name="remove_meta" value=""/>
6790 </section>
6791 <section name="id">
6792 <param name="remove_clashes" value="false"/>
6793 <param name="keep_best_score_id" value="false"/>
6794 <param name="sequences_whitelist" value=""/>
6795 <param name="sequence_comparison_method" value="substring"/>
6796 <param name="accessions_whitelist" value=""/>
6797 <param name="remove_annotated_features" value="true"/>
6798 <param name="remove_unannotated_features" value="false"/>
6799 <param name="remove_unassigned_ids" value="false"/>
6800 <param name="rt" value="0.1"/>
6801 <param name="mz" value="0.001"/>
6802 <param name="blacklist_imperfect" value="false"/>
6803 </section>
6804 <section name="algorithm">
6805 <section name="SignalToNoise">
6806 <param name="max_intensity" value="-1"/>
6807 <param name="auto_max_stdev_factor" value="3.0"/>
6808 <param name="auto_max_percentile" value="95"/>
6809 <param name="auto_mode" value="0"/>
6810 <param name="win_len" value="200.0"/>
6811 <param name="bin_count" value="30"/>
6812 <param name="min_required_elements" value="10"/>
6813 <param name="noise_for_empty_window" value="1e+20"/>
6814 <param name="write_log_messages" value="true"/>
6815 </section>
6816 </section>
6817 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6818 <output name="ctd_out" ftype="xml">
6819 <assert_contents>
6820 <is_valid_xml/>
6821 </assert_contents>
6822 </output>
6823 </test>
6824 <test expect_num_outputs="2">
6825 <conditional name="adv_opts_cond">
6826 <param name="adv_opts_selector" value="advanced"/>
6827 <param name="force" value="false"/>
6828 <param name="test" value="true"/>
6829 </conditional>
6830 <param name="in" value="FileFilter_18_input.consensusXML"/>
6831 <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
6832 <param name="out_type" value="consensusxml"/>
6833 <param name="rt" value=":"/>
6834 <param name="mz" value=":"/>
6835 <param name="int" value=":"/>
6836 <param name="sort" value="false"/>
6837 <section name="peak_options">
6838 <param name="sn" value="0.0"/>
6839 <param name="rm_pc_charge" value=""/>
6840 <param name="pc_mz_range" value=":"/>
6841 <param name="pc_mz_list" value=""/>
6842 <param name="level" value="1 2 3"/>
6843 <param name="sort_peaks" value="false"/>
6844 <param name="no_chromatograms" value="false"/>
6845 <param name="remove_chromatograms" value="false"/>
6846 <param name="remove_empty" value="false"/>
6847 <param name="mz_precision" value="64"/>
6848 <param name="int_precision" value="32"/>
6849 <param name="indexed_file" value="true"/>
6850 <param name="zlib_compression" value="false"/>
6851 <section name="numpress">
6852 <param name="masstime" value="none"/>
6853 <param name="lossy_mass_accuracy" value="-1.0"/>
6854 <param name="intensity" value="none"/>
6855 <param name="float_da" value="none"/>
6856 </section>
6857 </section>
6858 <section name="spectra">
6859 <param name="remove_zoom" value="false"/>
6860 <param name="remove_mode" value=""/>
6861 <param name="remove_activation" value=""/>
6862 <param name="remove_collision_energy" value=":"/>
6863 <param name="remove_isolation_window_width" value=":"/>
6864 <param name="select_zoom" value="false"/>
6865 <param name="select_mode" value=""/>
6866 <param name="select_activation" value=""/>
6867 <param name="select_collision_energy" value=":"/>
6868 <param name="select_isolation_window_width" value=":"/>
6869 <param name="select_polarity" value=""/>
6870 <section name="blackorwhitelist">
6871 <param name="similarity_threshold" value="-1.0"/>
6872 <param name="rt" value="0.01"/>
6873 <param name="mz" value="0.01"/>
6874 <param name="use_ppm_tolerance" value="false"/>
6875 <param name="blacklist" value="true"/>
6876 </section>
6877 </section>
6878 <section name="feature">
6879 <param name="q" value=":"/>
6880 </section>
6881 <section name="consensus">
6882 <param name="map" value=""/>
6883 <param name="map_and" value="false"/>
6884 <section name="blackorwhitelist">
6885 <param name="blacklist" value="true"/>
6886 <param name="maps" value=""/>
6887 <param name="rt" value="60.0"/>
6888 <param name="mz" value="0.01"/>
6889 <param name="use_ppm_tolerance" value="false"/>
6890 </section>
6891 </section>
6892 <section name="f_and_c">
6893 <param name="charge" value=":"/>
6894 <param name="size" value=":"/>
6895 <param name="remove_meta" value=""/>
6896 </section>
6897 <section name="id">
6898 <param name="remove_clashes" value="false"/>
6899 <param name="keep_best_score_id" value="false"/>
6900 <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
6901 <param name="sequence_comparison_method" value="substring"/>
6902 <param name="accessions_whitelist" value=""/>
6903 <param name="remove_annotated_features" value="false"/>
6904 <param name="remove_unannotated_features" value="false"/>
6905 <param name="remove_unassigned_ids" value="true"/>
6906 <param name="rt" value="0.1"/>
6907 <param name="mz" value="0.001"/>
6908 <param name="blacklist_imperfect" value="false"/>
6909 </section>
6910 <section name="algorithm">
6911 <section name="SignalToNoise">
6912 <param name="max_intensity" value="-1"/>
6913 <param name="auto_max_stdev_factor" value="3.0"/>
6914 <param name="auto_max_percentile" value="95"/>
6915 <param name="auto_mode" value="0"/>
6916 <param name="win_len" value="200.0"/>
6917 <param name="bin_count" value="30"/>
6918 <param name="min_required_elements" value="10"/>
6919 <param name="noise_for_empty_window" value="1e+20"/>
6920 <param name="write_log_messages" value="true"/>
6921 </section>
6922 </section>
6923 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6924 <output name="ctd_out" ftype="xml">
6925 <assert_contents>
6926 <is_valid_xml/>
6927 </assert_contents>
6928 </output>
6929 </test>
6930 <test expect_num_outputs="2">
6931 <conditional name="adv_opts_cond">
6932 <param name="adv_opts_selector" value="advanced"/>
6933 <param name="force" value="false"/>
6934 <param name="test" value="true"/>
6935 </conditional>
6936 <param name="in" value="FileFilter_18_input.consensusXML"/>
6937 <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
6938 <param name="out_type" value="consensusxml"/>
6939 <param name="rt" value="3000:4000"/>
6940 <param name="mz" value="400:600"/>
6941 <param name="int" value=":"/>
6942 <param name="sort" value="false"/>
6943 <section name="peak_options">
6944 <param name="sn" value="0.0"/>
6945 <param name="rm_pc_charge" value=""/>
6946 <param name="pc_mz_range" value=":"/>
6947 <param name="pc_mz_list" value=""/>
6948 <param name="level" value="1 2 3"/>
6949 <param name="sort_peaks" value="false"/>
6950 <param name="no_chromatograms" value="false"/>
6951 <param name="remove_chromatograms" value="false"/>
6952 <param name="remove_empty" value="false"/>
6953 <param name="mz_precision" value="64"/>
6954 <param name="int_precision" value="32"/>
6955 <param name="indexed_file" value="true"/>
6956 <param name="zlib_compression" value="false"/>
6957 <section name="numpress">
6958 <param name="masstime" value="none"/>
6959 <param name="lossy_mass_accuracy" value="-1.0"/>
6960 <param name="intensity" value="none"/>
6961 <param name="float_da" value="none"/>
6962 </section>
6963 </section>
6964 <section name="spectra">
6965 <param name="remove_zoom" value="false"/>
6966 <param name="remove_mode" value=""/>
6967 <param name="remove_activation" value=""/>
6968 <param name="remove_collision_energy" value=":"/>
6969 <param name="remove_isolation_window_width" value=":"/>
6970 <param name="select_zoom" value="false"/>
6971 <param name="select_mode" value=""/>
6972 <param name="select_activation" value=""/>
6973 <param name="select_collision_energy" value=":"/>
6974 <param name="select_isolation_window_width" value=":"/>
6975 <param name="select_polarity" value=""/>
6976 <section name="blackorwhitelist">
6977 <param name="similarity_threshold" value="-1.0"/>
6978 <param name="rt" value="0.01"/>
6979 <param name="mz" value="0.01"/>
6980 <param name="use_ppm_tolerance" value="false"/>
6981 <param name="blacklist" value="true"/>
6982 </section>
6983 </section>
6984 <section name="feature">
6985 <param name="q" value=":"/>
6986 </section>
6987 <section name="consensus">
6988 <param name="map" value=""/>
6989 <param name="map_and" value="false"/>
6990 <section name="blackorwhitelist">
6991 <param name="blacklist" value="true"/>
6992 <param name="maps" value=""/>
6993 <param name="rt" value="60.0"/>
6994 <param name="mz" value="0.01"/>
6995 <param name="use_ppm_tolerance" value="false"/>
6996 </section>
6997 </section>
6998 <section name="f_and_c">
6999 <param name="charge" value=":"/>
7000 <param name="size" value=":"/>
7001 <param name="remove_meta" value=""/>
7002 </section>
7003 <section name="id">
7004 <param name="remove_clashes" value="false"/>
7005 <param name="keep_best_score_id" value="false"/>
7006 <param name="sequences_whitelist" value=""/>
7007 <param name="sequence_comparison_method" value="substring"/>
7008 <param name="accessions_whitelist" value=""/>
7009 <param name="remove_annotated_features" value="false"/>
7010 <param name="remove_unannotated_features" value="true"/>
7011 <param name="remove_unassigned_ids" value="false"/>
7012 <param name="rt" value="0.1"/>
7013 <param name="mz" value="0.001"/>
7014 <param name="blacklist_imperfect" value="false"/>
7015 </section>
7016 <section name="algorithm">
7017 <section name="SignalToNoise">
7018 <param name="max_intensity" value="-1"/>
7019 <param name="auto_max_stdev_factor" value="3.0"/>
7020 <param name="auto_max_percentile" value="95"/>
7021 <param name="auto_mode" value="0"/>
7022 <param name="win_len" value="200.0"/>
7023 <param name="bin_count" value="30"/>
7024 <param name="min_required_elements" value="10"/>
7025 <param name="noise_for_empty_window" value="1e+20"/>
7026 <param name="write_log_messages" value="true"/>
7027 </section>
7028 </section>
7029 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7030 <output name="ctd_out" ftype="xml">
7031 <assert_contents>
7032 <is_valid_xml/>
7033 </assert_contents>
7034 </output>
7035 </test>
7036 <test expect_num_outputs="2">
7037 <conditional name="adv_opts_cond">
7038 <param name="adv_opts_selector" value="advanced"/>
7039 <param name="force" value="false"/>
7040 <param name="test" value="true"/>
7041 </conditional>
7042 <param name="in" value="FileFilter_15_input.featureXML"/>
7043 <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
7044 <param name="out_type" value="featurexml"/>
7045 <param name="rt" value=":"/>
7046 <param name="mz" value=":"/>
7047 <param name="int" value=":"/>
7048 <param name="sort" value="false"/>
7049 <section name="peak_options">
7050 <param name="sn" value="0.0"/>
7051 <param name="rm_pc_charge" value=""/>
7052 <param name="pc_mz_range" value=":"/>
7053 <param name="pc_mz_list" value=""/>
7054 <param name="level" value="1 2 3"/>
7055 <param name="sort_peaks" value="false"/>
7056 <param name="no_chromatograms" value="false"/>
7057 <param name="remove_chromatograms" value="false"/>
7058 <param name="remove_empty" value="false"/>
7059 <param name="mz_precision" value="64"/>
7060 <param name="int_precision" value="32"/>
7061 <param name="indexed_file" value="true"/>
7062 <param name="zlib_compression" value="false"/>
7063 <section name="numpress">
7064 <param name="masstime" value="none"/>
7065 <param name="lossy_mass_accuracy" value="-1.0"/>
7066 <param name="intensity" value="none"/>
7067 <param name="float_da" value="none"/>
7068 </section>
7069 </section>
7070 <section name="spectra">
7071 <param name="remove_zoom" value="false"/>
7072 <param name="remove_mode" value=""/>
7073 <param name="remove_activation" value=""/>
7074 <param name="remove_collision_energy" value=":"/>
7075 <param name="remove_isolation_window_width" value=":"/>
7076 <param name="select_zoom" value="false"/>
7077 <param name="select_mode" value=""/>
7078 <param name="select_activation" value=""/>
7079 <param name="select_collision_energy" value=":"/>
7080 <param name="select_isolation_window_width" value=":"/>
7081 <param name="select_polarity" value=""/>
7082 <section name="blackorwhitelist">
7083 <param name="similarity_threshold" value="-1.0"/>
7084 <param name="rt" value="0.01"/>
7085 <param name="mz" value="0.01"/>
7086 <param name="use_ppm_tolerance" value="false"/>
7087 <param name="blacklist" value="true"/>
7088 </section>
7089 </section>
7090 <section name="feature">
7091 <param name="q" value=":"/>
7092 </section>
7093 <section name="consensus">
7094 <param name="map" value=""/>
7095 <param name="map_and" value="false"/>
7096 <section name="blackorwhitelist">
7097 <param name="blacklist" value="true"/>
7098 <param name="maps" value=""/>
7099 <param name="rt" value="60.0"/>
7100 <param name="mz" value="0.01"/>
7101 <param name="use_ppm_tolerance" value="false"/>
7102 </section>
7103 </section>
7104 <section name="f_and_c">
7105 <param name="charge" value=":"/>
7106 <param name="size" value=":"/>
7107 <param name="remove_meta" value=""/>
7108 </section>
7109 <section name="id">
7110 <param name="remove_clashes" value="false"/>
7111 <param name="keep_best_score_id" value="false"/>
7112 <param name="sequences_whitelist" value=""/>
7113 <param name="sequence_comparison_method" value="substring"/>
7114 <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
7115 <param name="remove_annotated_features" value="false"/>
7116 <param name="remove_unannotated_features" value="false"/>
7117 <param name="remove_unassigned_ids" value="true"/>
7118 <param name="rt" value="0.1"/>
7119 <param name="mz" value="0.001"/>
7120 <param name="blacklist_imperfect" value="false"/>
7121 </section>
7122 <section name="algorithm">
7123 <section name="SignalToNoise">
7124 <param name="max_intensity" value="-1"/>
7125 <param name="auto_max_stdev_factor" value="3.0"/>
7126 <param name="auto_max_percentile" value="95"/>
7127 <param name="auto_mode" value="0"/>
7128 <param name="win_len" value="200.0"/>
7129 <param name="bin_count" value="30"/>
7130 <param name="min_required_elements" value="10"/>
7131 <param name="noise_for_empty_window" value="1e+20"/>
7132 <param name="write_log_messages" value="true"/>
7133 </section>
7134 </section>
7135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7136 <output name="ctd_out" ftype="xml">
7137 <assert_contents>
7138 <is_valid_xml/>
7139 </assert_contents>
7140 </output>
7141 </test>
7142 <test expect_num_outputs="2">
7143 <conditional name="adv_opts_cond">
7144 <param name="adv_opts_selector" value="advanced"/>
7145 <param name="force" value="false"/>
7146 <param name="test" value="true"/>
7147 </conditional>
7148 <param name="in" value="FileFilter_15_input.featureXML"/>
7149 <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
7150 <param name="out_type" value="featurexml"/>
7151 <param name="rt" value=":"/>
7152 <param name="mz" value=":"/>
7153 <param name="int" value=":"/>
7154 <param name="sort" value="false"/>
7155 <section name="peak_options">
7156 <param name="sn" value="0.0"/>
7157 <param name="rm_pc_charge" value=""/>
7158 <param name="pc_mz_range" value=":"/>
7159 <param name="pc_mz_list" value=""/>
7160 <param name="level" value="1 2 3"/>
7161 <param name="sort_peaks" value="false"/>
7162 <param name="no_chromatograms" value="false"/>
7163 <param name="remove_chromatograms" value="false"/>
7164 <param name="remove_empty" value="false"/>
7165 <param name="mz_precision" value="64"/>
7166 <param name="int_precision" value="32"/>
7167 <param name="indexed_file" value="true"/>
7168 <param name="zlib_compression" value="false"/>
7169 <section name="numpress">
7170 <param name="masstime" value="none"/>
7171 <param name="lossy_mass_accuracy" value="-1.0"/>
7172 <param name="intensity" value="none"/>
7173 <param name="float_da" value="none"/>
7174 </section>
7175 </section>
7176 <section name="spectra">
7177 <param name="remove_zoom" value="false"/>
7178 <param name="remove_mode" value=""/>
7179 <param name="remove_activation" value=""/>
7180 <param name="remove_collision_energy" value=":"/>
7181 <param name="remove_isolation_window_width" value=":"/>
7182 <param name="select_zoom" value="false"/>
7183 <param name="select_mode" value=""/>
7184 <param name="select_activation" value=""/>
7185 <param name="select_collision_energy" value=":"/>
7186 <param name="select_isolation_window_width" value=":"/>
7187 <param name="select_polarity" value=""/>
7188 <section name="blackorwhitelist">
7189 <param name="similarity_threshold" value="-1.0"/>
7190 <param name="rt" value="0.01"/>
7191 <param name="mz" value="0.01"/>
7192 <param name="use_ppm_tolerance" value="false"/>
7193 <param name="blacklist" value="true"/>
7194 </section>
7195 </section>
7196 <section name="feature">
7197 <param name="q" value=":"/>
7198 </section>
7199 <section name="consensus">
7200 <param name="map" value=""/>
7201 <param name="map_and" value="false"/>
7202 <section name="blackorwhitelist">
7203 <param name="blacklist" value="true"/>
7204 <param name="maps" value=""/>
7205 <param name="rt" value="60.0"/>
7206 <param name="mz" value="0.01"/>
7207 <param name="use_ppm_tolerance" value="false"/>
7208 </section>
7209 </section>
7210 <section name="f_and_c">
7211 <param name="charge" value=":"/>
7212 <param name="size" value=":"/>
7213 <param name="remove_meta" value=""/>
7214 </section>
7215 <section name="id">
7216 <param name="remove_clashes" value="false"/>
7217 <param name="keep_best_score_id" value="true"/>
7218 <param name="sequences_whitelist" value=""/>
7219 <param name="sequence_comparison_method" value="substring"/>
7220 <param name="accessions_whitelist" value=""/>
7221 <param name="remove_annotated_features" value="false"/>
7222 <param name="remove_unannotated_features" value="true"/>
7223 <param name="remove_unassigned_ids" value="true"/>
7224 <param name="rt" value="0.1"/>
7225 <param name="mz" value="0.001"/>
7226 <param name="blacklist_imperfect" value="false"/>
7227 </section>
7228 <section name="algorithm">
7229 <section name="SignalToNoise">
7230 <param name="max_intensity" value="-1"/>
7231 <param name="auto_max_stdev_factor" value="3.0"/>
7232 <param name="auto_max_percentile" value="95"/>
7233 <param name="auto_mode" value="0"/>
7234 <param name="win_len" value="200.0"/>
7235 <param name="bin_count" value="30"/>
7236 <param name="min_required_elements" value="10"/>
7237 <param name="noise_for_empty_window" value="1e+20"/>
7238 <param name="write_log_messages" value="true"/>
7239 </section>
7240 </section>
7241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7242 <output name="ctd_out" ftype="xml">
7243 <assert_contents>
7244 <is_valid_xml/>
7245 </assert_contents>
7246 </output>
7247 </test>
7248 <test expect_num_outputs="2">
7249 <conditional name="adv_opts_cond">
7250 <param name="adv_opts_selector" value="advanced"/>
7251 <param name="force" value="false"/>
7252 <param name="test" value="true"/>
7253 </conditional>
7254 <param name="in" value="FileFilter_22_input.consensusXML"/>
7255 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7256 <param name="out_type" value="consensusxml"/>
7257 <param name="rt" value=":"/>
7258 <param name="mz" value=":"/>
7259 <param name="int" value=":"/>
7260 <param name="sort" value="false"/>
7261 <section name="peak_options">
7262 <param name="sn" value="0.0"/>
7263 <param name="rm_pc_charge" value=""/>
7264 <param name="pc_mz_range" value=":"/>
7265 <param name="pc_mz_list" value=""/>
7266 <param name="level" value="1 2 3"/>
7267 <param name="sort_peaks" value="false"/>
7268 <param name="no_chromatograms" value="false"/>
7269 <param name="remove_chromatograms" value="false"/>
7270 <param name="remove_empty" value="false"/>
7271 <param name="mz_precision" value="64"/>
7272 <param name="int_precision" value="32"/>
7273 <param name="indexed_file" value="true"/>
7274 <param name="zlib_compression" value="false"/>
7275 <section name="numpress">
7276 <param name="masstime" value="none"/>
7277 <param name="lossy_mass_accuracy" value="-1.0"/>
7278 <param name="intensity" value="none"/>
7279 <param name="float_da" value="none"/>
7280 </section>
7281 </section>
7282 <section name="spectra">
7283 <param name="remove_zoom" value="false"/>
7284 <param name="remove_mode" value=""/>
7285 <param name="remove_activation" value=""/>
7286 <param name="remove_collision_energy" value=":"/>
7287 <param name="remove_isolation_window_width" value=":"/>
7288 <param name="select_zoom" value="false"/>
7289 <param name="select_mode" value=""/>
7290 <param name="select_activation" value=""/>
7291 <param name="select_collision_energy" value=":"/>
7292 <param name="select_isolation_window_width" value=":"/>
7293 <param name="select_polarity" value=""/>
7294 <section name="blackorwhitelist">
7295 <param name="similarity_threshold" value="-1.0"/>
7296 <param name="rt" value="0.01"/>
7297 <param name="mz" value="0.01"/>
7298 <param name="use_ppm_tolerance" value="false"/>
7299 <param name="blacklist" value="true"/>
7300 </section>
7301 </section>
7302 <section name="feature">
7303 <param name="q" value=":"/>
7304 </section>
7305 <section name="consensus">
7306 <param name="map" value=""/>
7307 <param name="map_and" value="false"/>
7308 <section name="blackorwhitelist">
7309 <param name="blacklist" value="true"/>
7310 <param name="maps" value=""/>
7311 <param name="rt" value="60.0"/>
7312 <param name="mz" value="0.01"/>
7313 <param name="use_ppm_tolerance" value="false"/>
7314 </section>
7315 </section>
7316 <section name="f_and_c">
7317 <param name="charge" value=":"/>
7318 <param name="size" value=":"/>
7319 <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
7320 </section>
7321 <section name="id">
7322 <param name="remove_clashes" value="false"/>
7323 <param name="keep_best_score_id" value="false"/>
7324 <param name="sequences_whitelist" value=""/>
7325 <param name="sequence_comparison_method" value="substring"/>
7326 <param name="accessions_whitelist" value=""/>
7327 <param name="remove_annotated_features" value="false"/>
7328 <param name="remove_unannotated_features" value="false"/>
7329 <param name="remove_unassigned_ids" value="false"/>
7330 <param name="rt" value="0.1"/>
7331 <param name="mz" value="0.001"/>
7332 <param name="blacklist_imperfect" value="false"/>
7333 </section>
7334 <section name="algorithm">
7335 <section name="SignalToNoise">
7336 <param name="max_intensity" value="-1"/>
7337 <param name="auto_max_stdev_factor" value="3.0"/>
7338 <param name="auto_max_percentile" value="95"/>
7339 <param name="auto_mode" value="0"/>
7340 <param name="win_len" value="200.0"/>
7341 <param name="bin_count" value="30"/>
7342 <param name="min_required_elements" value="10"/>
7343 <param name="noise_for_empty_window" value="1e+20"/>
7344 <param name="write_log_messages" value="true"/>
7345 </section>
7346 </section>
7347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7348 <output name="ctd_out" ftype="xml">
7349 <assert_contents>
7350 <is_valid_xml/>
7351 </assert_contents>
7352 </output>
7353 </test>
7354 <test expect_num_outputs="2">
7355 <conditional name="adv_opts_cond">
7356 <param name="adv_opts_selector" value="advanced"/>
7357 <param name="force" value="false"/>
7358 <param name="test" value="true"/>
7359 </conditional>
7360 <param name="in" value="FileFilter_22_input.consensusXML"/>
7361 <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7362 <param name="out_type" value="consensusxml"/>
7363 <param name="rt" value=":"/>
7364 <param name="mz" value=":"/>
7365 <param name="int" value=":"/>
7366 <param name="sort" value="false"/>
7367 <section name="peak_options">
7368 <param name="sn" value="0.0"/>
7369 <param name="rm_pc_charge" value=""/>
7370 <param name="pc_mz_range" value=":"/>
7371 <param name="pc_mz_list" value=""/>
7372 <param name="level" value="1 2 3"/>
7373 <param name="sort_peaks" value="false"/>
7374 <param name="no_chromatograms" value="false"/>
7375 <param name="remove_chromatograms" value="false"/>
7376 <param name="remove_empty" value="false"/>
7377 <param name="mz_precision" value="64"/>
7378 <param name="int_precision" value="32"/>
7379 <param name="indexed_file" value="true"/>
7380 <param name="zlib_compression" value="false"/>
7381 <section name="numpress">
7382 <param name="masstime" value="none"/>
7383 <param name="lossy_mass_accuracy" value="-1.0"/>
7384 <param name="intensity" value="none"/>
7385 <param name="float_da" value="none"/>
7386 </section>
7387 </section>
7388 <section name="spectra">
7389 <param name="remove_zoom" value="false"/>
7390 <param name="remove_mode" value=""/>
7391 <param name="remove_activation" value=""/>
7392 <param name="remove_collision_energy" value=":"/>
7393 <param name="remove_isolation_window_width" value=":"/>
7394 <param name="select_zoom" value="false"/>
7395 <param name="select_mode" value=""/>
7396 <param name="select_activation" value=""/>
7397 <param name="select_collision_energy" value=":"/>
7398 <param name="select_isolation_window_width" value=":"/>
7399 <param name="select_polarity" value=""/>
7400 <section name="blackorwhitelist">
7401 <param name="similarity_threshold" value="-1.0"/>
7402 <param name="rt" value="0.01"/>
7403 <param name="mz" value="0.01"/>
7404 <param name="use_ppm_tolerance" value="false"/>
7405 <param name="blacklist" value="true"/>
7406 </section>
7407 </section>
7408 <section name="feature">
7409 <param name="q" value=":"/>
7410 </section>
7411 <section name="consensus">
7412 <param name="map" value=""/>
7413 <param name="map_and" value="false"/>
7414 <section name="blackorwhitelist">
7415 <param name="blacklist" value="true"/>
7416 <param name="maps" value=""/>
7417 <param name="rt" value="60.0"/>
7418 <param name="mz" value="0.01"/>
7419 <param name="use_ppm_tolerance" value="false"/>
7420 </section>
7421 </section>
7422 <section name="f_and_c">
7423 <param name="charge" value=":"/>
7424 <param name="size" value=":"/>
7425 <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
7426 </section>
7427 <section name="id">
7428 <param name="remove_clashes" value="false"/>
7429 <param name="keep_best_score_id" value="false"/>
7430 <param name="sequences_whitelist" value=""/>
7431 <param name="sequence_comparison_method" value="substring"/>
7432 <param name="accessions_whitelist" value=""/>
7433 <param name="remove_annotated_features" value="false"/>
7434 <param name="remove_unannotated_features" value="false"/>
7435 <param name="remove_unassigned_ids" value="false"/>
7436 <param name="rt" value="0.1"/>
7437 <param name="mz" value="0.001"/>
7438 <param name="blacklist_imperfect" value="false"/>
7439 </section>
7440 <section name="algorithm">
7441 <section name="SignalToNoise">
7442 <param name="max_intensity" value="-1"/>
7443 <param name="auto_max_stdev_factor" value="3.0"/>
7444 <param name="auto_max_percentile" value="95"/>
7445 <param name="auto_mode" value="0"/>
7446 <param name="win_len" value="200.0"/>
7447 <param name="bin_count" value="30"/>
7448 <param name="min_required_elements" value="10"/>
7449 <param name="noise_for_empty_window" value="1e+20"/>
7450 <param name="write_log_messages" value="true"/>
7451 </section>
7452 </section>
7453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7454 <output name="ctd_out" ftype="xml">
7455 <assert_contents>
7456 <is_valid_xml/>
7457 </assert_contents>
7458 </output>
7459 </test>
7460 <test expect_num_outputs="2">
7461 <conditional name="adv_opts_cond">
7462 <param name="adv_opts_selector" value="advanced"/>
7463 <param name="force" value="false"/>
7464 <param name="test" value="true"/>
7465 </conditional>
7466 <param name="in" value="FileFilter_22_input.consensusXML"/>
7467 <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
7468 <param name="out_type" value="consensusxml"/>
7469 <param name="rt" value=":"/>
7470 <param name="mz" value=":"/>
7471 <param name="int" value=":"/>
7472 <param name="sort" value="false"/>
7473 <section name="peak_options">
7474 <param name="sn" value="0.0"/>
7475 <param name="rm_pc_charge" value=""/>
7476 <param name="pc_mz_range" value=":"/>
7477 <param name="pc_mz_list" value=""/>
7478 <param name="level" value="1 2 3"/>
7479 <param name="sort_peaks" value="false"/>
7480 <param name="no_chromatograms" value="false"/>
7481 <param name="remove_chromatograms" value="false"/>
7482 <param name="remove_empty" value="false"/>
7483 <param name="mz_precision" value="64"/>
7484 <param name="int_precision" value="32"/>
7485 <param name="indexed_file" value="true"/>
7486 <param name="zlib_compression" value="false"/>
7487 <section name="numpress">
7488 <param name="masstime" value="none"/>
7489 <param name="lossy_mass_accuracy" value="-1.0"/>
7490 <param name="intensity" value="none"/>
7491 <param name="float_da" value="none"/>
7492 </section>
7493 </section>
7494 <section name="spectra">
7495 <param name="remove_zoom" value="false"/>
7496 <param name="remove_mode" value=""/>
7497 <param name="remove_activation" value=""/>
7498 <param name="remove_collision_energy" value=":"/>
7499 <param name="remove_isolation_window_width" value=":"/>
7500 <param name="select_zoom" value="false"/>
7501 <param name="select_mode" value=""/>
7502 <param name="select_activation" value=""/>
7503 <param name="select_collision_energy" value=":"/>
7504 <param name="select_isolation_window_width" value=":"/>
7505 <param name="select_polarity" value=""/>
7506 <section name="blackorwhitelist">
7507 <param name="similarity_threshold" value="-1.0"/>
7508 <param name="rt" value="0.01"/>
7509 <param name="mz" value="0.01"/>
7510 <param name="use_ppm_tolerance" value="false"/>
7511 <param name="blacklist" value="true"/>
7512 </section>
7513 </section>
7514 <section name="feature">
7515 <param name="q" value=":"/>
7516 </section>
7517 <section name="consensus">
7518 <param name="map" value=""/>
7519 <param name="map_and" value="false"/>
7520 <section name="blackorwhitelist">
7521 <param name="blacklist" value="true"/>
7522 <param name="maps" value=""/>
7523 <param name="rt" value="60.0"/>
7524 <param name="mz" value="0.01"/>
7525 <param name="use_ppm_tolerance" value="false"/>
7526 </section>
7527 </section>
7528 <section name="f_and_c">
7529 <param name="charge" value=":"/>
7530 <param name="size" value=":"/>
7531 <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
7532 </section>
7533 <section name="id">
7534 <param name="remove_clashes" value="false"/>
7535 <param name="keep_best_score_id" value="false"/>
7536 <param name="sequences_whitelist" value=""/>
7537 <param name="sequence_comparison_method" value="substring"/>
7538 <param name="accessions_whitelist" value=""/>
7539 <param name="remove_annotated_features" value="false"/>
7540 <param name="remove_unannotated_features" value="false"/>
7541 <param name="remove_unassigned_ids" value="false"/>
7542 <param name="rt" value="0.1"/>
7543 <param name="mz" value="0.001"/>
7544 <param name="blacklist_imperfect" value="false"/>
7545 </section>
7546 <section name="algorithm">
7547 <section name="SignalToNoise">
7548 <param name="max_intensity" value="-1"/>
7549 <param name="auto_max_stdev_factor" value="3.0"/>
7550 <param name="auto_max_percentile" value="95"/>
7551 <param name="auto_mode" value="0"/>
7552 <param name="win_len" value="200.0"/>
7553 <param name="bin_count" value="30"/>
7554 <param name="min_required_elements" value="10"/>
7555 <param name="noise_for_empty_window" value="1e+20"/>
7556 <param name="write_log_messages" value="true"/>
7557 </section>
7558 </section>
7559 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7560 <output name="ctd_out" ftype="xml">
7561 <assert_contents>
7562 <is_valid_xml/>
7563 </assert_contents>
7564 </output>
7565 </test>
7566 <test expect_num_outputs="2">
7567 <conditional name="adv_opts_cond">
7568 <param name="adv_opts_selector" value="advanced"/>
7569 <param name="force" value="false"/>
7570 <param name="test" value="true"/>
7571 </conditional>
7572 <param name="in" value="FileFilter_25_input.mzML.gz"/>
7573 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7574 <param name="out_type" value="mzml"/>
7575 <param name="rt" value=":"/>
7576 <param name="mz" value=":"/>
7577 <param name="int" value=":"/>
7578 <param name="sort" value="false"/>
7579 <section name="peak_options">
7580 <param name="sn" value="0.0"/>
7581 <param name="rm_pc_charge" value=""/>
7582 <param name="pc_mz_range" value=":"/>
7583 <param name="pc_mz_list" value=""/>
7584 <param name="level" value="1 2 3"/>
7585 <param name="sort_peaks" value="false"/>
7586 <param name="no_chromatograms" value="false"/>
7587 <param name="remove_chromatograms" value="false"/>
7588 <param name="remove_empty" value="false"/>
7589 <param name="mz_precision" value="64"/>
7590 <param name="int_precision" value="32"/>
7591 <param name="indexed_file" value="true"/>
7592 <param name="zlib_compression" value="false"/>
7593 <section name="numpress">
7594 <param name="masstime" value="none"/>
7595 <param name="lossy_mass_accuracy" value="-1.0"/>
7596 <param name="intensity" value="none"/>
7597 <param name="float_da" value="none"/>
7598 </section>
7599 </section>
7600 <section name="spectra">
7601 <param name="remove_zoom" value="false"/>
7602 <param name="remove_mode" value=""/>
7603 <param name="remove_activation" value=""/>
7604 <param name="remove_collision_energy" value=":"/>
7605 <param name="remove_isolation_window_width" value=":"/>
7606 <param name="select_zoom" value="false"/>
7607 <param name="select_mode" value=""/>
7608 <param name="select_activation" value=""/>
7609 <param name="select_collision_energy" value=":"/>
7610 <param name="select_isolation_window_width" value=":"/>
7611 <param name="select_polarity" value=""/>
7612 <section name="blackorwhitelist">
7613 <param name="similarity_threshold" value="-1.0"/>
7614 <param name="rt" value="0.01"/>
7615 <param name="mz" value="0.01"/>
7616 <param name="use_ppm_tolerance" value="false"/>
7617 <param name="blacklist" value="true"/>
7618 </section>
7619 </section>
7620 <section name="feature">
7621 <param name="q" value=":"/>
7622 </section>
7623 <section name="consensus">
7624 <param name="map" value=""/>
7625 <param name="map_and" value="false"/>
7626 <section name="blackorwhitelist">
7627 <param name="blacklist" value="true"/>
7628 <param name="maps" value=""/>
7629 <param name="rt" value="60.0"/>
7630 <param name="mz" value="0.01"/>
7631 <param name="use_ppm_tolerance" value="false"/>
7632 </section>
7633 </section>
7634 <section name="f_and_c">
7635 <param name="charge" value=":"/>
7636 <param name="size" value=":"/>
7637 <param name="remove_meta" value=""/>
7638 </section>
7639 <section name="id">
7640 <param name="remove_clashes" value="false"/>
7641 <param name="keep_best_score_id" value="false"/>
7642 <param name="sequences_whitelist" value=""/>
7643 <param name="sequence_comparison_method" value="substring"/>
7644 <param name="accessions_whitelist" value=""/>
7645 <param name="remove_annotated_features" value="false"/>
7646 <param name="remove_unannotated_features" value="false"/>
7647 <param name="remove_unassigned_ids" value="false"/>
7648 <param name="blacklist" value="FileFilter_25_input.idXML"/>
7649 <param name="rt" value="1.0"/>
7650 <param name="mz" value="0.05"/>
7651 <param name="blacklist_imperfect" value="true"/>
7652 </section>
7653 <section name="algorithm">
7654 <section name="SignalToNoise">
7655 <param name="max_intensity" value="-1"/>
7656 <param name="auto_max_stdev_factor" value="3.0"/>
7657 <param name="auto_max_percentile" value="95"/>
7658 <param name="auto_mode" value="0"/>
7659 <param name="win_len" value="200.0"/>
7660 <param name="bin_count" value="30"/>
7661 <param name="min_required_elements" value="10"/>
7662 <param name="noise_for_empty_window" value="1e+20"/>
7663 <param name="write_log_messages" value="true"/>
7664 </section>
7665 </section>
7666 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7667 <output name="ctd_out" ftype="xml">
7668 <assert_contents>
7669 <is_valid_xml/>
7670 </assert_contents>
7671 </output>
7672 </test>
7673 <test expect_num_outputs="2">
7674 <conditional name="adv_opts_cond">
7675 <param name="adv_opts_selector" value="advanced"/>
7676 <param name="force" value="false"/>
7677 <param name="test" value="true"/>
7678 </conditional>
7679 <param name="in" value="FileFilter_25_input.mzML.gz"/>
7680 <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7681 <param name="out_type" value="mzml"/>
7682 <param name="rt" value=":"/>
7683 <param name="mz" value=":"/>
7684 <param name="int" value=":"/>
7685 <param name="sort" value="false"/>
7686 <section name="peak_options">
7687 <param name="sn" value="0.0"/>
7688 <param name="rm_pc_charge" value=""/>
7689 <param name="pc_mz_range" value=":"/>
7690 <param name="pc_mz_list" value=""/>
7691 <param name="level" value="1 2 3"/>
7692 <param name="sort_peaks" value="false"/>
7693 <param name="no_chromatograms" value="false"/>
7694 <param name="remove_chromatograms" value="false"/>
7695 <param name="remove_empty" value="false"/>
7696 <param name="mz_precision" value="64"/>
7697 <param name="int_precision" value="32"/>
7698 <param name="indexed_file" value="true"/>
7699 <param name="zlib_compression" value="false"/>
7700 <section name="numpress">
7701 <param name="masstime" value="none"/>
7702 <param name="lossy_mass_accuracy" value="-1.0"/>
7703 <param name="intensity" value="none"/>
7704 <param name="float_da" value="none"/>
7705 </section>
7706 </section>
7707 <section name="spectra">
7708 <param name="remove_zoom" value="false"/>
7709 <param name="remove_mode" value=""/>
7710 <param name="remove_activation" value=""/>
7711 <param name="remove_collision_energy" value=":"/>
7712 <param name="remove_isolation_window_width" value=":"/>
7713 <param name="select_zoom" value="false"/>
7714 <param name="select_mode" value=""/>
7715 <param name="select_activation" value=""/>
7716 <param name="select_collision_energy" value=":"/>
7717 <param name="select_isolation_window_width" value=":"/>
7718 <param name="select_polarity" value=""/>
7719 <section name="blackorwhitelist">
7720 <param name="similarity_threshold" value="-1.0"/>
7721 <param name="rt" value="0.01"/>
7722 <param name="mz" value="0.01"/>
7723 <param name="use_ppm_tolerance" value="false"/>
7724 <param name="blacklist" value="true"/>
7725 </section>
7726 </section>
7727 <section name="feature">
7728 <param name="q" value=":"/>
7729 </section>
7730 <section name="consensus">
7731 <param name="map" value=""/>
7732 <param name="map_and" value="false"/>
7733 <section name="blackorwhitelist">
7734 <param name="blacklist" value="true"/>
7735 <param name="maps" value=""/>
7736 <param name="rt" value="60.0"/>
7737 <param name="mz" value="0.01"/>
7738 <param name="use_ppm_tolerance" value="false"/>
7739 </section>
7740 </section>
7741 <section name="f_and_c">
7742 <param name="charge" value=":"/>
7743 <param name="size" value=":"/>
7744 <param name="remove_meta" value=""/>
7745 </section>
7746 <section name="id">
7747 <param name="remove_clashes" value="false"/>
7748 <param name="keep_best_score_id" value="false"/>
7749 <param name="sequences_whitelist" value=""/>
7750 <param name="sequence_comparison_method" value="substring"/>
7751 <param name="accessions_whitelist" value=""/>
7752 <param name="remove_annotated_features" value="false"/>
7753 <param name="remove_unannotated_features" value="false"/>
7754 <param name="remove_unassigned_ids" value="false"/>
7755 <param name="blacklist" value="FileFilter_25_input.idXML"/>
7756 <param name="rt" value="0.1"/>
7757 <param name="mz" value="0.001"/>
7758 <param name="blacklist_imperfect" value="true"/>
7759 </section>
7760 <section name="algorithm">
7761 <section name="SignalToNoise">
7762 <param name="max_intensity" value="-1"/>
7763 <param name="auto_max_stdev_factor" value="3.0"/>
7764 <param name="auto_max_percentile" value="95"/>
7765 <param name="auto_mode" value="0"/>
7766 <param name="win_len" value="200.0"/>
7767 <param name="bin_count" value="30"/>
7768 <param name="min_required_elements" value="10"/>
7769 <param name="noise_for_empty_window" value="1e+20"/>
7770 <param name="write_log_messages" value="true"/>
7771 </section>
7772 </section>
7773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7774 <output name="ctd_out" ftype="xml">
7775 <assert_contents>
7776 <is_valid_xml/>
7777 </assert_contents>
7778 </output>
7779 </test>
7780 <test expect_num_outputs="2">
7781 <conditional name="adv_opts_cond">
7782 <param name="adv_opts_selector" value="advanced"/>
7783 <param name="force" value="false"/>
7784 <param name="test" value="true"/>
7785 </conditional>
7786 <param name="in" value="FileFilter_28_input.mzML.gz"/>
7787 <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7788 <param name="out_type" value="mzml"/>
7789 <param name="rt" value=":"/>
7790 <param name="mz" value=":"/>
7791 <param name="int" value=":"/>
7792 <param name="sort" value="false"/>
7793 <section name="peak_options">
7794 <param name="sn" value="0.0"/>
7795 <param name="rm_pc_charge" value=""/>
7796 <param name="pc_mz_range" value="832:836"/>
7797 <param name="pc_mz_list" value=""/>
7798 <param name="level" value="2"/>
7799 <param name="sort_peaks" value="false"/>
7800 <param name="no_chromatograms" value="false"/>
7801 <param name="remove_chromatograms" value="false"/>
7802 <param name="remove_empty" value="false"/>
7803 <param name="mz_precision" value="64"/>
7804 <param name="int_precision" value="32"/>
7805 <param name="indexed_file" value="true"/>
7806 <param name="zlib_compression" value="false"/>
7807 <section name="numpress">
7808 <param name="masstime" value="none"/>
7809 <param name="lossy_mass_accuracy" value="-1.0"/>
7810 <param name="intensity" value="none"/>
7811 <param name="float_da" value="none"/>
7812 </section>
7813 </section>
7814 <section name="spectra">
7815 <param name="remove_zoom" value="false"/>
7816 <param name="remove_mode" value=""/>
7817 <param name="remove_activation" value=""/>
7818 <param name="remove_collision_energy" value=":"/>
7819 <param name="remove_isolation_window_width" value=":"/>
7820 <param name="select_zoom" value="false"/>
7821 <param name="select_mode" value=""/>
7822 <param name="select_activation" value=""/>
7823 <param name="select_collision_energy" value=":"/>
7824 <param name="select_isolation_window_width" value=":"/>
7825 <param name="select_polarity" value=""/>
7826 <section name="blackorwhitelist">
7827 <param name="similarity_threshold" value="-1.0"/>
7828 <param name="rt" value="0.01"/>
7829 <param name="mz" value="0.01"/>
7830 <param name="use_ppm_tolerance" value="false"/>
7831 <param name="blacklist" value="true"/>
7832 </section>
7833 </section>
7834 <section name="feature">
7835 <param name="q" value=":"/>
7836 </section>
7837 <section name="consensus">
7838 <param name="map" value=""/>
7839 <param name="map_and" value="false"/>
7840 <section name="blackorwhitelist">
7841 <param name="blacklist" value="true"/>
7842 <param name="maps" value=""/>
7843 <param name="rt" value="60.0"/>
7844 <param name="mz" value="0.01"/>
7845 <param name="use_ppm_tolerance" value="false"/>
7846 </section>
7847 </section>
7848 <section name="f_and_c">
7849 <param name="charge" value=":"/>
7850 <param name="size" value=":"/>
7851 <param name="remove_meta" value=""/>
7852 </section>
7853 <section name="id">
7854 <param name="remove_clashes" value="false"/>
7855 <param name="keep_best_score_id" value="false"/>
7856 <param name="sequences_whitelist" value=""/>
7857 <param name="sequence_comparison_method" value="substring"/>
7858 <param name="accessions_whitelist" value=""/>
7859 <param name="remove_annotated_features" value="false"/>
7860 <param name="remove_unannotated_features" value="false"/>
7861 <param name="remove_unassigned_ids" value="false"/>
7862 <param name="rt" value="0.1"/>
7863 <param name="mz" value="0.001"/>
7864 <param name="blacklist_imperfect" value="false"/>
7865 </section>
7866 <section name="algorithm">
7867 <section name="SignalToNoise">
7868 <param name="max_intensity" value="-1"/>
7869 <param name="auto_max_stdev_factor" value="3.0"/>
7870 <param name="auto_max_percentile" value="95"/>
7871 <param name="auto_mode" value="0"/>
7872 <param name="win_len" value="200.0"/>
7873 <param name="bin_count" value="30"/>
7874 <param name="min_required_elements" value="10"/>
7875 <param name="noise_for_empty_window" value="1e+20"/>
7876 <param name="write_log_messages" value="true"/>
7877 </section>
7878 </section>
7879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7880 <output name="ctd_out" ftype="xml">
7881 <assert_contents>
7882 <is_valid_xml/>
7883 </assert_contents>
7884 </output>
7885 </test>
7886 <test expect_num_outputs="2">
7887 <conditional name="adv_opts_cond">
7888 <param name="adv_opts_selector" value="advanced"/>
7889 <param name="force" value="false"/>
7890 <param name="test" value="true"/>
7891 </conditional>
7892 <param name="in" value="FileFilter_28_input.mzML.gz"/>
7893 <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
7894 <param name="out_type" value="mzml"/>
7895 <param name="rt" value=":"/>
7896 <param name="mz" value=":"/>
7897 <param name="int" value=":"/>
7898 <param name="sort" value="false"/>
7899 <section name="peak_options">
7900 <param name="sn" value="0.0"/>
7901 <param name="rm_pc_charge" value=""/>
7902 <param name="pc_mz_range" value="832:836"/>
7903 <param name="pc_mz_list" value=""/>
7904 <param name="level" value="1 2"/>
7905 <param name="sort_peaks" value="false"/>
7906 <param name="no_chromatograms" value="false"/>
7907 <param name="remove_chromatograms" value="false"/>
7908 <param name="remove_empty" value="false"/>
7909 <param name="mz_precision" value="64"/>
7910 <param name="int_precision" value="32"/>
7911 <param name="indexed_file" value="true"/>
7912 <param name="zlib_compression" value="false"/>
7913 <section name="numpress">
7914 <param name="masstime" value="none"/>
7915 <param name="lossy_mass_accuracy" value="-1.0"/>
7916 <param name="intensity" value="none"/>
7917 <param name="float_da" value="none"/>
7918 </section>
7919 </section>
7920 <section name="spectra">
7921 <param name="remove_zoom" value="false"/>
7922 <param name="remove_mode" value=""/>
7923 <param name="remove_activation" value=""/>
7924 <param name="remove_collision_energy" value=":"/>
7925 <param name="remove_isolation_window_width" value=":"/>
7926 <param name="select_zoom" value="false"/>
7927 <param name="select_mode" value=""/>
7928 <param name="select_activation" value=""/>
7929 <param name="select_collision_energy" value=":"/>
7930 <param name="select_isolation_window_width" value=":"/>
7931 <param name="select_polarity" value=""/>
7932 <section name="blackorwhitelist">
7933 <param name="similarity_threshold" value="-1.0"/>
7934 <param name="rt" value="0.01"/>
7935 <param name="mz" value="0.01"/>
7936 <param name="use_ppm_tolerance" value="false"/>
7937 <param name="blacklist" value="true"/>
7938 </section>
7939 </section>
7940 <section name="feature">
7941 <param name="q" value=":"/>
7942 </section>
7943 <section name="consensus">
7944 <param name="map" value=""/>
7945 <param name="map_and" value="false"/>
7946 <section name="blackorwhitelist">
7947 <param name="blacklist" value="true"/>
7948 <param name="maps" value=""/>
7949 <param name="rt" value="60.0"/>
7950 <param name="mz" value="0.01"/>
7951 <param name="use_ppm_tolerance" value="false"/>
7952 </section>
7953 </section>
7954 <section name="f_and_c">
7955 <param name="charge" value=":"/>
7956 <param name="size" value=":"/>
7957 <param name="remove_meta" value=""/>
7958 </section>
7959 <section name="id">
7960 <param name="remove_clashes" value="false"/>
7961 <param name="keep_best_score_id" value="false"/>
7962 <param name="sequences_whitelist" value=""/>
7963 <param name="sequence_comparison_method" value="substring"/>
7964 <param name="accessions_whitelist" value=""/>
7965 <param name="remove_annotated_features" value="false"/>
7966 <param name="remove_unannotated_features" value="false"/>
7967 <param name="remove_unassigned_ids" value="false"/>
7968 <param name="rt" value="0.1"/>
7969 <param name="mz" value="0.001"/>
7970 <param name="blacklist_imperfect" value="false"/>
7971 </section>
7972 <section name="algorithm">
7973 <section name="SignalToNoise">
7974 <param name="max_intensity" value="-1"/>
7975 <param name="auto_max_stdev_factor" value="3.0"/>
7976 <param name="auto_max_percentile" value="95"/>
7977 <param name="auto_mode" value="0"/>
7978 <param name="win_len" value="200.0"/>
7979 <param name="bin_count" value="30"/>
7980 <param name="min_required_elements" value="10"/>
7981 <param name="noise_for_empty_window" value="1e+20"/>
7982 <param name="write_log_messages" value="true"/>
7983 </section>
7984 </section>
7985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
7986 <output name="ctd_out" ftype="xml">
7987 <assert_contents>
7988 <is_valid_xml/>
7989 </assert_contents>
7990 </output>
7991 </test>
7992 <test expect_num_outputs="2">
7993 <conditional name="adv_opts_cond">
7994 <param name="adv_opts_selector" value="advanced"/>
7995 <param name="force" value="false"/>
7996 <param name="test" value="true"/>
7997 </conditional>
7998 <param name="in" value="FileFilter_28_input.mzML.gz"/>
7999 <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8000 <param name="out_type" value="mzml"/>
8001 <param name="rt" value=":"/>
8002 <param name="mz" value=":"/>
8003 <param name="int" value=":"/>
8004 <param name="sort" value="false"/>
8005 <section name="peak_options">
8006 <param name="sn" value="0.0"/>
8007 <param name="rm_pc_charge" value=""/>
8008 <param name="pc_mz_range" value="832:836"/>
8009 <param name="pc_mz_list" value=""/>
8010 <param name="level" value="1 2"/>
8011 <param name="sort_peaks" value="false"/>
8012 <param name="no_chromatograms" value="false"/>
8013 <param name="remove_chromatograms" value="false"/>
8014 <param name="remove_empty" value="false"/>
8015 <param name="mz_precision" value="64"/>
8016 <param name="int_precision" value="32"/>
8017 <param name="indexed_file" value="true"/>
8018 <param name="zlib_compression" value="false"/>
8019 <section name="numpress">
8020 <param name="masstime" value="none"/>
8021 <param name="lossy_mass_accuracy" value="-1.0"/>
8022 <param name="intensity" value="none"/>
8023 <param name="float_da" value="none"/>
8024 </section>
8025 </section>
8026 <section name="spectra">
8027 <param name="remove_zoom" value="false"/>
8028 <param name="remove_mode" value=""/>
8029 <param name="remove_activation" value=""/>
8030 <param name="remove_collision_energy" value=":"/>
8031 <param name="remove_isolation_window_width" value=":"/>
8032 <param name="select_zoom" value="false"/>
8033 <param name="select_mode" value=""/>
8034 <param name="select_activation" value=""/>
8035 <param name="select_collision_energy" value=":"/>
8036 <param name="select_isolation_window_width" value=":"/>
8037 <param name="select_polarity" value=""/>
8038 <section name="blackorwhitelist">
8039 <param name="similarity_threshold" value="-1.0"/>
8040 <param name="rt" value="0.01"/>
8041 <param name="mz" value="0.01"/>
8042 <param name="use_ppm_tolerance" value="false"/>
8043 <param name="blacklist" value="true"/>
8044 </section>
8045 </section>
8046 <section name="feature">
8047 <param name="q" value=":"/>
8048 </section>
8049 <section name="consensus">
8050 <param name="map" value=""/>
8051 <param name="map_and" value="false"/>
8052 <section name="blackorwhitelist">
8053 <param name="blacklist" value="true"/>
8054 <param name="maps" value=""/>
8055 <param name="rt" value="60.0"/>
8056 <param name="mz" value="0.01"/>
8057 <param name="use_ppm_tolerance" value="false"/>
8058 </section>
8059 </section>
8060 <section name="f_and_c">
8061 <param name="charge" value=":"/>
8062 <param name="size" value=":"/>
8063 <param name="remove_meta" value=""/>
8064 </section>
8065 <section name="id">
8066 <param name="remove_clashes" value="false"/>
8067 <param name="keep_best_score_id" value="false"/>
8068 <param name="sequences_whitelist" value=""/>
8069 <param name="sequence_comparison_method" value="substring"/>
8070 <param name="accessions_whitelist" value=""/>
8071 <param name="remove_annotated_features" value="false"/>
8072 <param name="remove_unannotated_features" value="false"/>
8073 <param name="remove_unassigned_ids" value="false"/>
8074 <param name="rt" value="0.1"/>
8075 <param name="mz" value="0.001"/>
8076 <param name="blacklist_imperfect" value="false"/>
8077 </section>
8078 <section name="algorithm">
8079 <section name="SignalToNoise">
8080 <param name="max_intensity" value="-1"/>
8081 <param name="auto_max_stdev_factor" value="3.0"/>
8082 <param name="auto_max_percentile" value="95"/>
8083 <param name="auto_mode" value="0"/>
8084 <param name="win_len" value="200.0"/>
8085 <param name="bin_count" value="30"/>
8086 <param name="min_required_elements" value="10"/>
8087 <param name="noise_for_empty_window" value="1e+20"/>
8088 <param name="write_log_messages" value="true"/>
8089 </section>
8090 </section>
8091 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8092 <output name="ctd_out" ftype="xml">
8093 <assert_contents>
8094 <is_valid_xml/>
8095 </assert_contents>
8096 </output>
8097 </test>
8098 <test expect_num_outputs="2">
8099 <conditional name="adv_opts_cond">
8100 <param name="adv_opts_selector" value="advanced"/>
8101 <param name="force" value="false"/>
8102 <param name="test" value="true"/>
8103 </conditional>
8104 <param name="in" value="FileFilter_31_34_input.mzML"/>
8105 <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8106 <param name="out_type" value="mzml"/>
8107 <param name="rt" value=":"/>
8108 <param name="mz" value=":"/>
8109 <param name="int" value=":"/>
8110 <param name="sort" value="false"/>
8111 <section name="peak_options">
8112 <param name="sn" value="0.0"/>
8113 <param name="rm_pc_charge" value=""/>
8114 <param name="pc_mz_range" value=":"/>
8115 <param name="pc_mz_list" value=""/>
8116 <param name="level" value="1 2 3"/>
8117 <param name="sort_peaks" value="false"/>
8118 <param name="no_chromatograms" value="false"/>
8119 <param name="remove_chromatograms" value="false"/>
8120 <param name="remove_empty" value="false"/>
8121 <param name="mz_precision" value="64"/>
8122 <param name="int_precision" value="32"/>
8123 <param name="indexed_file" value="true"/>
8124 <param name="zlib_compression" value="false"/>
8125 <section name="numpress">
8126 <param name="masstime" value="none"/>
8127 <param name="lossy_mass_accuracy" value="-1.0"/>
8128 <param name="intensity" value="none"/>
8129 <param name="float_da" value="none"/>
8130 </section>
8131 </section>
8132 <section name="spectra">
8133 <param name="remove_zoom" value="false"/>
8134 <param name="remove_mode" value=""/>
8135 <param name="remove_activation" value=""/>
8136 <param name="remove_collision_energy" value=":"/>
8137 <param name="remove_isolation_window_width" value=":2"/>
8138 <param name="select_zoom" value="false"/>
8139 <param name="select_mode" value=""/>
8140 <param name="select_activation" value=""/>
8141 <param name="select_collision_energy" value=":"/>
8142 <param name="select_isolation_window_width" value=":"/>
8143 <param name="select_polarity" value=""/>
8144 <section name="blackorwhitelist">
8145 <param name="similarity_threshold" value="-1.0"/>
8146 <param name="rt" value="0.01"/>
8147 <param name="mz" value="0.01"/>
8148 <param name="use_ppm_tolerance" value="false"/>
8149 <param name="blacklist" value="true"/>
8150 </section>
8151 </section>
8152 <section name="feature">
8153 <param name="q" value=":"/>
8154 </section>
8155 <section name="consensus">
8156 <param name="map" value=""/>
8157 <param name="map_and" value="false"/>
8158 <section name="blackorwhitelist">
8159 <param name="blacklist" value="true"/>
8160 <param name="maps" value=""/>
8161 <param name="rt" value="60.0"/>
8162 <param name="mz" value="0.01"/>
8163 <param name="use_ppm_tolerance" value="false"/>
8164 </section>
8165 </section>
8166 <section name="f_and_c">
8167 <param name="charge" value=":"/>
8168 <param name="size" value=":"/>
8169 <param name="remove_meta" value=""/>
8170 </section>
8171 <section name="id">
8172 <param name="remove_clashes" value="false"/>
8173 <param name="keep_best_score_id" value="false"/>
8174 <param name="sequences_whitelist" value=""/>
8175 <param name="sequence_comparison_method" value="substring"/>
8176 <param name="accessions_whitelist" value=""/>
8177 <param name="remove_annotated_features" value="false"/>
8178 <param name="remove_unannotated_features" value="false"/>
8179 <param name="remove_unassigned_ids" value="false"/>
8180 <param name="rt" value="0.1"/>
8181 <param name="mz" value="0.001"/>
8182 <param name="blacklist_imperfect" value="false"/>
8183 </section>
8184 <section name="algorithm">
8185 <section name="SignalToNoise">
8186 <param name="max_intensity" value="-1"/>
8187 <param name="auto_max_stdev_factor" value="3.0"/>
8188 <param name="auto_max_percentile" value="95"/>
8189 <param name="auto_mode" value="0"/>
8190 <param name="win_len" value="200.0"/>
8191 <param name="bin_count" value="30"/>
8192 <param name="min_required_elements" value="10"/>
8193 <param name="noise_for_empty_window" value="1e+20"/>
8194 <param name="write_log_messages" value="true"/>
8195 </section>
8196 </section>
8197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8198 <output name="ctd_out" ftype="xml">
8199 <assert_contents>
8200 <is_valid_xml/>
8201 </assert_contents>
8202 </output>
8203 </test>
8204 <test expect_num_outputs="2">
8205 <conditional name="adv_opts_cond">
8206 <param name="adv_opts_selector" value="advanced"/>
8207 <param name="force" value="false"/>
8208 <param name="test" value="true"/>
8209 </conditional>
8210 <param name="in" value="FileFilter_31_34_input.mzML"/>
8211 <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8212 <param name="out_type" value="mzml"/>
8213 <param name="rt" value=":"/>
8214 <param name="mz" value=":"/>
8215 <param name="int" value=":"/>
8216 <param name="sort" value="false"/>
8217 <section name="peak_options">
8218 <param name="sn" value="0.0"/>
8219 <param name="rm_pc_charge" value=""/>
8220 <param name="pc_mz_range" value=":"/>
8221 <param name="pc_mz_list" value=""/>
8222 <param name="level" value="1 2 3"/>
8223 <param name="sort_peaks" value="false"/>
8224 <param name="no_chromatograms" value="false"/>
8225 <param name="remove_chromatograms" value="false"/>
8226 <param name="remove_empty" value="false"/>
8227 <param name="mz_precision" value="64"/>
8228 <param name="int_precision" value="32"/>
8229 <param name="indexed_file" value="true"/>
8230 <param name="zlib_compression" value="false"/>
8231 <section name="numpress">
8232 <param name="masstime" value="none"/>
8233 <param name="lossy_mass_accuracy" value="-1.0"/>
8234 <param name="intensity" value="none"/>
8235 <param name="float_da" value="none"/>
8236 </section>
8237 </section>
8238 <section name="spectra">
8239 <param name="remove_zoom" value="false"/>
8240 <param name="remove_mode" value=""/>
8241 <param name="remove_activation" value=""/>
8242 <param name="remove_collision_energy" value=":"/>
8243 <param name="remove_isolation_window_width" value=":"/>
8244 <param name="select_zoom" value="false"/>
8245 <param name="select_mode" value=""/>
8246 <param name="select_activation" value=""/>
8247 <param name="select_collision_energy" value=":"/>
8248 <param name="select_isolation_window_width" value=":2"/>
8249 <param name="select_polarity" value=""/>
8250 <section name="blackorwhitelist">
8251 <param name="similarity_threshold" value="-1.0"/>
8252 <param name="rt" value="0.01"/>
8253 <param name="mz" value="0.01"/>
8254 <param name="use_ppm_tolerance" value="false"/>
8255 <param name="blacklist" value="true"/>
8256 </section>
8257 </section>
8258 <section name="feature">
8259 <param name="q" value=":"/>
8260 </section>
8261 <section name="consensus">
8262 <param name="map" value=""/>
8263 <param name="map_and" value="false"/>
8264 <section name="blackorwhitelist">
8265 <param name="blacklist" value="true"/>
8266 <param name="maps" value=""/>
8267 <param name="rt" value="60.0"/>
8268 <param name="mz" value="0.01"/>
8269 <param name="use_ppm_tolerance" value="false"/>
8270 </section>
8271 </section>
8272 <section name="f_and_c">
8273 <param name="charge" value=":"/>
8274 <param name="size" value=":"/>
8275 <param name="remove_meta" value=""/>
8276 </section>
8277 <section name="id">
8278 <param name="remove_clashes" value="false"/>
8279 <param name="keep_best_score_id" value="false"/>
8280 <param name="sequences_whitelist" value=""/>
8281 <param name="sequence_comparison_method" value="substring"/>
8282 <param name="accessions_whitelist" value=""/>
8283 <param name="remove_annotated_features" value="false"/>
8284 <param name="remove_unannotated_features" value="false"/>
8285 <param name="remove_unassigned_ids" value="false"/>
8286 <param name="rt" value="0.1"/>
8287 <param name="mz" value="0.001"/>
8288 <param name="blacklist_imperfect" value="false"/>
8289 </section>
8290 <section name="algorithm">
8291 <section name="SignalToNoise">
8292 <param name="max_intensity" value="-1"/>
8293 <param name="auto_max_stdev_factor" value="3.0"/>
8294 <param name="auto_max_percentile" value="95"/>
8295 <param name="auto_mode" value="0"/>
8296 <param name="win_len" value="200.0"/>
8297 <param name="bin_count" value="30"/>
8298 <param name="min_required_elements" value="10"/>
8299 <param name="noise_for_empty_window" value="1e+20"/>
8300 <param name="write_log_messages" value="true"/>
8301 </section>
8302 </section>
8303 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8304 <output name="ctd_out" ftype="xml">
8305 <assert_contents>
8306 <is_valid_xml/>
8307 </assert_contents>
8308 </output>
8309 </test>
8310 <test expect_num_outputs="2">
8311 <conditional name="adv_opts_cond">
8312 <param name="adv_opts_selector" value="advanced"/>
8313 <param name="force" value="false"/>
8314 <param name="test" value="true"/>
8315 </conditional>
8316 <param name="in" value="FileFilter_31_34_input.mzML"/>
8317 <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8318 <param name="out_type" value="mzml"/>
8319 <param name="rt" value=":"/>
8320 <param name="mz" value=":"/>
8321 <param name="int" value=":"/>
8322 <param name="sort" value="false"/>
8323 <section name="peak_options">
8324 <param name="sn" value="0.0"/>
8325 <param name="rm_pc_charge" value=""/>
8326 <param name="pc_mz_range" value=":"/>
8327 <param name="pc_mz_list" value=""/>
8328 <param name="level" value="1 2 3"/>
8329 <param name="sort_peaks" value="false"/>
8330 <param name="no_chromatograms" value="false"/>
8331 <param name="remove_chromatograms" value="false"/>
8332 <param name="remove_empty" value="false"/>
8333 <param name="mz_precision" value="64"/>
8334 <param name="int_precision" value="32"/>
8335 <param name="indexed_file" value="true"/>
8336 <param name="zlib_compression" value="false"/>
8337 <section name="numpress">
8338 <param name="masstime" value="none"/>
8339 <param name="lossy_mass_accuracy" value="-1.0"/>
8340 <param name="intensity" value="none"/>
8341 <param name="float_da" value="none"/>
8342 </section>
8343 </section>
8344 <section name="spectra">
8345 <param name="remove_zoom" value="false"/>
8346 <param name="remove_mode" value=""/>
8347 <param name="remove_activation" value=""/>
8348 <param name="remove_collision_energy" value=":35"/>
8349 <param name="remove_isolation_window_width" value=":"/>
8350 <param name="select_zoom" value="false"/>
8351 <param name="select_mode" value=""/>
8352 <param name="select_activation" value=""/>
8353 <param name="select_collision_energy" value=":"/>
8354 <param name="select_isolation_window_width" value=":"/>
8355 <param name="select_polarity" value=""/>
8356 <section name="blackorwhitelist">
8357 <param name="similarity_threshold" value="-1.0"/>
8358 <param name="rt" value="0.01"/>
8359 <param name="mz" value="0.01"/>
8360 <param name="use_ppm_tolerance" value="false"/>
8361 <param name="blacklist" value="true"/>
8362 </section>
8363 </section>
8364 <section name="feature">
8365 <param name="q" value=":"/>
8366 </section>
8367 <section name="consensus">
8368 <param name="map" value=""/>
8369 <param name="map_and" value="false"/>
8370 <section name="blackorwhitelist">
8371 <param name="blacklist" value="true"/>
8372 <param name="maps" value=""/>
8373 <param name="rt" value="60.0"/>
8374 <param name="mz" value="0.01"/>
8375 <param name="use_ppm_tolerance" value="false"/>
8376 </section>
8377 </section>
8378 <section name="f_and_c">
8379 <param name="charge" value=":"/>
8380 <param name="size" value=":"/>
8381 <param name="remove_meta" value=""/>
8382 </section>
8383 <section name="id">
8384 <param name="remove_clashes" value="false"/>
8385 <param name="keep_best_score_id" value="false"/>
8386 <param name="sequences_whitelist" value=""/>
8387 <param name="sequence_comparison_method" value="substring"/>
8388 <param name="accessions_whitelist" value=""/>
8389 <param name="remove_annotated_features" value="false"/>
8390 <param name="remove_unannotated_features" value="false"/>
8391 <param name="remove_unassigned_ids" value="false"/>
8392 <param name="rt" value="0.1"/>
8393 <param name="mz" value="0.001"/>
8394 <param name="blacklist_imperfect" value="false"/>
8395 </section>
8396 <section name="algorithm">
8397 <section name="SignalToNoise">
8398 <param name="max_intensity" value="-1"/>
8399 <param name="auto_max_stdev_factor" value="3.0"/>
8400 <param name="auto_max_percentile" value="95"/>
8401 <param name="auto_mode" value="0"/>
8402 <param name="win_len" value="200.0"/>
8403 <param name="bin_count" value="30"/>
8404 <param name="min_required_elements" value="10"/>
8405 <param name="noise_for_empty_window" value="1e+20"/>
8406 <param name="write_log_messages" value="true"/>
8407 </section>
8408 </section>
8409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8410 <output name="ctd_out" ftype="xml">
8411 <assert_contents>
8412 <is_valid_xml/>
8413 </assert_contents>
8414 </output>
8415 </test>
8416 <test expect_num_outputs="2">
8417 <conditional name="adv_opts_cond">
8418 <param name="adv_opts_selector" value="advanced"/>
8419 <param name="force" value="false"/>
8420 <param name="test" value="true"/>
8421 </conditional>
8422 <param name="in" value="FileFilter_31_34_input.mzML"/>
8423 <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8424 <param name="out_type" value="mzml"/>
8425 <param name="rt" value=":"/>
8426 <param name="mz" value=":"/>
8427 <param name="int" value=":"/>
8428 <param name="sort" value="false"/>
8429 <section name="peak_options">
8430 <param name="sn" value="0.0"/>
8431 <param name="rm_pc_charge" value=""/>
8432 <param name="pc_mz_range" value=":"/>
8433 <param name="pc_mz_list" value=""/>
8434 <param name="level" value="1 2 3"/>
8435 <param name="sort_peaks" value="false"/>
8436 <param name="no_chromatograms" value="false"/>
8437 <param name="remove_chromatograms" value="false"/>
8438 <param name="remove_empty" value="false"/>
8439 <param name="mz_precision" value="64"/>
8440 <param name="int_precision" value="32"/>
8441 <param name="indexed_file" value="true"/>
8442 <param name="zlib_compression" value="false"/>
8443 <section name="numpress">
8444 <param name="masstime" value="none"/>
8445 <param name="lossy_mass_accuracy" value="-1.0"/>
8446 <param name="intensity" value="none"/>
8447 <param name="float_da" value="none"/>
8448 </section>
8449 </section>
8450 <section name="spectra">
8451 <param name="remove_zoom" value="false"/>
8452 <param name="remove_mode" value=""/>
8453 <param name="remove_activation" value=""/>
8454 <param name="remove_collision_energy" value=":"/>
8455 <param name="remove_isolation_window_width" value=":"/>
8456 <param name="select_zoom" value="false"/>
8457 <param name="select_mode" value=""/>
8458 <param name="select_activation" value=""/>
8459 <param name="select_collision_energy" value=":35"/>
8460 <param name="select_isolation_window_width" value=":"/>
8461 <param name="select_polarity" value=""/>
8462 <section name="blackorwhitelist">
8463 <param name="similarity_threshold" value="-1.0"/>
8464 <param name="rt" value="0.01"/>
8465 <param name="mz" value="0.01"/>
8466 <param name="use_ppm_tolerance" value="false"/>
8467 <param name="blacklist" value="true"/>
8468 </section>
8469 </section>
8470 <section name="feature">
8471 <param name="q" value=":"/>
8472 </section>
8473 <section name="consensus">
8474 <param name="map" value=""/>
8475 <param name="map_and" value="false"/>
8476 <section name="blackorwhitelist">
8477 <param name="blacklist" value="true"/>
8478 <param name="maps" value=""/>
8479 <param name="rt" value="60.0"/>
8480 <param name="mz" value="0.01"/>
8481 <param name="use_ppm_tolerance" value="false"/>
8482 </section>
8483 </section>
8484 <section name="f_and_c">
8485 <param name="charge" value=":"/>
8486 <param name="size" value=":"/>
8487 <param name="remove_meta" value=""/>
8488 </section>
8489 <section name="id">
8490 <param name="remove_clashes" value="false"/>
8491 <param name="keep_best_score_id" value="false"/>
8492 <param name="sequences_whitelist" value=""/>
8493 <param name="sequence_comparison_method" value="substring"/>
8494 <param name="accessions_whitelist" value=""/>
8495 <param name="remove_annotated_features" value="false"/>
8496 <param name="remove_unannotated_features" value="false"/>
8497 <param name="remove_unassigned_ids" value="false"/>
8498 <param name="rt" value="0.1"/>
8499 <param name="mz" value="0.001"/>
8500 <param name="blacklist_imperfect" value="false"/>
8501 </section>
8502 <section name="algorithm">
8503 <section name="SignalToNoise">
8504 <param name="max_intensity" value="-1"/>
8505 <param name="auto_max_stdev_factor" value="3.0"/>
8506 <param name="auto_max_percentile" value="95"/>
8507 <param name="auto_mode" value="0"/>
8508 <param name="win_len" value="200.0"/>
8509 <param name="bin_count" value="30"/>
8510 <param name="min_required_elements" value="10"/>
8511 <param name="noise_for_empty_window" value="1e+20"/>
8512 <param name="write_log_messages" value="true"/>
8513 </section>
8514 </section>
8515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8516 <output name="ctd_out" ftype="xml">
8517 <assert_contents>
8518 <is_valid_xml/>
8519 </assert_contents>
8520 </output>
8521 </test>
8522 <test expect_num_outputs="2">
8523 <conditional name="adv_opts_cond">
8524 <param name="adv_opts_selector" value="advanced"/>
8525 <param name="force" value="false"/>
8526 <param name="test" value="true"/>
8527 </conditional>
8528 <param name="in" value="FileFilter_1_input.mzML"/>
8529 <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8530 <param name="out_type" value="mzML"/>
8531 <param name="rt" value=":"/>
8532 <param name="mz" value=":"/>
8533 <param name="int" value=":"/>
8534 <param name="sort" value="false"/>
8535 <section name="peak_options">
8536 <param name="sn" value="0.0"/>
8537 <param name="rm_pc_charge" value=""/>
8538 <param name="pc_mz_range" value=":"/>
8539 <param name="pc_mz_list" value=""/>
8540 <param name="level" value="1 2 3"/>
8541 <param name="sort_peaks" value="false"/>
8542 <param name="no_chromatograms" value="false"/>
8543 <param name="remove_chromatograms" value="false"/>
8544 <param name="remove_empty" value="false"/>
8545 <param name="mz_precision" value="64"/>
8546 <param name="int_precision" value="32"/>
8547 <param name="indexed_file" value="true"/>
8548 <param name="zlib_compression" value="false"/>
8549 <section name="numpress">
8550 <param name="masstime" value="none"/>
8551 <param name="lossy_mass_accuracy" value="-1.0"/>
8552 <param name="intensity" value="none"/>
8553 <param name="float_da" value="none"/>
8554 </section>
8555 </section>
8556 <section name="spectra">
8557 <param name="remove_zoom" value="false"/>
8558 <param name="remove_mode" value=""/>
8559 <param name="remove_activation" value=""/>
8560 <param name="remove_collision_energy" value=":"/>
8561 <param name="remove_isolation_window_width" value=":"/>
8562 <param name="select_zoom" value="false"/>
8563 <param name="select_mode" value=""/>
8564 <param name="select_activation" value=""/>
8565 <param name="select_collision_energy" value=":"/>
8566 <param name="select_isolation_window_width" value=":"/>
8567 <param name="select_polarity" value=""/>
8568 <section name="blackorwhitelist">
8569 <param name="similarity_threshold" value="-1.0"/>
8570 <param name="rt" value="0.01"/>
8571 <param name="mz" value="0.01"/>
8572 <param name="use_ppm_tolerance" value="false"/>
8573 <param name="blacklist" value="true"/>
8574 </section>
8575 </section>
8576 <section name="feature">
8577 <param name="q" value=":"/>
8578 </section>
8579 <section name="consensus">
8580 <param name="map" value=""/>
8581 <param name="map_and" value="false"/>
8582 <section name="blackorwhitelist">
8583 <param name="blacklist" value="true"/>
8584 <param name="maps" value=""/>
8585 <param name="rt" value="60.0"/>
8586 <param name="mz" value="0.01"/>
8587 <param name="use_ppm_tolerance" value="false"/>
8588 </section>
8589 </section>
8590 <section name="f_and_c">
8591 <param name="charge" value=":"/>
8592 <param name="size" value=":"/>
8593 <param name="remove_meta" value=""/>
8594 </section>
8595 <section name="id">
8596 <param name="remove_clashes" value="false"/>
8597 <param name="keep_best_score_id" value="false"/>
8598 <param name="sequences_whitelist" value=""/>
8599 <param name="sequence_comparison_method" value="substring"/>
8600 <param name="accessions_whitelist" value=""/>
8601 <param name="remove_annotated_features" value="false"/>
8602 <param name="remove_unannotated_features" value="false"/>
8603 <param name="remove_unassigned_ids" value="false"/>
8604 <param name="rt" value="0.1"/>
8605 <param name="mz" value="0.001"/>
8606 <param name="blacklist_imperfect" value="false"/>
8607 </section>
8608 <section name="algorithm">
8609 <section name="SignalToNoise">
8610 <param name="max_intensity" value="-1"/>
8611 <param name="auto_max_stdev_factor" value="3.0"/>
8612 <param name="auto_max_percentile" value="95"/>
8613 <param name="auto_mode" value="0"/>
8614 <param name="win_len" value="200.0"/>
8615 <param name="bin_count" value="30"/>
8616 <param name="min_required_elements" value="10"/>
8617 <param name="noise_for_empty_window" value="1e+20"/>
8618 <param name="write_log_messages" value="true"/>
8619 </section>
8620 </section>
8621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8622 <output name="ctd_out" ftype="xml">
8623 <assert_contents>
8624 <is_valid_xml/>
8625 </assert_contents>
8626 </output>
8627 </test>
8628 <test expect_num_outputs="2">
8629 <conditional name="adv_opts_cond">
8630 <param name="adv_opts_selector" value="advanced"/>
8631 <param name="force" value="false"/>
8632 <param name="test" value="true"/>
8633 </conditional>
8634 <param name="in" value="FileFilter_1_input.mzML"/>
8635 <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8636 <param name="out_type" value="mzML"/>
8637 <param name="rt" value=":"/>
8638 <param name="mz" value=":"/>
8639 <param name="int" value=":"/>
8640 <param name="sort" value="false"/>
8641 <section name="peak_options">
8642 <param name="sn" value="0.0"/>
8643 <param name="rm_pc_charge" value=""/>
8644 <param name="pc_mz_range" value=":"/>
8645 <param name="pc_mz_list" value=""/>
8646 <param name="level" value="1 2 3"/>
8647 <param name="sort_peaks" value="false"/>
8648 <param name="no_chromatograms" value="false"/>
8649 <param name="remove_chromatograms" value="false"/>
8650 <param name="remove_empty" value="false"/>
8651 <param name="mz_precision" value="64"/>
8652 <param name="int_precision" value="32"/>
8653 <param name="indexed_file" value="false"/>
8654 <param name="zlib_compression" value="false"/>
8655 <section name="numpress">
8656 <param name="masstime" value="none"/>
8657 <param name="lossy_mass_accuracy" value="-1.0"/>
8658 <param name="intensity" value="none"/>
8659 <param name="float_da" value="none"/>
8660 </section>
8661 </section>
8662 <section name="spectra">
8663 <param name="remove_zoom" value="false"/>
8664 <param name="remove_mode" value=""/>
8665 <param name="remove_activation" value=""/>
8666 <param name="remove_collision_energy" value=":"/>
8667 <param name="remove_isolation_window_width" value=":"/>
8668 <param name="select_zoom" value="false"/>
8669 <param name="select_mode" value=""/>
8670 <param name="select_activation" value=""/>
8671 <param name="select_collision_energy" value=":"/>
8672 <param name="select_isolation_window_width" value=":"/>
8673 <param name="select_polarity" value=""/>
8674 <section name="blackorwhitelist">
8675 <param name="similarity_threshold" value="-1.0"/>
8676 <param name="rt" value="0.01"/>
8677 <param name="mz" value="0.01"/>
8678 <param name="use_ppm_tolerance" value="false"/>
8679 <param name="blacklist" value="true"/>
8680 </section>
8681 </section>
8682 <section name="feature">
8683 <param name="q" value=":"/>
8684 </section>
8685 <section name="consensus">
8686 <param name="map" value=""/>
8687 <param name="map_and" value="false"/>
8688 <section name="blackorwhitelist">
8689 <param name="blacklist" value="true"/>
8690 <param name="maps" value=""/>
8691 <param name="rt" value="60.0"/>
8692 <param name="mz" value="0.01"/>
8693 <param name="use_ppm_tolerance" value="false"/>
8694 </section>
8695 </section>
8696 <section name="f_and_c">
8697 <param name="charge" value=":"/>
8698 <param name="size" value=":"/>
8699 <param name="remove_meta" value=""/>
8700 </section>
8701 <section name="id">
8702 <param name="remove_clashes" value="false"/>
8703 <param name="keep_best_score_id" value="false"/>
8704 <param name="sequences_whitelist" value=""/>
8705 <param name="sequence_comparison_method" value="substring"/>
8706 <param name="accessions_whitelist" value=""/>
8707 <param name="remove_annotated_features" value="false"/>
8708 <param name="remove_unannotated_features" value="false"/>
8709 <param name="remove_unassigned_ids" value="false"/>
8710 <param name="rt" value="0.1"/>
8711 <param name="mz" value="0.001"/>
8712 <param name="blacklist_imperfect" value="false"/>
8713 </section>
8714 <section name="algorithm">
8715 <section name="SignalToNoise">
8716 <param name="max_intensity" value="-1"/>
8717 <param name="auto_max_stdev_factor" value="3.0"/>
8718 <param name="auto_max_percentile" value="95"/>
8719 <param name="auto_mode" value="0"/>
8720 <param name="win_len" value="200.0"/>
8721 <param name="bin_count" value="30"/>
8722 <param name="min_required_elements" value="10"/>
8723 <param name="noise_for_empty_window" value="1e+20"/>
8724 <param name="write_log_messages" value="true"/>
8725 </section>
8726 </section>
8727 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8728 <output name="ctd_out" ftype="xml">
8729 <assert_contents>
8730 <is_valid_xml/>
8731 </assert_contents>
8732 </output>
8733 </test>
8734 <test expect_num_outputs="2">
8735 <conditional name="adv_opts_cond">
8736 <param name="adv_opts_selector" value="advanced"/>
8737 <param name="force" value="false"/>
8738 <param name="test" value="true"/>
8739 </conditional>
8740 <param name="in" value="FileFilter_1_input.mzML"/>
8741 <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8742 <param name="out_type" value="mzML"/>
8743 <param name="rt" value=":"/>
8744 <param name="mz" value=":"/>
8745 <param name="int" value=":"/>
8746 <param name="sort" value="false"/>
8747 <section name="peak_options">
8748 <param name="sn" value="0.0"/>
8749 <param name="rm_pc_charge" value=""/>
8750 <param name="pc_mz_range" value=":"/>
8751 <param name="pc_mz_list" value=""/>
8752 <param name="level" value="1 2 3"/>
8753 <param name="sort_peaks" value="false"/>
8754 <param name="no_chromatograms" value="false"/>
8755 <param name="remove_chromatograms" value="false"/>
8756 <param name="remove_empty" value="false"/>
8757 <param name="mz_precision" value="64"/>
8758 <param name="int_precision" value="32"/>
8759 <param name="indexed_file" value="true"/>
8760 <param name="zlib_compression" value="false"/>
8761 <section name="numpress">
8762 <param name="masstime" value="linear"/>
8763 <param name="lossy_mass_accuracy" value="0.0001"/>
8764 <param name="intensity" value="slof"/>
8765 <param name="float_da" value="none"/>
8766 </section>
8767 </section>
8768 <section name="spectra">
8769 <param name="remove_zoom" value="false"/>
8770 <param name="remove_mode" value=""/>
8771 <param name="remove_activation" value=""/>
8772 <param name="remove_collision_energy" value=":"/>
8773 <param name="remove_isolation_window_width" value=":"/>
8774 <param name="select_zoom" value="false"/>
8775 <param name="select_mode" value=""/>
8776 <param name="select_activation" value=""/>
8777 <param name="select_collision_energy" value=":"/>
8778 <param name="select_isolation_window_width" value=":"/>
8779 <param name="select_polarity" value=""/>
8780 <section name="blackorwhitelist">
8781 <param name="similarity_threshold" value="-1.0"/>
8782 <param name="rt" value="0.01"/>
8783 <param name="mz" value="0.01"/>
8784 <param name="use_ppm_tolerance" value="false"/>
8785 <param name="blacklist" value="true"/>
8786 </section>
8787 </section>
8788 <section name="feature">
8789 <param name="q" value=":"/>
8790 </section>
8791 <section name="consensus">
8792 <param name="map" value=""/>
8793 <param name="map_and" value="false"/>
8794 <section name="blackorwhitelist">
8795 <param name="blacklist" value="true"/>
8796 <param name="maps" value=""/>
8797 <param name="rt" value="60.0"/>
8798 <param name="mz" value="0.01"/>
8799 <param name="use_ppm_tolerance" value="false"/>
8800 </section>
8801 </section>
8802 <section name="f_and_c">
8803 <param name="charge" value=":"/>
8804 <param name="size" value=":"/>
8805 <param name="remove_meta" value=""/>
8806 </section>
8807 <section name="id">
8808 <param name="remove_clashes" value="false"/>
8809 <param name="keep_best_score_id" value="false"/>
8810 <param name="sequences_whitelist" value=""/>
8811 <param name="sequence_comparison_method" value="substring"/>
8812 <param name="accessions_whitelist" value=""/>
8813 <param name="remove_annotated_features" value="false"/>
8814 <param name="remove_unannotated_features" value="false"/>
8815 <param name="remove_unassigned_ids" value="false"/>
8816 <param name="rt" value="0.1"/>
8817 <param name="mz" value="0.001"/>
8818 <param name="blacklist_imperfect" value="false"/>
8819 </section>
8820 <section name="algorithm">
8821 <section name="SignalToNoise">
8822 <param name="max_intensity" value="-1"/>
8823 <param name="auto_max_stdev_factor" value="3.0"/>
8824 <param name="auto_max_percentile" value="95"/>
8825 <param name="auto_mode" value="0"/>
8826 <param name="win_len" value="200.0"/>
8827 <param name="bin_count" value="30"/>
8828 <param name="min_required_elements" value="10"/>
8829 <param name="noise_for_empty_window" value="1e+20"/>
8830 <param name="write_log_messages" value="true"/>
8831 </section>
8832 </section>
8833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8834 <output name="ctd_out" ftype="xml">
8835 <assert_contents>
8836 <is_valid_xml/>
8837 </assert_contents>
8838 </output>
8839 </test>
8840 <test expect_num_outputs="2">
8841 <conditional name="adv_opts_cond">
8842 <param name="adv_opts_selector" value="advanced"/>
8843 <param name="force" value="false"/>
8844 <param name="test" value="true"/>
8845 </conditional>
8846 <param name="in" value="FileFilter_1_input.mzML"/>
8847 <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8848 <param name="out_type" value="mzML"/>
8849 <param name="rt" value=":"/>
8850 <param name="mz" value=":"/>
8851 <param name="int" value=":"/>
8852 <param name="sort" value="false"/>
8853 <section name="peak_options">
8854 <param name="sn" value="0.0"/>
8855 <param name="rm_pc_charge" value=""/>
8856 <param name="pc_mz_range" value=":"/>
8857 <param name="pc_mz_list" value=""/>
8858 <param name="level" value="1 2 3"/>
8859 <param name="sort_peaks" value="false"/>
8860 <param name="no_chromatograms" value="false"/>
8861 <param name="remove_chromatograms" value="false"/>
8862 <param name="remove_empty" value="false"/>
8863 <param name="mz_precision" value="64"/>
8864 <param name="int_precision" value="32"/>
8865 <param name="indexed_file" value="true"/>
8866 <param name="zlib_compression" value="false"/>
8867 <section name="numpress">
8868 <param name="masstime" value="linear"/>
8869 <param name="lossy_mass_accuracy" value="0.0001"/>
8870 <param name="intensity" value="pic"/>
8871 <param name="float_da" value="none"/>
8872 </section>
8873 </section>
8874 <section name="spectra">
8875 <param name="remove_zoom" value="false"/>
8876 <param name="remove_mode" value=""/>
8877 <param name="remove_activation" value=""/>
8878 <param name="remove_collision_energy" value=":"/>
8879 <param name="remove_isolation_window_width" value=":"/>
8880 <param name="select_zoom" value="false"/>
8881 <param name="select_mode" value=""/>
8882 <param name="select_activation" value=""/>
8883 <param name="select_collision_energy" value=":"/>
8884 <param name="select_isolation_window_width" value=":"/>
8885 <param name="select_polarity" value=""/>
8886 <section name="blackorwhitelist">
8887 <param name="similarity_threshold" value="-1.0"/>
8888 <param name="rt" value="0.01"/>
8889 <param name="mz" value="0.01"/>
8890 <param name="use_ppm_tolerance" value="false"/>
8891 <param name="blacklist" value="true"/>
8892 </section>
8893 </section>
8894 <section name="feature">
8895 <param name="q" value=":"/>
8896 </section>
8897 <section name="consensus">
8898 <param name="map" value=""/>
8899 <param name="map_and" value="false"/>
8900 <section name="blackorwhitelist">
8901 <param name="blacklist" value="true"/>
8902 <param name="maps" value=""/>
8903 <param name="rt" value="60.0"/>
8904 <param name="mz" value="0.01"/>
8905 <param name="use_ppm_tolerance" value="false"/>
8906 </section>
8907 </section>
8908 <section name="f_and_c">
8909 <param name="charge" value=":"/>
8910 <param name="size" value=":"/>
8911 <param name="remove_meta" value=""/>
8912 </section>
8913 <section name="id">
8914 <param name="remove_clashes" value="false"/>
8915 <param name="keep_best_score_id" value="false"/>
8916 <param name="sequences_whitelist" value=""/>
8917 <param name="sequence_comparison_method" value="substring"/>
8918 <param name="accessions_whitelist" value=""/>
8919 <param name="remove_annotated_features" value="false"/>
8920 <param name="remove_unannotated_features" value="false"/>
8921 <param name="remove_unassigned_ids" value="false"/>
8922 <param name="rt" value="0.1"/>
8923 <param name="mz" value="0.001"/>
8924 <param name="blacklist_imperfect" value="false"/>
8925 </section>
8926 <section name="algorithm">
8927 <section name="SignalToNoise">
8928 <param name="max_intensity" value="-1"/>
8929 <param name="auto_max_stdev_factor" value="3.0"/>
8930 <param name="auto_max_percentile" value="95"/>
8931 <param name="auto_mode" value="0"/>
8932 <param name="win_len" value="200.0"/>
8933 <param name="bin_count" value="30"/>
8934 <param name="min_required_elements" value="10"/>
8935 <param name="noise_for_empty_window" value="1e+20"/>
8936 <param name="write_log_messages" value="true"/>
8937 </section>
8938 </section>
8939 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
8940 <output name="ctd_out" ftype="xml">
8941 <assert_contents>
8942 <is_valid_xml/>
8943 </assert_contents>
8944 </output>
8945 </test>
8946 <test expect_num_outputs="2">
8947 <conditional name="adv_opts_cond">
8948 <param name="adv_opts_selector" value="advanced"/>
8949 <param name="force" value="false"/>
8950 <param name="test" value="true"/>
8951 </conditional>
8952 <param name="in" value="FileFilter_40_input.mzML"/>
8953 <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
8954 <param name="out_type" value="mzML"/>
8955 <param name="rt" value=":"/>
8956 <param name="mz" value=":"/>
8957 <param name="int" value=":"/>
8958 <param name="sort" value="false"/>
8959 <section name="peak_options">
8960 <param name="sn" value="0.0"/>
8961 <param name="rm_pc_charge" value=""/>
8962 <param name="pc_mz_range" value=":"/>
8963 <param name="pc_mz_list" value=""/>
8964 <param name="level" value="1 2 3"/>
8965 <param name="sort_peaks" value="false"/>
8966 <param name="no_chromatograms" value="false"/>
8967 <param name="remove_chromatograms" value="false"/>
8968 <param name="remove_empty" value="false"/>
8969 <param name="mz_precision" value="64"/>
8970 <param name="int_precision" value="32"/>
8971 <param name="indexed_file" value="true"/>
8972 <param name="zlib_compression" value="false"/>
8973 <section name="numpress">
8974 <param name="masstime" value="none"/>
8975 <param name="lossy_mass_accuracy" value="-1.0"/>
8976 <param name="intensity" value="none"/>
8977 <param name="float_da" value="none"/>
8978 </section>
8979 </section>
8980 <section name="spectra">
8981 <param name="remove_zoom" value="false"/>
8982 <param name="remove_mode" value=""/>
8983 <param name="remove_activation" value=""/>
8984 <param name="remove_collision_energy" value=":"/>
8985 <param name="remove_isolation_window_width" value=":"/>
8986 <param name="select_zoom" value="false"/>
8987 <param name="select_mode" value=""/>
8988 <param name="select_activation" value=""/>
8989 <param name="select_collision_energy" value=":"/>
8990 <param name="select_isolation_window_width" value=":"/>
8991 <param name="select_polarity" value="positive"/>
8992 <section name="blackorwhitelist">
8993 <param name="similarity_threshold" value="-1.0"/>
8994 <param name="rt" value="0.01"/>
8995 <param name="mz" value="0.01"/>
8996 <param name="use_ppm_tolerance" value="false"/>
8997 <param name="blacklist" value="true"/>
8998 </section>
8999 </section>
9000 <section name="feature">
9001 <param name="q" value=":"/>
9002 </section>
9003 <section name="consensus">
9004 <param name="map" value=""/>
9005 <param name="map_and" value="false"/>
9006 <section name="blackorwhitelist">
9007 <param name="blacklist" value="true"/>
9008 <param name="maps" value=""/>
9009 <param name="rt" value="60.0"/>
9010 <param name="mz" value="0.01"/>
9011 <param name="use_ppm_tolerance" value="false"/>
9012 </section>
9013 </section>
9014 <section name="f_and_c">
9015 <param name="charge" value=":"/>
9016 <param name="size" value=":"/>
9017 <param name="remove_meta" value=""/>
9018 </section>
9019 <section name="id">
9020 <param name="remove_clashes" value="false"/>
9021 <param name="keep_best_score_id" value="false"/>
9022 <param name="sequences_whitelist" value=""/>
9023 <param name="sequence_comparison_method" value="substring"/>
9024 <param name="accessions_whitelist" value=""/>
9025 <param name="remove_annotated_features" value="false"/>
9026 <param name="remove_unannotated_features" value="false"/>
9027 <param name="remove_unassigned_ids" value="false"/>
9028 <param name="rt" value="0.1"/>
9029 <param name="mz" value="0.001"/>
9030 <param name="blacklist_imperfect" value="false"/>
9031 </section>
9032 <section name="algorithm">
9033 <section name="SignalToNoise">
9034 <param name="max_intensity" value="-1"/>
9035 <param name="auto_max_stdev_factor" value="3.0"/>
9036 <param name="auto_max_percentile" value="95"/>
9037 <param name="auto_mode" value="0"/>
9038 <param name="win_len" value="200.0"/>
9039 <param name="bin_count" value="30"/>
9040 <param name="min_required_elements" value="10"/>
9041 <param name="noise_for_empty_window" value="1e+20"/>
9042 <param name="write_log_messages" value="true"/>
9043 </section>
9044 </section>
9045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9046 <output name="ctd_out" ftype="xml">
9047 <assert_contents>
9048 <is_valid_xml/>
9049 </assert_contents>
9050 </output>
9051 </test>
9052 <test expect_num_outputs="2">
9053 <conditional name="adv_opts_cond">
9054 <param name="adv_opts_selector" value="advanced"/>
9055 <param name="force" value="false"/>
9056 <param name="test" value="true"/>
9057 </conditional>
9058 <param name="in" value="FileFilter_40_input.mzML"/>
9059 <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9060 <param name="out_type" value="mzML"/>
9061 <param name="rt" value=":"/>
9062 <param name="mz" value=":"/>
9063 <param name="int" value=":"/>
9064 <param name="sort" value="false"/>
9065 <section name="peak_options">
9066 <param name="sn" value="0.0"/>
9067 <param name="rm_pc_charge" value=""/>
9068 <param name="pc_mz_range" value=":"/>
9069 <param name="pc_mz_list" value=""/>
9070 <param name="level" value="1 2 3"/>
9071 <param name="sort_peaks" value="false"/>
9072 <param name="no_chromatograms" value="false"/>
9073 <param name="remove_chromatograms" value="false"/>
9074 <param name="remove_empty" value="false"/>
9075 <param name="mz_precision" value="64"/>
9076 <param name="int_precision" value="32"/>
9077 <param name="indexed_file" value="true"/>
9078 <param name="zlib_compression" value="false"/>
9079 <section name="numpress">
9080 <param name="masstime" value="none"/>
9081 <param name="lossy_mass_accuracy" value="-1.0"/>
9082 <param name="intensity" value="none"/>
9083 <param name="float_da" value="none"/>
9084 </section>
9085 </section>
9086 <section name="spectra">
9087 <param name="remove_zoom" value="false"/>
9088 <param name="remove_mode" value=""/>
9089 <param name="remove_activation" value=""/>
9090 <param name="remove_collision_energy" value=":"/>
9091 <param name="remove_isolation_window_width" value=":"/>
9092 <param name="select_zoom" value="false"/>
9093 <param name="select_mode" value=""/>
9094 <param name="select_activation" value=""/>
9095 <param name="select_collision_energy" value=":"/>
9096 <param name="select_isolation_window_width" value=":"/>
9097 <param name="select_polarity" value="negative"/>
9098 <section name="blackorwhitelist">
9099 <param name="similarity_threshold" value="-1.0"/>
9100 <param name="rt" value="0.01"/>
9101 <param name="mz" value="0.01"/>
9102 <param name="use_ppm_tolerance" value="false"/>
9103 <param name="blacklist" value="true"/>
9104 </section>
9105 </section>
9106 <section name="feature">
9107 <param name="q" value=":"/>
9108 </section>
9109 <section name="consensus">
9110 <param name="map" value=""/>
9111 <param name="map_and" value="false"/>
9112 <section name="blackorwhitelist">
9113 <param name="blacklist" value="true"/>
9114 <param name="maps" value=""/>
9115 <param name="rt" value="60.0"/>
9116 <param name="mz" value="0.01"/>
9117 <param name="use_ppm_tolerance" value="false"/>
9118 </section>
9119 </section>
9120 <section name="f_and_c">
9121 <param name="charge" value=":"/>
9122 <param name="size" value=":"/>
9123 <param name="remove_meta" value=""/>
9124 </section>
9125 <section name="id">
9126 <param name="remove_clashes" value="false"/>
9127 <param name="keep_best_score_id" value="false"/>
9128 <param name="sequences_whitelist" value=""/>
9129 <param name="sequence_comparison_method" value="substring"/>
9130 <param name="accessions_whitelist" value=""/>
9131 <param name="remove_annotated_features" value="false"/>
9132 <param name="remove_unannotated_features" value="false"/>
9133 <param name="remove_unassigned_ids" value="false"/>
9134 <param name="rt" value="0.1"/>
9135 <param name="mz" value="0.001"/>
9136 <param name="blacklist_imperfect" value="false"/>
9137 </section>
9138 <section name="algorithm">
9139 <section name="SignalToNoise">
9140 <param name="max_intensity" value="-1"/>
9141 <param name="auto_max_stdev_factor" value="3.0"/>
9142 <param name="auto_max_percentile" value="95"/>
9143 <param name="auto_mode" value="0"/>
9144 <param name="win_len" value="200.0"/>
9145 <param name="bin_count" value="30"/>
9146 <param name="min_required_elements" value="10"/>
9147 <param name="noise_for_empty_window" value="1e+20"/>
9148 <param name="write_log_messages" value="true"/>
9149 </section>
9150 </section>
9151 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9152 <output name="ctd_out" ftype="xml">
9153 <assert_contents>
9154 <is_valid_xml/>
9155 </assert_contents>
9156 </output>
9157 </test>
9158 <test expect_num_outputs="2">
9159 <conditional name="adv_opts_cond">
9160 <param name="adv_opts_selector" value="advanced"/>
9161 <param name="force" value="false"/>
9162 <param name="test" value="true"/>
9163 </conditional>
9164 <param name="in" value="FileFilter_40_input.mzML"/>
9165 <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9166 <param name="out_type" value="mzML"/>
9167 <param name="rt" value=":"/>
9168 <param name="mz" value=":"/>
9169 <param name="int" value=":"/>
9170 <param name="sort" value="false"/>
9171 <section name="peak_options">
9172 <param name="sn" value="0.0"/>
9173 <param name="rm_pc_charge" value=""/>
9174 <param name="pc_mz_range" value=":"/>
9175 <param name="pc_mz_list" value=""/>
9176 <param name="level" value="1 2 3"/>
9177 <param name="sort_peaks" value="false"/>
9178 <param name="no_chromatograms" value="false"/>
9179 <param name="remove_chromatograms" value="false"/>
9180 <param name="remove_empty" value="false"/>
9181 <param name="mz_precision" value="64"/>
9182 <param name="int_precision" value="32"/>
9183 <param name="indexed_file" value="true"/>
9184 <param name="zlib_compression" value="false"/>
9185 <section name="numpress">
9186 <param name="masstime" value="none"/>
9187 <param name="lossy_mass_accuracy" value="-1.0"/>
9188 <param name="intensity" value="none"/>
9189 <param name="float_da" value="none"/>
9190 </section>
9191 </section>
9192 <section name="spectra">
9193 <param name="remove_zoom" value="false"/>
9194 <param name="remove_mode" value=""/>
9195 <param name="remove_activation" value=""/>
9196 <param name="remove_collision_energy" value=":"/>
9197 <param name="remove_isolation_window_width" value=":"/>
9198 <param name="select_zoom" value="false"/>
9199 <param name="select_mode" value=""/>
9200 <param name="select_activation" value=""/>
9201 <param name="select_collision_energy" value=":"/>
9202 <param name="select_isolation_window_width" value=":"/>
9203 <param name="select_polarity" value=""/>
9204 <section name="blackorwhitelist">
9205 <param name="similarity_threshold" value="-1.0"/>
9206 <param name="rt" value="0.01"/>
9207 <param name="mz" value="0.01"/>
9208 <param name="use_ppm_tolerance" value="false"/>
9209 <param name="blacklist" value="true"/>
9210 </section>
9211 </section>
9212 <section name="feature">
9213 <param name="q" value=":"/>
9214 </section>
9215 <section name="consensus">
9216 <param name="map" value=""/>
9217 <param name="map_and" value="false"/>
9218 <section name="blackorwhitelist">
9219 <param name="blacklist" value="true"/>
9220 <param name="maps" value=""/>
9221 <param name="rt" value="60.0"/>
9222 <param name="mz" value="0.01"/>
9223 <param name="use_ppm_tolerance" value="false"/>
9224 </section>
9225 </section>
9226 <section name="f_and_c">
9227 <param name="charge" value=":"/>
9228 <param name="size" value=":"/>
9229 <param name="remove_meta" value=""/>
9230 </section>
9231 <section name="id">
9232 <param name="remove_clashes" value="false"/>
9233 <param name="keep_best_score_id" value="false"/>
9234 <param name="sequences_whitelist" value=""/>
9235 <param name="sequence_comparison_method" value="substring"/>
9236 <param name="accessions_whitelist" value=""/>
9237 <param name="remove_annotated_features" value="false"/>
9238 <param name="remove_unannotated_features" value="false"/>
9239 <param name="remove_unassigned_ids" value="false"/>
9240 <param name="rt" value="0.1"/>
9241 <param name="mz" value="0.001"/>
9242 <param name="blacklist_imperfect" value="false"/>
9243 </section>
9244 <section name="algorithm">
9245 <section name="SignalToNoise">
9246 <param name="max_intensity" value="-1"/>
9247 <param name="auto_max_stdev_factor" value="3.0"/>
9248 <param name="auto_max_percentile" value="95"/>
9249 <param name="auto_mode" value="0"/>
9250 <param name="win_len" value="200.0"/>
9251 <param name="bin_count" value="30"/>
9252 <param name="min_required_elements" value="10"/>
9253 <param name="noise_for_empty_window" value="1e+20"/>
9254 <param name="write_log_messages" value="true"/>
9255 </section>
9256 </section>
9257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9258 <output name="ctd_out" ftype="xml">
9259 <assert_contents>
9260 <is_valid_xml/>
9261 </assert_contents>
9262 </output>
9263 </test>
9264 <test expect_num_outputs="2">
9265 <conditional name="adv_opts_cond">
9266 <param name="adv_opts_selector" value="advanced"/>
9267 <param name="force" value="false"/>
9268 <param name="test" value="true"/>
9269 </conditional>
9270 <param name="in" value="FileFilter_43_input.mzML"/>
9271 <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9272 <param name="out_type" value="mzML"/>
9273 <param name="rt" value=":"/>
9274 <param name="mz" value=":"/>
9275 <param name="int" value=":"/>
9276 <param name="sort" value="false"/>
9277 <section name="peak_options">
9278 <param name="sn" value="0.0"/>
9279 <param name="rm_pc_charge" value=""/>
9280 <param name="pc_mz_range" value=":"/>
9281 <param name="pc_mz_list" value=""/>
9282 <param name="level" value="1 2 3"/>
9283 <param name="sort_peaks" value="false"/>
9284 <param name="no_chromatograms" value="false"/>
9285 <param name="remove_chromatograms" value="false"/>
9286 <param name="remove_empty" value="false"/>
9287 <param name="mz_precision" value="64"/>
9288 <param name="int_precision" value="32"/>
9289 <param name="indexed_file" value="true"/>
9290 <param name="zlib_compression" value="false"/>
9291 <section name="numpress">
9292 <param name="masstime" value="none"/>
9293 <param name="lossy_mass_accuracy" value="-1.0"/>
9294 <param name="intensity" value="none"/>
9295 <param name="float_da" value="none"/>
9296 </section>
9297 </section>
9298 <section name="spectra">
9299 <param name="remove_zoom" value="false"/>
9300 <param name="remove_mode" value=""/>
9301 <param name="remove_activation" value=""/>
9302 <param name="remove_collision_energy" value=":"/>
9303 <param name="remove_isolation_window_width" value=":"/>
9304 <param name="select_zoom" value="false"/>
9305 <param name="select_mode" value=""/>
9306 <param name="select_activation" value=""/>
9307 <param name="select_collision_energy" value=":"/>
9308 <param name="select_isolation_window_width" value=":"/>
9309 <param name="select_polarity" value=""/>
9310 <section name="blackorwhitelist">
9311 <param name="similarity_threshold" value="-1.0"/>
9312 <param name="rt" value="0.01"/>
9313 <param name="mz" value="0.01"/>
9314 <param name="use_ppm_tolerance" value="false"/>
9315 <param name="blacklist" value="true"/>
9316 </section>
9317 </section>
9318 <section name="feature">
9319 <param name="q" value=":"/>
9320 </section>
9321 <section name="consensus">
9322 <param name="map" value=""/>
9323 <param name="map_and" value="false"/>
9324 <section name="blackorwhitelist">
9325 <param name="blacklist" value="true"/>
9326 <param name="maps" value=""/>
9327 <param name="rt" value="60.0"/>
9328 <param name="mz" value="0.01"/>
9329 <param name="use_ppm_tolerance" value="false"/>
9330 </section>
9331 </section>
9332 <section name="f_and_c">
9333 <param name="charge" value=":"/>
9334 <param name="size" value=":"/>
9335 <param name="remove_meta" value=""/>
9336 </section>
9337 <section name="id">
9338 <param name="remove_clashes" value="false"/>
9339 <param name="keep_best_score_id" value="false"/>
9340 <param name="sequences_whitelist" value=""/>
9341 <param name="sequence_comparison_method" value="substring"/>
9342 <param name="accessions_whitelist" value=""/>
9343 <param name="remove_annotated_features" value="false"/>
9344 <param name="remove_unannotated_features" value="false"/>
9345 <param name="remove_unassigned_ids" value="false"/>
9346 <param name="rt" value="0.1"/>
9347 <param name="mz" value="0.001"/>
9348 <param name="blacklist_imperfect" value="false"/>
9349 </section>
9350 <section name="algorithm">
9351 <section name="SignalToNoise">
9352 <param name="max_intensity" value="-1"/>
9353 <param name="auto_max_stdev_factor" value="3.0"/>
9354 <param name="auto_max_percentile" value="95"/>
9355 <param name="auto_mode" value="0"/>
9356 <param name="win_len" value="200.0"/>
9357 <param name="bin_count" value="30"/>
9358 <param name="min_required_elements" value="10"/>
9359 <param name="noise_for_empty_window" value="1e+20"/>
9360 <param name="write_log_messages" value="true"/>
9361 </section>
9362 </section>
9363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9364 <output name="ctd_out" ftype="xml">
9365 <assert_contents>
9366 <is_valid_xml/>
9367 </assert_contents>
9368 </output>
9369 </test>
9370 <test expect_num_outputs="2">
9371 <conditional name="adv_opts_cond">
9372 <param name="adv_opts_selector" value="advanced"/>
9373 <param name="force" value="false"/>
9374 <param name="test" value="true"/>
9375 </conditional>
9376 <param name="in" value="FileFilter_43.tmp.mzML"/>
9377 <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/>
9378 <param name="out_type" value="mzML"/>
9379 <param name="rt" value=":"/>
9380 <param name="mz" value=":"/>
9381 <param name="int" value=":"/>
9382 <param name="sort" value="false"/>
9383 <section name="peak_options">
9384 <param name="sn" value="0.0"/>
9385 <param name="rm_pc_charge" value=""/>
9386 <param name="pc_mz_range" value=":"/>
9387 <param name="pc_mz_list" value=""/>
9388 <param name="level" value="1 2 3"/>
9389 <param name="sort_peaks" value="false"/>
9390 <param name="no_chromatograms" value="false"/>
9391 <param name="remove_chromatograms" value="false"/>
9392 <param name="remove_empty" value="false"/>
9393 <param name="mz_precision" value="64"/>
9394 <param name="int_precision" value="32"/>
9395 <param name="indexed_file" value="true"/>
9396 <param name="zlib_compression" value="false"/>
9397 <section name="numpress">
9398 <param name="masstime" value="none"/>
9399 <param name="lossy_mass_accuracy" value="-1.0"/>
9400 <param name="intensity" value="none"/>
9401 <param name="float_da" value="none"/>
9402 </section>
9403 </section>
9404 <section name="spectra">
9405 <param name="remove_zoom" value="false"/>
9406 <param name="remove_mode" value=""/>
9407 <param name="remove_activation" value=""/>
9408 <param name="remove_collision_energy" value=":"/>
9409 <param name="remove_isolation_window_width" value=":"/>
9410 <param name="select_zoom" value="false"/>
9411 <param name="select_mode" value=""/>
9412 <param name="select_activation" value=""/>
9413 <param name="select_collision_energy" value=":"/>
9414 <param name="select_isolation_window_width" value=":"/>
9415 <param name="select_polarity" value=""/>
9416 <section name="blackorwhitelist">
9417 <param name="similarity_threshold" value="-1.0"/>
9418 <param name="rt" value="0.01"/>
9419 <param name="mz" value="0.01"/>
9420 <param name="use_ppm_tolerance" value="false"/>
9421 <param name="blacklist" value="true"/>
9422 </section>
9423 </section>
9424 <section name="feature">
9425 <param name="q" value=":"/>
9426 </section>
9427 <section name="consensus">
9428 <param name="map" value=""/>
9429 <param name="map_and" value="false"/>
9430 <section name="blackorwhitelist">
9431 <param name="blacklist" value="true"/>
9432 <param name="maps" value=""/>
9433 <param name="rt" value="60.0"/>
9434 <param name="mz" value="0.01"/>
9435 <param name="use_ppm_tolerance" value="false"/>
9436 </section>
9437 </section>
9438 <section name="f_and_c">
9439 <param name="charge" value=":"/>
9440 <param name="size" value=":"/>
9441 <param name="remove_meta" value=""/>
9442 </section>
9443 <section name="id">
9444 <param name="remove_clashes" value="false"/>
9445 <param name="keep_best_score_id" value="false"/>
9446 <param name="sequences_whitelist" value=""/>
9447 <param name="sequence_comparison_method" value="substring"/>
9448 <param name="accessions_whitelist" value=""/>
9449 <param name="remove_annotated_features" value="false"/>
9450 <param name="remove_unannotated_features" value="false"/>
9451 <param name="remove_unassigned_ids" value="false"/>
9452 <param name="rt" value="0.1"/>
9453 <param name="mz" value="0.001"/>
9454 <param name="blacklist_imperfect" value="false"/>
9455 </section>
9456 <section name="algorithm">
9457 <section name="SignalToNoise">
9458 <param name="max_intensity" value="-1"/>
9459 <param name="auto_max_stdev_factor" value="3.0"/>
9460 <param name="auto_max_percentile" value="95"/>
9461 <param name="auto_mode" value="0"/>
9462 <param name="win_len" value="200.0"/>
9463 <param name="bin_count" value="30"/>
9464 <param name="min_required_elements" value="10"/>
9465 <param name="noise_for_empty_window" value="1e+20"/>
9466 <param name="write_log_messages" value="true"/>
9467 </section>
9468 </section>
9469 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9470 <output name="ctd_out" ftype="xml">
9471 <assert_contents>
9472 <is_valid_xml/>
9473 </assert_contents>
9474 </output>
9475 </test>
9476 <test expect_num_outputs="2">
9477 <conditional name="adv_opts_cond">
9478 <param name="adv_opts_selector" value="advanced"/>
9479 <param name="force" value="false"/>
9480 <param name="test" value="true"/>
9481 </conditional>
9482 <param name="in" value="FileFilter_44_input.mzML"/>
9483 <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9484 <param name="out_type" value="mzML"/>
9485 <param name="rt" value=":"/>
9486 <param name="mz" value=":"/>
9487 <param name="int" value=":"/>
9488 <param name="sort" value="false"/>
9489 <section name="peak_options">
9490 <param name="sn" value="0.0"/>
9491 <param name="rm_pc_charge" value=""/>
9492 <param name="pc_mz_range" value=":"/>
9493 <param name="pc_mz_list" value=""/>
9494 <param name="level" value="1 2 3"/>
9495 <param name="sort_peaks" value="false"/>
9496 <param name="no_chromatograms" value="false"/>
9497 <param name="remove_chromatograms" value="false"/>
9498 <param name="remove_empty" value="false"/>
9499 <param name="mz_precision" value="64"/>
9500 <param name="int_precision" value="32"/>
9501 <param name="indexed_file" value="true"/>
9502 <param name="zlib_compression" value="false"/>
9503 <section name="numpress">
9504 <param name="masstime" value="none"/>
9505 <param name="lossy_mass_accuracy" value="-1.0"/>
9506 <param name="intensity" value="none"/>
9507 <param name="float_da" value="none"/>
9508 </section>
9509 </section>
9510 <section name="spectra">
9511 <param name="remove_zoom" value="false"/>
9512 <param name="remove_mode" value=""/>
9513 <param name="remove_activation" value=""/>
9514 <param name="remove_collision_energy" value=":"/>
9515 <param name="remove_isolation_window_width" value=":"/>
9516 <param name="select_zoom" value="false"/>
9517 <param name="select_mode" value=""/>
9518 <param name="select_activation" value=""/>
9519 <param name="select_collision_energy" value=":"/>
9520 <param name="select_isolation_window_width" value=":"/>
9521 <param name="select_polarity" value=""/>
9522 <section name="blackorwhitelist">
9523 <param name="similarity_threshold" value="-1.0"/>
9524 <param name="rt" value="0.01"/>
9525 <param name="mz" value="0.01"/>
9526 <param name="use_ppm_tolerance" value="false"/>
9527 <param name="blacklist" value="true"/>
9528 </section>
9529 </section>
9530 <section name="feature">
9531 <param name="q" value=":"/>
9532 </section>
9533 <section name="consensus">
9534 <param name="map" value=""/>
9535 <param name="map_and" value="false"/>
9536 <section name="blackorwhitelist">
9537 <param name="blacklist" value="true"/>
9538 <param name="maps" value=""/>
9539 <param name="rt" value="60.0"/>
9540 <param name="mz" value="0.01"/>
9541 <param name="use_ppm_tolerance" value="false"/>
9542 </section>
9543 </section>
9544 <section name="f_and_c">
9545 <param name="charge" value=":"/>
9546 <param name="size" value=":"/>
9547 <param name="remove_meta" value=""/>
9548 </section>
9549 <section name="id">
9550 <param name="remove_clashes" value="false"/>
9551 <param name="keep_best_score_id" value="false"/>
9552 <param name="sequences_whitelist" value=""/>
9553 <param name="sequence_comparison_method" value="substring"/>
9554 <param name="accessions_whitelist" value=""/>
9555 <param name="remove_annotated_features" value="false"/>
9556 <param name="remove_unannotated_features" value="false"/>
9557 <param name="remove_unassigned_ids" value="false"/>
9558 <param name="rt" value="0.1"/>
9559 <param name="mz" value="0.001"/>
9560 <param name="blacklist_imperfect" value="false"/>
9561 </section>
9562 <section name="algorithm">
9563 <section name="SignalToNoise">
9564 <param name="max_intensity" value="-1"/>
9565 <param name="auto_max_stdev_factor" value="3.0"/>
9566 <param name="auto_max_percentile" value="95"/>
9567 <param name="auto_mode" value="0"/>
9568 <param name="win_len" value="200.0"/>
9569 <param name="bin_count" value="30"/>
9570 <param name="min_required_elements" value="10"/>
9571 <param name="noise_for_empty_window" value="1e+20"/>
9572 <param name="write_log_messages" value="true"/>
9573 </section>
9574 </section>
9575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9576 <output name="ctd_out" ftype="xml">
9577 <assert_contents>
9578 <is_valid_xml/>
9579 </assert_contents>
9580 </output>
9581 </test>
9582 <test expect_num_outputs="2">
9583 <conditional name="adv_opts_cond">
9584 <param name="adv_opts_selector" value="advanced"/>
9585 <param name="force" value="false"/>
9586 <param name="test" value="true"/>
9587 </conditional>
9588 <param name="in" value="FileFilter_45_input.featureXML"/>
9589 <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
9590 <param name="out_type" value="featurexml"/>
9591 <param name="rt" value=":"/>
9592 <param name="mz" value=":"/>
9593 <param name="int" value=":"/>
9594 <param name="sort" value="false"/>
9595 <section name="peak_options">
9596 <param name="sn" value="0.0"/>
9597 <param name="rm_pc_charge" value=""/>
9598 <param name="pc_mz_range" value=":"/>
9599 <param name="pc_mz_list" value=""/>
9600 <param name="level" value="1 2 3"/>
9601 <param name="sort_peaks" value="false"/>
9602 <param name="no_chromatograms" value="false"/>
9603 <param name="remove_chromatograms" value="false"/>
9604 <param name="remove_empty" value="false"/>
9605 <param name="mz_precision" value="64"/>
9606 <param name="int_precision" value="32"/>
9607 <param name="indexed_file" value="true"/>
9608 <param name="zlib_compression" value="false"/>
9609 <section name="numpress">
9610 <param name="masstime" value="none"/>
9611 <param name="lossy_mass_accuracy" value="-1.0"/>
9612 <param name="intensity" value="none"/>
9613 <param name="float_da" value="none"/>
9614 </section>
9615 </section>
9616 <section name="spectra">
9617 <param name="remove_zoom" value="false"/>
9618 <param name="remove_mode" value=""/>
9619 <param name="remove_activation" value=""/>
9620 <param name="remove_collision_energy" value=":"/>
9621 <param name="remove_isolation_window_width" value=":"/>
9622 <param name="select_zoom" value="false"/>
9623 <param name="select_mode" value=""/>
9624 <param name="select_activation" value=""/>
9625 <param name="select_collision_energy" value=":"/>
9626 <param name="select_isolation_window_width" value=":"/>
9627 <param name="select_polarity" value=""/>
9628 <section name="blackorwhitelist">
9629 <param name="similarity_threshold" value="-1.0"/>
9630 <param name="rt" value="0.01"/>
9631 <param name="mz" value="0.01"/>
9632 <param name="use_ppm_tolerance" value="false"/>
9633 <param name="blacklist" value="true"/>
9634 </section>
9635 </section>
9636 <section name="feature">
9637 <param name="q" value=":"/>
9638 </section>
9639 <section name="consensus">
9640 <param name="map" value=""/>
9641 <param name="map_and" value="false"/>
9642 <section name="blackorwhitelist">
9643 <param name="blacklist" value="true"/>
9644 <param name="maps" value=""/>
9645 <param name="rt" value="60.0"/>
9646 <param name="mz" value="0.01"/>
9647 <param name="use_ppm_tolerance" value="false"/>
9648 </section>
9649 </section>
9650 <section name="f_and_c">
9651 <param name="charge" value=":"/>
9652 <param name="size" value=":"/>
9653 <param name="remove_meta" value=""/>
9654 </section>
9655 <section name="id">
9656 <param name="remove_clashes" value="false"/>
9657 <param name="keep_best_score_id" value="false"/>
9658 <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
9659 <param name="sequence_comparison_method" value="substring"/>
9660 <param name="accessions_whitelist" value=""/>
9661 <param name="remove_annotated_features" value="false"/>
9662 <param name="remove_unannotated_features" value="false"/>
9663 <param name="remove_unassigned_ids" value="false"/>
9664 <param name="rt" value="0.1"/>
9665 <param name="mz" value="0.001"/>
9666 <param name="blacklist_imperfect" value="false"/>
9667 </section>
9668 <section name="algorithm">
9669 <section name="SignalToNoise">
9670 <param name="max_intensity" value="-1"/>
9671 <param name="auto_max_stdev_factor" value="3.0"/>
9672 <param name="auto_max_percentile" value="95"/>
9673 <param name="auto_mode" value="0"/>
9674 <param name="win_len" value="200.0"/>
9675 <param name="bin_count" value="30"/>
9676 <param name="min_required_elements" value="10"/>
9677 <param name="noise_for_empty_window" value="1e+20"/>
9678 <param name="write_log_messages" value="true"/>
9679 </section>
9680 </section>
9681 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9682 <output name="ctd_out" ftype="xml">
9683 <assert_contents>
9684 <is_valid_xml/>
9685 </assert_contents>
9686 </output>
9687 </test>
9688 <test expect_num_outputs="2">
9689 <conditional name="adv_opts_cond">
9690 <param name="adv_opts_selector" value="advanced"/>
9691 <param name="force" value="false"/>
9692 <param name="test" value="true"/>
9693 </conditional>
9694 <param name="in" value="FileFilter_46_input.featureXML"/>
9695 <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
9696 <param name="out_type" value="featurexml"/>
9697 <param name="rt" value=":"/>
9698 <param name="mz" value=":"/>
9699 <param name="int" value=":"/>
9700 <param name="sort" value="false"/>
9701 <section name="peak_options">
9702 <param name="sn" value="0.0"/>
9703 <param name="rm_pc_charge" value=""/>
9704 <param name="pc_mz_range" value=":"/>
9705 <param name="pc_mz_list" value=""/>
9706 <param name="level" value="1 2 3"/>
9707 <param name="sort_peaks" value="false"/>
9708 <param name="no_chromatograms" value="false"/>
9709 <param name="remove_chromatograms" value="false"/>
9710 <param name="remove_empty" value="false"/>
9711 <param name="mz_precision" value="64"/>
9712 <param name="int_precision" value="32"/>
9713 <param name="indexed_file" value="true"/>
9714 <param name="zlib_compression" value="false"/>
9715 <section name="numpress">
9716 <param name="masstime" value="none"/>
9717 <param name="lossy_mass_accuracy" value="-1.0"/>
9718 <param name="intensity" value="none"/>
9719 <param name="float_da" value="none"/>
9720 </section>
9721 </section>
9722 <section name="spectra">
9723 <param name="remove_zoom" value="false"/>
9724 <param name="remove_mode" value=""/>
9725 <param name="remove_activation" value=""/>
9726 <param name="remove_collision_energy" value=":"/>
9727 <param name="remove_isolation_window_width" value=":"/>
9728 <param name="select_zoom" value="false"/>
9729 <param name="select_mode" value=""/>
9730 <param name="select_activation" value=""/>
9731 <param name="select_collision_energy" value=":"/>
9732 <param name="select_isolation_window_width" value=":"/>
9733 <param name="select_polarity" value=""/>
9734 <section name="blackorwhitelist">
9735 <param name="similarity_threshold" value="-1.0"/>
9736 <param name="rt" value="0.01"/>
9737 <param name="mz" value="0.01"/>
9738 <param name="use_ppm_tolerance" value="false"/>
9739 <param name="blacklist" value="true"/>
9740 </section>
9741 </section>
9742 <section name="feature">
9743 <param name="q" value=":"/>
9744 </section>
9745 <section name="consensus">
9746 <param name="map" value=""/>
9747 <param name="map_and" value="false"/>
9748 <section name="blackorwhitelist">
9749 <param name="blacklist" value="true"/>
9750 <param name="maps" value=""/>
9751 <param name="rt" value="60.0"/>
9752 <param name="mz" value="0.01"/>
9753 <param name="use_ppm_tolerance" value="false"/>
9754 </section>
9755 </section>
9756 <section name="f_and_c">
9757 <param name="charge" value=":"/>
9758 <param name="size" value=":"/>
9759 <param name="remove_meta" value=""/>
9760 </section>
9761 <section name="id">
9762 <param name="remove_clashes" value="false"/>
9763 <param name="keep_best_score_id" value="false"/>
9764 <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
9765 <param name="sequence_comparison_method" value="exact"/>
9766 <param name="accessions_whitelist" value=""/>
9767 <param name="remove_annotated_features" value="false"/>
9768 <param name="remove_unannotated_features" value="false"/>
9769 <param name="remove_unassigned_ids" value="false"/>
9770 <param name="rt" value="0.1"/>
9771 <param name="mz" value="0.001"/>
9772 <param name="blacklist_imperfect" value="false"/>
9773 </section>
9774 <section name="algorithm">
9775 <section name="SignalToNoise">
9776 <param name="max_intensity" value="-1"/>
9777 <param name="auto_max_stdev_factor" value="3.0"/>
9778 <param name="auto_max_percentile" value="95"/>
9779 <param name="auto_mode" value="0"/>
9780 <param name="win_len" value="200.0"/>
9781 <param name="bin_count" value="30"/>
9782 <param name="min_required_elements" value="10"/>
9783 <param name="noise_for_empty_window" value="1e+20"/>
9784 <param name="write_log_messages" value="true"/>
9785 </section>
9786 </section>
9787 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9788 <output name="ctd_out" ftype="xml">
9789 <assert_contents>
9790 <is_valid_xml/>
9791 </assert_contents>
9792 </output>
9793 </test>
9794 <test expect_num_outputs="2">
9795 <conditional name="adv_opts_cond">
9796 <param name="adv_opts_selector" value="advanced"/>
9797 <param name="force" value="false"/>
9798 <param name="test" value="true"/>
9799 </conditional>
9800 <param name="in" value="FileFilter_47_input.mzML"/>
9801 <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9802 <param name="out_type" value="mzml"/>
9803 <param name="rt" value=":"/>
9804 <param name="mz" value=":"/>
9805 <param name="int" value=":"/>
9806 <param name="sort" value="false"/>
9807 <section name="peak_options">
9808 <param name="sn" value="0.0"/>
9809 <param name="rm_pc_charge" value=""/>
9810 <param name="pc_mz_range" value=":"/>
9811 <param name="pc_mz_list" value=""/>
9812 <param name="level" value="1 2 3"/>
9813 <param name="sort_peaks" value="false"/>
9814 <param name="no_chromatograms" value="false"/>
9815 <param name="remove_chromatograms" value="false"/>
9816 <param name="remove_empty" value="false"/>
9817 <param name="mz_precision" value="64"/>
9818 <param name="int_precision" value="32"/>
9819 <param name="indexed_file" value="true"/>
9820 <param name="zlib_compression" value="false"/>
9821 <section name="numpress">
9822 <param name="masstime" value="none"/>
9823 <param name="lossy_mass_accuracy" value="-1.0"/>
9824 <param name="intensity" value="none"/>
9825 <param name="float_da" value="none"/>
9826 </section>
9827 </section>
9828 <section name="spectra">
9829 <param name="remove_zoom" value="false"/>
9830 <param name="remove_mode" value=""/>
9831 <param name="remove_activation" value=""/>
9832 <param name="remove_collision_energy" value=":"/>
9833 <param name="remove_isolation_window_width" value=":"/>
9834 <param name="select_zoom" value="false"/>
9835 <param name="select_mode" value=""/>
9836 <param name="select_activation" value=""/>
9837 <param name="select_collision_energy" value=":"/>
9838 <param name="select_isolation_window_width" value=":"/>
9839 <param name="select_polarity" value=""/>
9840 <section name="blackorwhitelist">
9841 <param name="file" value="FileFilter_47_input_select.mzML"/>
9842 <param name="similarity_threshold" value="0.9"/>
9843 <param name="rt" value="0.01"/>
9844 <param name="mz" value="0.01"/>
9845 <param name="use_ppm_tolerance" value="false"/>
9846 <param name="blacklist" value="true"/>
9847 </section>
9848 </section>
9849 <section name="feature">
9850 <param name="q" value=":"/>
9851 </section>
9852 <section name="consensus">
9853 <param name="map" value=""/>
9854 <param name="map_and" value="false"/>
9855 <section name="blackorwhitelist">
9856 <param name="blacklist" value="true"/>
9857 <param name="maps" value=""/>
9858 <param name="rt" value="60.0"/>
9859 <param name="mz" value="0.01"/>
9860 <param name="use_ppm_tolerance" value="false"/>
9861 </section>
9862 </section>
9863 <section name="f_and_c">
9864 <param name="charge" value=":"/>
9865 <param name="size" value=":"/>
9866 <param name="remove_meta" value=""/>
9867 </section>
9868 <section name="id">
9869 <param name="remove_clashes" value="false"/>
9870 <param name="keep_best_score_id" value="false"/>
9871 <param name="sequences_whitelist" value=""/>
9872 <param name="sequence_comparison_method" value="substring"/>
9873 <param name="accessions_whitelist" value=""/>
9874 <param name="remove_annotated_features" value="false"/>
9875 <param name="remove_unannotated_features" value="false"/>
9876 <param name="remove_unassigned_ids" value="false"/>
9877 <param name="rt" value="0.1"/>
9878 <param name="mz" value="0.001"/>
9879 <param name="blacklist_imperfect" value="false"/>
9880 </section>
9881 <section name="algorithm">
9882 <section name="SignalToNoise">
9883 <param name="max_intensity" value="-1"/>
9884 <param name="auto_max_stdev_factor" value="3.0"/>
9885 <param name="auto_max_percentile" value="95"/>
9886 <param name="auto_mode" value="0"/>
9887 <param name="win_len" value="200.0"/>
9888 <param name="bin_count" value="30"/>
9889 <param name="min_required_elements" value="10"/>
9890 <param name="noise_for_empty_window" value="1e+20"/>
9891 <param name="write_log_messages" value="true"/>
9892 </section>
9893 </section>
9894 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
9895 <output name="ctd_out" ftype="xml">
9896 <assert_contents>
9897 <is_valid_xml/>
9898 </assert_contents>
9899 </output>
9900 </test>
9901 <test expect_num_outputs="2">
9902 <conditional name="adv_opts_cond">
9903 <param name="adv_opts_selector" value="advanced"/>
9904 <param name="force" value="false"/>
9905 <param name="test" value="true"/>
9906 </conditional>
9907 <param name="in" value="FileFilter_47_input.mzML"/>
9908 <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
9909 <param name="out_type" value="mzml"/>
9910 <param name="rt" value=":"/>
9911 <param name="mz" value=":"/>
9912 <param name="int" value=":"/>
9913 <param name="sort" value="false"/>
9914 <section name="peak_options">
9915 <param name="sn" value="0.0"/>
9916 <param name="rm_pc_charge" value=""/>
9917 <param name="pc_mz_range" value=":"/>
9918 <param name="pc_mz_list" value=""/>
9919 <param name="level" value="1 2 3"/>
9920 <param name="sort_peaks" value="false"/>
9921 <param name="no_chromatograms" value="false"/>
9922 <param name="remove_chromatograms" value="false"/>
9923 <param name="remove_empty" value="false"/>
9924 <param name="mz_precision" value="64"/>
9925 <param name="int_precision" value="32"/>
9926 <param name="indexed_file" value="true"/>
9927 <param name="zlib_compression" value="false"/>
9928 <section name="numpress">
9929 <param name="masstime" value="none"/>
9930 <param name="lossy_mass_accuracy" value="-1.0"/>
9931 <param name="intensity" value="none"/>
9932 <param name="float_da" value="none"/>
9933 </section>
9934 </section>
9935 <section name="spectra">
9936 <param name="remove_zoom" value="false"/>
9937 <param name="remove_mode" value=""/>
9938 <param name="remove_activation" value=""/>
9939 <param name="remove_collision_energy" value=":"/>
9940 <param name="remove_isolation_window_width" value=":"/>
9941 <param name="select_zoom" value="false"/>
9942 <param name="select_mode" value=""/>
9943 <param name="select_activation" value=""/>
9944 <param name="select_collision_energy" value=":"/>
9945 <param name="select_isolation_window_width" value=":"/>
9946 <param name="select_polarity" value=""/>
9947 <section name="blackorwhitelist">
9948 <param name="file" value="FileFilter_47_input_select.mzML"/>
9949 <param name="similarity_threshold" value="0.9"/>
9950 <param name="rt" value="0.01"/>
9951 <param name="mz" value="0.01"/>
9952 <param name="use_ppm_tolerance" value="false"/>
9953 <param name="blacklist" value="false"/>
9954 </section>
9955 </section>
9956 <section name="feature">
9957 <param name="q" value=":"/>
9958 </section>
9959 <section name="consensus">
9960 <param name="map" value=""/>
9961 <param name="map_and" value="false"/>
9962 <section name="blackorwhitelist">
9963 <param name="blacklist" value="true"/>
9964 <param name="maps" value=""/>
9965 <param name="rt" value="60.0"/>
9966 <param name="mz" value="0.01"/>
9967 <param name="use_ppm_tolerance" value="false"/>
9968 </section>
9969 </section>
9970 <section name="f_and_c">
9971 <param name="charge" value=":"/>
9972 <param name="size" value=":"/>
9973 <param name="remove_meta" value=""/>
9974 </section>
9975 <section name="id">
9976 <param name="remove_clashes" value="false"/>
9977 <param name="keep_best_score_id" value="false"/>
9978 <param name="sequences_whitelist" value=""/>
9979 <param name="sequence_comparison_method" value="substring"/>
9980 <param name="accessions_whitelist" value=""/>
9981 <param name="remove_annotated_features" value="false"/>
9982 <param name="remove_unannotated_features" value="false"/>
9983 <param name="remove_unassigned_ids" value="false"/>
9984 <param name="rt" value="0.1"/>
9985 <param name="mz" value="0.001"/>
9986 <param name="blacklist_imperfect" value="false"/>
9987 </section>
9988 <section name="algorithm">
9989 <section name="SignalToNoise">
9990 <param name="max_intensity" value="-1"/>
9991 <param name="auto_max_stdev_factor" value="3.0"/>
9992 <param name="auto_max_percentile" value="95"/>
9993 <param name="auto_mode" value="0"/>
9994 <param name="win_len" value="200.0"/>
9995 <param name="bin_count" value="30"/>
9996 <param name="min_required_elements" value="10"/>
9997 <param name="noise_for_empty_window" value="1e+20"/>
9998 <param name="write_log_messages" value="true"/>
9999 </section>
10000 </section>
10001 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10002 <output name="ctd_out" ftype="xml">
10003 <assert_contents>
10004 <is_valid_xml/>
10005 </assert_contents>
10006 </output>
10007 </test>
10008 <test expect_num_outputs="2">
10009 <conditional name="adv_opts_cond">
10010 <param name="adv_opts_selector" value="advanced"/>
10011 <param name="force" value="false"/>
10012 <param name="test" value="true"/>
10013 </conditional>
10014 <param name="in" value="FileFilter_49_input.mzML"/>
10015 <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10016 <param name="out_type" value="mzml"/>
10017 <param name="rt" value=":"/>
10018 <param name="mz" value=":"/>
10019 <param name="int" value=":"/>
10020 <param name="sort" value="false"/>
10021 <section name="peak_options">
10022 <param name="sn" value="0.0"/>
10023 <param name="rm_pc_charge" value=""/>
10024 <param name="pc_mz_range" value=":"/>
10025 <param name="pc_mz_list" value=""/>
10026 <param name="level" value="1 2 3"/>
10027 <param name="sort_peaks" value="false"/>
10028 <param name="no_chromatograms" value="false"/>
10029 <param name="remove_chromatograms" value="false"/>
10030 <param name="remove_empty" value="false"/>
10031 <param name="mz_precision" value="64"/>
10032 <param name="int_precision" value="32"/>
10033 <param name="indexed_file" value="true"/>
10034 <param name="zlib_compression" value="true"/>
10035 <section name="numpress">
10036 <param name="masstime" value="linear"/>
10037 <param name="lossy_mass_accuracy" value="-1.0"/>
10038 <param name="intensity" value="pic"/>
10039 <param name="float_da" value="slof"/>
10040 </section>
10041 </section>
10042 <section name="spectra">
10043 <param name="remove_zoom" value="false"/>
10044 <param name="remove_mode" value=""/>
10045 <param name="remove_activation" value=""/>
10046 <param name="remove_collision_energy" value=":"/>
10047 <param name="remove_isolation_window_width" value=":"/>
10048 <param name="select_zoom" value="false"/>
10049 <param name="select_mode" value=""/>
10050 <param name="select_activation" value=""/>
10051 <param name="select_collision_energy" value=":"/>
10052 <param name="select_isolation_window_width" value=":"/>
10053 <param name="select_polarity" value=""/>
10054 <section name="blackorwhitelist">
10055 <param name="similarity_threshold" value="-1.0"/>
10056 <param name="rt" value="0.01"/>
10057 <param name="mz" value="0.01"/>
10058 <param name="use_ppm_tolerance" value="false"/>
10059 <param name="blacklist" value="true"/>
10060 </section>
10061 </section>
10062 <section name="feature">
10063 <param name="q" value=":"/>
10064 </section>
10065 <section name="consensus">
10066 <param name="map" value=""/>
10067 <param name="map_and" value="false"/>
10068 <section name="blackorwhitelist">
10069 <param name="blacklist" value="true"/>
10070 <param name="maps" value=""/>
10071 <param name="rt" value="60.0"/>
10072 <param name="mz" value="0.01"/>
10073 <param name="use_ppm_tolerance" value="false"/>
10074 </section>
10075 </section>
10076 <section name="f_and_c">
10077 <param name="charge" value=":"/>
10078 <param name="size" value=":"/>
10079 <param name="remove_meta" value=""/>
10080 </section>
10081 <section name="id">
10082 <param name="remove_clashes" value="false"/>
10083 <param name="keep_best_score_id" value="false"/>
10084 <param name="sequences_whitelist" value=""/>
10085 <param name="sequence_comparison_method" value="substring"/>
10086 <param name="accessions_whitelist" value=""/>
10087 <param name="remove_annotated_features" value="false"/>
10088 <param name="remove_unannotated_features" value="false"/>
10089 <param name="remove_unassigned_ids" value="false"/>
10090 <param name="rt" value="0.1"/>
10091 <param name="mz" value="0.001"/>
10092 <param name="blacklist_imperfect" value="false"/>
10093 </section>
10094 <section name="algorithm">
10095 <section name="SignalToNoise">
10096 <param name="max_intensity" value="-1"/>
10097 <param name="auto_max_stdev_factor" value="3.0"/>
10098 <param name="auto_max_percentile" value="95"/>
10099 <param name="auto_mode" value="0"/>
10100 <param name="win_len" value="200.0"/>
10101 <param name="bin_count" value="30"/>
10102 <param name="min_required_elements" value="10"/>
10103 <param name="noise_for_empty_window" value="1e+20"/>
10104 <param name="write_log_messages" value="true"/>
10105 </section>
10106 </section>
10107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10108 <output name="ctd_out" ftype="xml">
10109 <assert_contents>
10110 <is_valid_xml/>
10111 </assert_contents>
10112 </output>
10113 </test>
10114 </xml>
10115 <xml name="autotest_FileInfo">
10116 <test expect_num_outputs="2">
10117 <conditional name="adv_opts_cond">
10118 <param name="adv_opts_selector" value="advanced"/>
10119 <param name="force" value="false"/>
10120 <param name="test" value="true"/>
10121 </conditional>
10122 <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
10123 <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10124 <param name="m" value="false"/>
10125 <param name="p" value="false"/>
10126 <param name="s" value="false"/>
10127 <param name="d" value="false"/>
10128 <param name="c" value="false"/>
10129 <param name="v" value="false"/>
10130 <param name="i" value="false"/>
10131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10132 <output name="ctd_out" ftype="xml">
10133 <assert_contents>
10134 <is_valid_xml/>
10135 </assert_contents>
10136 </output>
10137 </test>
10138 <test expect_num_outputs="2">
10139 <conditional name="adv_opts_cond">
10140 <param name="adv_opts_selector" value="advanced"/>
10141 <param name="force" value="false"/>
10142 <param name="test" value="true"/>
10143 </conditional>
10144 <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
10145 <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10146 <param name="m" value="false"/>
10147 <param name="p" value="false"/>
10148 <param name="s" value="false"/>
10149 <param name="d" value="false"/>
10150 <param name="c" value="false"/>
10151 <param name="v" value="false"/>
10152 <param name="i" value="false"/>
10153 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10154 <output name="ctd_out" ftype="xml">
10155 <assert_contents>
10156 <is_valid_xml/>
10157 </assert_contents>
10158 </output>
10159 </test>
10160 <test expect_num_outputs="2">
10161 <conditional name="adv_opts_cond">
10162 <param name="adv_opts_selector" value="advanced"/>
10163 <param name="force" value="false"/>
10164 <param name="test" value="true"/>
10165 </conditional>
10166 <param name="in" value="FileInfo_3_input.featureXML"/>
10167 <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10168 <param name="m" value="true"/>
10169 <param name="p" value="true"/>
10170 <param name="s" value="true"/>
10171 <param name="d" value="false"/>
10172 <param name="c" value="false"/>
10173 <param name="v" value="false"/>
10174 <param name="i" value="false"/>
10175 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10176 <output name="ctd_out" ftype="xml">
10177 <assert_contents>
10178 <is_valid_xml/>
10179 </assert_contents>
10180 </output>
10181 </test>
10182 <test expect_num_outputs="2">
10183 <conditional name="adv_opts_cond">
10184 <param name="adv_opts_selector" value="advanced"/>
10185 <param name="force" value="false"/>
10186 <param name="test" value="true"/>
10187 </conditional>
10188 <param name="in" value="FileInfo_4_input.mzXML"/>
10189 <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10190 <param name="m" value="true"/>
10191 <param name="p" value="false"/>
10192 <param name="s" value="false"/>
10193 <param name="d" value="false"/>
10194 <param name="c" value="false"/>
10195 <param name="v" value="false"/>
10196 <param name="i" value="false"/>
10197 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10198 <output name="ctd_out" ftype="xml">
10199 <assert_contents>
10200 <is_valid_xml/>
10201 </assert_contents>
10202 </output>
10203 </test>
10204 <test expect_num_outputs="2">
10205 <conditional name="adv_opts_cond">
10206 <param name="adv_opts_selector" value="advanced"/>
10207 <param name="force" value="false"/>
10208 <param name="test" value="true"/>
10209 </conditional>
10210 <param name="in" value="FileInfo_5_input.mzDat"/>
10211 <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10212 <param name="m" value="true"/>
10213 <param name="p" value="false"/>
10214 <param name="s" value="true"/>
10215 <param name="d" value="false"/>
10216 <param name="c" value="false"/>
10217 <param name="v" value="false"/>
10218 <param name="i" value="false"/>
10219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10220 <output name="ctd_out" ftype="xml">
10221 <assert_contents>
10222 <is_valid_xml/>
10223 </assert_contents>
10224 </output>
10225 </test>
10226 <test expect_num_outputs="2">
10227 <conditional name="adv_opts_cond">
10228 <param name="adv_opts_selector" value="advanced"/>
10229 <param name="force" value="false"/>
10230 <param name="test" value="true"/>
10231 </conditional>
10232 <param name="in" value="FileInfo_6_input.mzData"/>
10233 <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10234 <param name="m" value="false"/>
10235 <param name="p" value="false"/>
10236 <param name="s" value="true"/>
10237 <param name="d" value="true"/>
10238 <param name="c" value="false"/>
10239 <param name="v" value="false"/>
10240 <param name="i" value="false"/>
10241 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10242 <output name="ctd_out" ftype="xml">
10243 <assert_contents>
10244 <is_valid_xml/>
10245 </assert_contents>
10246 </output>
10247 </test>
10248 <test expect_num_outputs="2">
10249 <conditional name="adv_opts_cond">
10250 <param name="adv_opts_selector" value="advanced"/>
10251 <param name="force" value="false"/>
10252 <param name="test" value="true"/>
10253 </conditional>
10254 <param name="in" value="FileInfo_7_input.consensusXML"/>
10255 <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10256 <param name="m" value="true"/>
10257 <param name="p" value="true"/>
10258 <param name="s" value="true"/>
10259 <param name="d" value="false"/>
10260 <param name="c" value="false"/>
10261 <param name="v" value="false"/>
10262 <param name="i" value="false"/>
10263 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10264 <output name="ctd_out" ftype="xml">
10265 <assert_contents>
10266 <is_valid_xml/>
10267 </assert_contents>
10268 </output>
10269 </test>
10270 <test expect_num_outputs="2">
10271 <conditional name="adv_opts_cond">
10272 <param name="adv_opts_selector" value="advanced"/>
10273 <param name="force" value="false"/>
10274 <param name="test" value="true"/>
10275 </conditional>
10276 <param name="in" value="FileInfo_9_input.mzML"/>
10277 <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10278 <param name="m" value="true"/>
10279 <param name="p" value="true"/>
10280 <param name="s" value="true"/>
10281 <param name="d" value="false"/>
10282 <param name="c" value="false"/>
10283 <param name="v" value="false"/>
10284 <param name="i" value="false"/>
10285 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10286 <output name="ctd_out" ftype="xml">
10287 <assert_contents>
10288 <is_valid_xml/>
10289 </assert_contents>
10290 </output>
10291 </test>
10292 <test expect_num_outputs="2">
10293 <conditional name="adv_opts_cond">
10294 <param name="adv_opts_selector" value="advanced"/>
10295 <param name="force" value="false"/>
10296 <param name="test" value="true"/>
10297 </conditional>
10298 <param name="in" value="FileInfo_10_input.idXML"/>
10299 <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10300 <param name="m" value="false"/>
10301 <param name="p" value="false"/>
10302 <param name="s" value="false"/>
10303 <param name="d" value="false"/>
10304 <param name="c" value="false"/>
10305 <param name="v" value="false"/>
10306 <param name="i" value="false"/>
10307 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10308 <output name="ctd_out" ftype="xml">
10309 <assert_contents>
10310 <is_valid_xml/>
10311 </assert_contents>
10312 </output>
10313 </test>
10314 <test expect_num_outputs="2">
10315 <conditional name="adv_opts_cond">
10316 <param name="adv_opts_selector" value="advanced"/>
10317 <param name="force" value="false"/>
10318 <param name="test" value="true"/>
10319 </conditional>
10320 <param name="in" value="FileInfo_12_input.mzML"/>
10321 <param name="m" value="false"/>
10322 <param name="p" value="false"/>
10323 <param name="s" value="false"/>
10324 <param name="d" value="false"/>
10325 <param name="c" value="false"/>
10326 <param name="v" value="false"/>
10327 <param name="i" value="true"/>
10328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10329 <output name="ctd_out" ftype="xml">
10330 <assert_contents>
10331 <is_valid_xml/>
10332 </assert_contents>
10333 </output>
10334 </test>
10335 <test expect_num_outputs="2">
10336 <conditional name="adv_opts_cond">
10337 <param name="adv_opts_selector" value="advanced"/>
10338 <param name="force" value="false"/>
10339 <param name="test" value="true"/>
10340 </conditional>
10341 <param name="in" value="FileInfo_13_input.consensusXML"/>
10342 <param name="m" value="false"/>
10343 <param name="p" value="false"/>
10344 <param name="s" value="false"/>
10345 <param name="d" value="false"/>
10346 <param name="c" value="false"/>
10347 <param name="v" value="false"/>
10348 <param name="i" value="false"/>
10349 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10350 <output name="ctd_out" ftype="xml">
10351 <assert_contents>
10352 <is_valid_xml/>
10353 </assert_contents>
10354 </output>
10355 </test>
10356 <test expect_num_outputs="2">
10357 <conditional name="adv_opts_cond">
10358 <param name="adv_opts_selector" value="advanced"/>
10359 <param name="force" value="false"/>
10360 <param name="test" value="true"/>
10361 </conditional>
10362 <param name="in" value="FileInfo_14_input.mzid"/>
10363 <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10364 <param name="m" value="false"/>
10365 <param name="p" value="false"/>
10366 <param name="s" value="false"/>
10367 <param name="d" value="false"/>
10368 <param name="c" value="false"/>
10369 <param name="v" value="true"/>
10370 <param name="i" value="false"/>
10371 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10372 <output name="ctd_out" ftype="xml">
10373 <assert_contents>
10374 <is_valid_xml/>
10375 </assert_contents>
10376 </output>
10377 </test>
10378 <test expect_num_outputs="2">
10379 <conditional name="adv_opts_cond">
10380 <param name="adv_opts_selector" value="advanced"/>
10381 <param name="force" value="false"/>
10382 <param name="test" value="true"/>
10383 </conditional>
10384 <param name="in" value="FileInfo_15_input.mzid"/>
10385 <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10386 <param name="m" value="false"/>
10387 <param name="p" value="false"/>
10388 <param name="s" value="false"/>
10389 <param name="d" value="false"/>
10390 <param name="c" value="false"/>
10391 <param name="v" value="true"/>
10392 <param name="i" value="false"/>
10393 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10394 <output name="ctd_out" ftype="xml">
10395 <assert_contents>
10396 <is_valid_xml/>
10397 </assert_contents>
10398 </output>
10399 </test>
10400 <test expect_num_outputs="2">
10401 <conditional name="adv_opts_cond">
10402 <param name="adv_opts_selector" value="advanced"/>
10403 <param name="force" value="false"/>
10404 <param name="test" value="true"/>
10405 </conditional>
10406 <param name="in" value="FileInfo_16_input.trafoXML"/>
10407 <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10408 <param name="m" value="false"/>
10409 <param name="p" value="false"/>
10410 <param name="s" value="false"/>
10411 <param name="d" value="false"/>
10412 <param name="c" value="false"/>
10413 <param name="v" value="false"/>
10414 <param name="i" value="false"/>
10415 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10416 <output name="ctd_out" ftype="xml">
10417 <assert_contents>
10418 <is_valid_xml/>
10419 </assert_contents>
10420 </output>
10421 </test>
10422 <test expect_num_outputs="2">
10423 <conditional name="adv_opts_cond">
10424 <param name="adv_opts_selector" value="advanced"/>
10425 <param name="force" value="false"/>
10426 <param name="test" value="true"/>
10427 </conditional>
10428 <param name="in" value="FileInfo_17_input.fasta"/>
10429 <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10430 <param name="m" value="false"/>
10431 <param name="p" value="false"/>
10432 <param name="s" value="false"/>
10433 <param name="d" value="false"/>
10434 <param name="c" value="false"/>
10435 <param name="v" value="false"/>
10436 <param name="i" value="false"/>
10437 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10438 <output name="ctd_out" ftype="xml">
10439 <assert_contents>
10440 <is_valid_xml/>
10441 </assert_contents>
10442 </output>
10443 </test>
10444 <test expect_num_outputs="2">
10445 <conditional name="adv_opts_cond">
10446 <param name="adv_opts_selector" value="advanced"/>
10447 <param name="force" value="false"/>
10448 <param name="test" value="true"/>
10449 </conditional>
10450 <param name="in" value="FileInfo_18_input.fasta"/>
10451 <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
10452 <param name="m" value="false"/>
10453 <param name="p" value="false"/>
10454 <param name="s" value="false"/>
10455 <param name="d" value="false"/>
10456 <param name="c" value="false"/>
10457 <param name="v" value="false"/>
10458 <param name="i" value="false"/>
10459 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10460 <output name="ctd_out" ftype="xml">
10461 <assert_contents>
10462 <is_valid_xml/>
10463 </assert_contents>
10464 </output>
10465 </test>
10466 </xml>
10467 <xml name="autotest_FileMerger">
10468 <test expect_num_outputs="2">
10469 <conditional name="adv_opts_cond">
10470 <param name="adv_opts_selector" value="advanced"/>
10471 <param name="force" value="false"/>
10472 <param name="test" value="true"/>
10473 </conditional>
10474 <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
10475 <param name="out_type" value="mzML"/>
10476 <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10477 <param name="annotate_file_origin" value="false"/>
10478 <param name="append_method" value="append_rows"/>
10479 <section name="rt_concat">
10480 <param name="gap" value="0.0"/>
10481 </section>
10482 <section name="raw">
10483 <param name="rt_auto" value="false"/>
10484 <param name="rt_custom" value="5.0 10.0"/>
10485 <param name="rt_filename" value="false"/>
10486 <param name="ms_level" value="0"/>
10487 </section>
10488 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10489 <output name="ctd_out" ftype="xml">
10490 <assert_contents>
10491 <is_valid_xml/>
10492 </assert_contents>
10493 </output>
10494 </test>
10495 <test expect_num_outputs="2">
10496 <conditional name="adv_opts_cond">
10497 <param name="adv_opts_selector" value="advanced"/>
10498 <param name="force" value="false"/>
10499 <param name="test" value="true"/>
10500 </conditional>
10501 <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
10502 <param name="out_type" value="mzML"/>
10503 <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10504 <param name="annotate_file_origin" value="false"/>
10505 <param name="append_method" value="append_rows"/>
10506 <section name="rt_concat">
10507 <param name="gap" value="0.0"/>
10508 </section>
10509 <section name="raw">
10510 <param name="rt_auto" value="true"/>
10511 <param name="rt_custom" value=""/>
10512 <param name="rt_filename" value="false"/>
10513 <param name="ms_level" value="0"/>
10514 </section>
10515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10516 <output name="ctd_out" ftype="xml">
10517 <assert_contents>
10518 <is_valid_xml/>
10519 </assert_contents>
10520 </output>
10521 </test>
10522 <test expect_num_outputs="2">
10523 <conditional name="adv_opts_cond">
10524 <param name="adv_opts_selector" value="advanced"/>
10525 <param name="force" value="false"/>
10526 <param name="test" value="true"/>
10527 </conditional>
10528 <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
10529 <param name="out_type" value="mzML"/>
10530 <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10531 <param name="annotate_file_origin" value="false"/>
10532 <param name="append_method" value="append_rows"/>
10533 <section name="rt_concat">
10534 <param name="gap" value="0.0"/>
10535 </section>
10536 <section name="raw">
10537 <param name="rt_auto" value="false"/>
10538 <param name="rt_custom" value=""/>
10539 <param name="rt_filename" value="false"/>
10540 <param name="ms_level" value="0"/>
10541 </section>
10542 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10543 <output name="ctd_out" ftype="xml">
10544 <assert_contents>
10545 <is_valid_xml/>
10546 </assert_contents>
10547 </output>
10548 </test>
10549 <test expect_num_outputs="2">
10550 <conditional name="adv_opts_cond">
10551 <param name="adv_opts_selector" value="advanced"/>
10552 <param name="force" value="false"/>
10553 <param name="test" value="true"/>
10554 </conditional>
10555 <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
10556 <param name="out_type" value="mzML"/>
10557 <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10558 <param name="annotate_file_origin" value="false"/>
10559 <param name="append_method" value="append_rows"/>
10560 <section name="rt_concat">
10561 <param name="gap" value="0.0"/>
10562 </section>
10563 <section name="raw">
10564 <param name="rt_auto" value="false"/>
10565 <param name="rt_custom" value=""/>
10566 <param name="rt_filename" value="true"/>
10567 <param name="ms_level" value="2"/>
10568 </section>
10569 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10570 <output name="ctd_out" ftype="xml">
10571 <assert_contents>
10572 <is_valid_xml/>
10573 </assert_contents>
10574 </output>
10575 </test>
10576 <test expect_num_outputs="2">
10577 <conditional name="adv_opts_cond">
10578 <param name="adv_opts_selector" value="advanced"/>
10579 <param name="force" value="false"/>
10580 <param name="test" value="true"/>
10581 </conditional>
10582 <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
10583 <param name="out_type" value="mzML"/>
10584 <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10585 <param name="annotate_file_origin" value="false"/>
10586 <param name="append_method" value="append_rows"/>
10587 <section name="rt_concat">
10588 <param name="gap" value="0.0"/>
10589 </section>
10590 <section name="raw">
10591 <param name="rt_auto" value="false"/>
10592 <param name="rt_custom" value=""/>
10593 <param name="rt_filename" value="false"/>
10594 <param name="ms_level" value="0"/>
10595 </section>
10596 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10597 <output name="ctd_out" ftype="xml">
10598 <assert_contents>
10599 <is_valid_xml/>
10600 </assert_contents>
10601 </output>
10602 </test>
10603 <test expect_num_outputs="2">
10604 <conditional name="adv_opts_cond">
10605 <param name="adv_opts_selector" value="advanced"/>
10606 <param name="force" value="false"/>
10607 <param name="test" value="true"/>
10608 </conditional>
10609 <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
10610 <param name="out_type" value="featureXML"/>
10611 <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
10612 <param name="annotate_file_origin" value="false"/>
10613 <param name="append_method" value="append_rows"/>
10614 <section name="rt_concat">
10615 <param name="gap" value="0.0"/>
10616 </section>
10617 <section name="raw">
10618 <param name="rt_auto" value="false"/>
10619 <param name="rt_custom" value=""/>
10620 <param name="rt_filename" value="false"/>
10621 <param name="ms_level" value="0"/>
10622 </section>
10623 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10624 <output name="ctd_out" ftype="xml">
10625 <assert_contents>
10626 <is_valid_xml/>
10627 </assert_contents>
10628 </output>
10629 </test>
10630 <test expect_num_outputs="2">
10631 <conditional name="adv_opts_cond">
10632 <param name="adv_opts_selector" value="advanced"/>
10633 <param name="force" value="false"/>
10634 <param name="test" value="true"/>
10635 </conditional>
10636 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
10637 <param name="out_type" value="consensusXML"/>
10638 <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
10639 <param name="annotate_file_origin" value="false"/>
10640 <param name="append_method" value="append_rows"/>
10641 <section name="rt_concat">
10642 <param name="gap" value="0.0"/>
10643 </section>
10644 <section name="raw">
10645 <param name="rt_auto" value="false"/>
10646 <param name="rt_custom" value=""/>
10647 <param name="rt_filename" value="false"/>
10648 <param name="ms_level" value="0"/>
10649 </section>
10650 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10651 <output name="ctd_out" ftype="xml">
10652 <assert_contents>
10653 <is_valid_xml/>
10654 </assert_contents>
10655 </output>
10656 </test>
10657 <test expect_num_outputs="2">
10658 <conditional name="adv_opts_cond">
10659 <param name="adv_opts_selector" value="advanced"/>
10660 <param name="force" value="false"/>
10661 <param name="test" value="true"/>
10662 </conditional>
10663 <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
10664 <param name="out_type" value="traML"/>
10665 <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/>
10666 <param name="annotate_file_origin" value="false"/>
10667 <param name="append_method" value="append_rows"/>
10668 <section name="rt_concat">
10669 <param name="gap" value="0.0"/>
10670 </section>
10671 <section name="raw">
10672 <param name="rt_auto" value="false"/>
10673 <param name="rt_custom" value=""/>
10674 <param name="rt_filename" value="false"/>
10675 <param name="ms_level" value="0"/>
10676 </section>
10677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10678 <output name="ctd_out" ftype="xml">
10679 <assert_contents>
10680 <is_valid_xml/>
10681 </assert_contents>
10682 </output>
10683 </test>
10684 <test expect_num_outputs="3">
10685 <conditional name="adv_opts_cond">
10686 <param name="adv_opts_selector" value="advanced"/>
10687 <param name="force" value="false"/>
10688 <param name="test" value="true"/>
10689 </conditional>
10690 <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
10691 <param name="out_type" value="mzML"/>
10692 <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10693 <param name="annotate_file_origin" value="false"/>
10694 <param name="append_method" value="append_rows"/>
10695 <section name="rt_concat">
10696 <param name="gap" value="10.0"/>
10697 </section>
10698 <output_collection name="rt_concat_trafo_out" count="2"/>
10699 <section name="raw">
10700 <param name="rt_auto" value="false"/>
10701 <param name="rt_custom" value=""/>
10702 <param name="rt_filename" value="false"/>
10703 <param name="ms_level" value="0"/>
10704 </section>
10705 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
10706 <output name="ctd_out" ftype="xml">
10707 <assert_contents>
10708 <is_valid_xml/>
10709 </assert_contents>
10710 </output>
10711 </test>
10712 <test expect_num_outputs="2">
10713 <conditional name="adv_opts_cond">
10714 <param name="adv_opts_selector" value="advanced"/>
10715 <param name="force" value="false"/>
10716 <param name="test" value="true"/>
10717 </conditional>
10718 <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
10719 <param name="out_type" value="consensusXML"/>
10720 <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
10721 <param name="annotate_file_origin" value="false"/>
10722 <param name="append_method" value="append_cols"/>
10723 <section name="rt_concat">
10724 <param name="gap" value="0.0"/>
10725 </section>
10726 <section name="raw">
10727 <param name="rt_auto" value="false"/>
10728 <param name="rt_custom" value=""/>
10729 <param name="rt_filename" value="false"/>
10730 <param name="ms_level" value="0"/>
10731 </section>
10732 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10733 <output name="ctd_out" ftype="xml">
10734 <assert_contents>
10735 <is_valid_xml/>
10736 </assert_contents>
10737 </output>
10738 </test>
10739 </xml>
10740 <xml name="autotest_FuzzyDiff">
10741 <test expect_num_outputs="1">
10742 <conditional name="adv_opts_cond">
10743 <param name="adv_opts_selector" value="advanced"/>
10744 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
10745 <param name="matched_whitelist" value=""/>
10746 <param name="force" value="false"/>
10747 <param name="test" value="true"/>
10748 </conditional>
10749 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
10750 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
10751 <param name="ratio" value="1.01"/>
10752 <param name="absdiff" value="0.01"/>
10753 <param name="verbose" value="1"/>
10754 <param name="tab_width" value="8"/>
10755 <param name="first_column" value="1"/>
10756 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10757 <output name="ctd_out" ftype="xml">
10758 <assert_contents>
10759 <is_valid_xml/>
10760 </assert_contents>
10761 </output>
10762 </test>
10763 </xml>
10764 <xml name="autotest_GNPSExport">
10765 <test expect_num_outputs="2">
10766 <conditional name="adv_opts_cond">
10767 <param name="adv_opts_selector" value="advanced"/>
10768 <param name="force" value="false"/>
10769 <param name="test" value="true"/>
10770 </conditional>
10771 <param name="in_cm" value="GNPSExport_single.consensusXML"/>
10772 <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
10773 <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
10774 <param name="output_type" value="full_spectra"/>
10775 <param name="precursor_mz_tolerance" value="0.0001"/>
10776 <param name="precursor_rt_tolerance" value="5.0"/>
10777 <section name="merged_spectra">
10778 <param name="cos_similarity" value="0.95"/>
10779 </section>
10780 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10781 <output name="ctd_out" ftype="xml">
10782 <assert_contents>
10783 <is_valid_xml/>
10784 </assert_contents>
10785 </output>
10786 </test>
10787 <test expect_num_outputs="2">
10788 <conditional name="adv_opts_cond">
10789 <param name="adv_opts_selector" value="advanced"/>
10790 <param name="force" value="false"/>
10791 <param name="test" value="true"/>
10792 </conditional>
10793 <param name="in_cm" value="GNPSExport_single.consensusXML"/>
10794 <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
10795 <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
10796 <param name="output_type" value="merged_spectra"/>
10797 <param name="precursor_mz_tolerance" value="0.0001"/>
10798 <param name="precursor_rt_tolerance" value="5.0"/>
10799 <section name="merged_spectra">
10800 <param name="cos_similarity" value="0.95"/>
10801 </section>
10802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10803 <output name="ctd_out" ftype="xml">
10804 <assert_contents>
10805 <is_valid_xml/>
10806 </assert_contents>
10807 </output>
10808 </test>
10809 <test expect_num_outputs="2">
10810 <conditional name="adv_opts_cond">
10811 <param name="adv_opts_selector" value="advanced"/>
10812 <param name="force" value="false"/>
10813 <param name="test" value="true"/>
10814 </conditional>
10815 <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
10816 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
10817 <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
10818 <param name="output_type" value="full_spectra"/>
10819 <param name="precursor_mz_tolerance" value="0.0001"/>
10820 <param name="precursor_rt_tolerance" value="5.0"/>
10821 <section name="merged_spectra">
10822 <param name="cos_similarity" value="0.95"/>
10823 </section>
10824 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10825 <output name="ctd_out" ftype="xml">
10826 <assert_contents>
10827 <is_valid_xml/>
10828 </assert_contents>
10829 </output>
10830 </test>
10831 <test expect_num_outputs="2">
10832 <conditional name="adv_opts_cond">
10833 <param name="adv_opts_selector" value="advanced"/>
10834 <param name="force" value="false"/>
10835 <param name="test" value="true"/>
10836 </conditional>
10837 <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
10838 <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
10839 <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
10840 <param name="output_type" value="full_spectra"/>
10841 <param name="precursor_mz_tolerance" value="0.0001"/>
10842 <param name="precursor_rt_tolerance" value="5.0"/>
10843 <section name="merged_spectra">
10844 <param name="cos_similarity" value="0.95"/>
10845 </section>
10846 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10847 <output name="ctd_out" ftype="xml">
10848 <assert_contents>
10849 <is_valid_xml/>
10850 </assert_contents>
10851 </output>
10852 </test>
10853 </xml>
10854 <xml name="autotest_HighResPrecursorMassCorrector">
10855 <test expect_num_outputs="2">
10856 <conditional name="adv_opts_cond">
10857 <param name="adv_opts_selector" value="advanced"/>
10858 <param name="force" value="false"/>
10859 <param name="test" value="true"/>
10860 </conditional>
10861 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
10862 <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10863 <section name="feature">
10864 <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
10865 <param name="mz_tolerance" value="5.0"/>
10866 <param name="mz_tolerance_unit" value="ppm"/>
10867 <param name="rt_tolerance" value="0.0"/>
10868 <param name="max_trace" value="2"/>
10869 <param name="believe_charge" value="false"/>
10870 <param name="keep_original" value="false"/>
10871 <param name="assign_all_matching" value="false"/>
10872 </section>
10873 <section name="nearest_peak">
10874 <param name="mz_tolerance" value="0.0"/>
10875 <param name="mz_tolerance_unit" value="ppm"/>
10876 </section>
10877 <section name="highest_intensity_peak">
10878 <param name="mz_tolerance" value="0.0"/>
10879 <param name="mz_tolerance_unit" value="ppm"/>
10880 </section>
10881 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10882 <output name="ctd_out" ftype="xml">
10883 <assert_contents>
10884 <is_valid_xml/>
10885 </assert_contents>
10886 </output>
10887 </test>
10888 <test expect_num_outputs="2">
10889 <conditional name="adv_opts_cond">
10890 <param name="adv_opts_selector" value="advanced"/>
10891 <param name="force" value="false"/>
10892 <param name="test" value="true"/>
10893 </conditional>
10894 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
10895 <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10896 <section name="feature">
10897 <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
10898 <param name="mz_tolerance" value="10.0"/>
10899 <param name="mz_tolerance_unit" value="ppm"/>
10900 <param name="rt_tolerance" value="0.0"/>
10901 <param name="max_trace" value="4"/>
10902 <param name="believe_charge" value="false"/>
10903 <param name="keep_original" value="false"/>
10904 <param name="assign_all_matching" value="false"/>
10905 </section>
10906 <section name="nearest_peak">
10907 <param name="mz_tolerance" value="0.0"/>
10908 <param name="mz_tolerance_unit" value="ppm"/>
10909 </section>
10910 <section name="highest_intensity_peak">
10911 <param name="mz_tolerance" value="0.0"/>
10912 <param name="mz_tolerance_unit" value="ppm"/>
10913 </section>
10914 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10915 <output name="ctd_out" ftype="xml">
10916 <assert_contents>
10917 <is_valid_xml/>
10918 </assert_contents>
10919 </output>
10920 </test>
10921 <test expect_num_outputs="2">
10922 <conditional name="adv_opts_cond">
10923 <param name="adv_opts_selector" value="advanced"/>
10924 <param name="force" value="false"/>
10925 <param name="test" value="true"/>
10926 </conditional>
10927 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
10928 <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10929 <section name="feature">
10930 <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
10931 <param name="mz_tolerance" value="5.0"/>
10932 <param name="mz_tolerance_unit" value="ppm"/>
10933 <param name="rt_tolerance" value="0.0"/>
10934 <param name="max_trace" value="2"/>
10935 <param name="believe_charge" value="false"/>
10936 <param name="keep_original" value="false"/>
10937 <param name="assign_all_matching" value="false"/>
10938 </section>
10939 <section name="nearest_peak">
10940 <param name="mz_tolerance" value="0.0"/>
10941 <param name="mz_tolerance_unit" value="ppm"/>
10942 </section>
10943 <section name="highest_intensity_peak">
10944 <param name="mz_tolerance" value="0.0"/>
10945 <param name="mz_tolerance_unit" value="ppm"/>
10946 </section>
10947 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10948 <output name="ctd_out" ftype="xml">
10949 <assert_contents>
10950 <is_valid_xml/>
10951 </assert_contents>
10952 </output>
10953 </test>
10954 <test expect_num_outputs="2">
10955 <conditional name="adv_opts_cond">
10956 <param name="adv_opts_selector" value="advanced"/>
10957 <param name="force" value="false"/>
10958 <param name="test" value="true"/>
10959 </conditional>
10960 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
10961 <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10962 <section name="feature">
10963 <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
10964 <param name="mz_tolerance" value="5.0"/>
10965 <param name="mz_tolerance_unit" value="ppm"/>
10966 <param name="rt_tolerance" value="0.0"/>
10967 <param name="max_trace" value="2"/>
10968 <param name="believe_charge" value="false"/>
10969 <param name="keep_original" value="false"/>
10970 <param name="assign_all_matching" value="false"/>
10971 </section>
10972 <section name="nearest_peak">
10973 <param name="mz_tolerance" value="0.0"/>
10974 <param name="mz_tolerance_unit" value="ppm"/>
10975 </section>
10976 <section name="highest_intensity_peak">
10977 <param name="mz_tolerance" value="0.0"/>
10978 <param name="mz_tolerance_unit" value="ppm"/>
10979 </section>
10980 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
10981 <output name="ctd_out" ftype="xml">
10982 <assert_contents>
10983 <is_valid_xml/>
10984 </assert_contents>
10985 </output>
10986 </test>
10987 <test expect_num_outputs="2">
10988 <conditional name="adv_opts_cond">
10989 <param name="adv_opts_selector" value="advanced"/>
10990 <param name="force" value="false"/>
10991 <param name="test" value="true"/>
10992 </conditional>
10993 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
10994 <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
10995 <section name="feature">
10996 <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
10997 <param name="mz_tolerance" value="5.0"/>
10998 <param name="mz_tolerance_unit" value="ppm"/>
10999 <param name="rt_tolerance" value="0.0"/>
11000 <param name="max_trace" value="2"/>
11001 <param name="believe_charge" value="false"/>
11002 <param name="keep_original" value="false"/>
11003 <param name="assign_all_matching" value="false"/>
11004 </section>
11005 <section name="nearest_peak">
11006 <param name="mz_tolerance" value="0.0"/>
11007 <param name="mz_tolerance_unit" value="ppm"/>
11008 </section>
11009 <section name="highest_intensity_peak">
11010 <param name="mz_tolerance" value="0.0"/>
11011 <param name="mz_tolerance_unit" value="ppm"/>
11012 </section>
11013 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11014 <output name="ctd_out" ftype="xml">
11015 <assert_contents>
11016 <is_valid_xml/>
11017 </assert_contents>
11018 </output>
11019 </test>
11020 <test expect_num_outputs="2">
11021 <conditional name="adv_opts_cond">
11022 <param name="adv_opts_selector" value="advanced"/>
11023 <param name="force" value="false"/>
11024 <param name="test" value="true"/>
11025 </conditional>
11026 <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
11027 <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
11028 <section name="feature">
11029 <param name="mz_tolerance" value="5.0"/>
11030 <param name="mz_tolerance_unit" value="ppm"/>
11031 <param name="rt_tolerance" value="0.0"/>
11032 <param name="max_trace" value="2"/>
11033 <param name="believe_charge" value="false"/>
11034 <param name="keep_original" value="false"/>
11035 <param name="assign_all_matching" value="false"/>
11036 </section>
11037 <section name="nearest_peak">
11038 <param name="mz_tolerance" value="0.0"/>
11039 <param name="mz_tolerance_unit" value="ppm"/>
11040 </section>
11041 <section name="highest_intensity_peak">
11042 <param name="mz_tolerance" value="0.2"/>
11043 <param name="mz_tolerance_unit" value="ppm"/>
11044 </section>
11045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11046 <output name="ctd_out" ftype="xml">
11047 <assert_contents>
11048 <is_valid_xml/>
11049 </assert_contents>
11050 </output>
11051 </test>
11052 </xml>
11053 <xml name="autotest_IDConflictResolver">
11054 <test expect_num_outputs="2">
11055 <conditional name="adv_opts_cond">
11056 <param name="adv_opts_selector" value="advanced"/>
11057 <param name="force" value="false"/>
11058 <param name="test" value="true"/>
11059 </conditional>
11060 <param name="in" value="IDConflictResolver_1_input.featureXML"/>
11061 <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
11062 <param name="resolve_between_features" value="off"/>
11063 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11064 <output name="ctd_out" ftype="xml">
11065 <assert_contents>
11066 <is_valid_xml/>
11067 </assert_contents>
11068 </output>
11069 </test>
11070 <test expect_num_outputs="2">
11071 <conditional name="adv_opts_cond">
11072 <param name="adv_opts_selector" value="advanced"/>
11073 <param name="force" value="false"/>
11074 <param name="test" value="true"/>
11075 </conditional>
11076 <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
11077 <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
11078 <param name="resolve_between_features" value="off"/>
11079 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11080 <output name="ctd_out" ftype="xml">
11081 <assert_contents>
11082 <is_valid_xml/>
11083 </assert_contents>
11084 </output>
11085 </test>
11086 <test expect_num_outputs="2">
11087 <conditional name="adv_opts_cond">
11088 <param name="adv_opts_selector" value="advanced"/>
11089 <param name="force" value="false"/>
11090 <param name="test" value="true"/>
11091 </conditional>
11092 <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
11093 <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
11094 <param name="resolve_between_features" value="off"/>
11095 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11096 <output name="ctd_out" ftype="xml">
11097 <assert_contents>
11098 <is_valid_xml/>
11099 </assert_contents>
11100 </output>
11101 </test>
11102 <test expect_num_outputs="2">
11103 <conditional name="adv_opts_cond">
11104 <param name="adv_opts_selector" value="advanced"/>
11105 <param name="force" value="false"/>
11106 <param name="test" value="true"/>
11107 </conditional>
11108 <param name="in" value="IDConflictResolver_4_input.featureXML"/>
11109 <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
11110 <param name="resolve_between_features" value="highest_intensity"/>
11111 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11112 <output name="ctd_out" ftype="xml">
11113 <assert_contents>
11114 <is_valid_xml/>
11115 </assert_contents>
11116 </output>
11117 </test>
11118 </xml>
11119 <xml name="autotest_IDExtractor">
11120 </xml>
11121 <xml name="autotest_IDFileConverter">
11122 <test expect_num_outputs="2">
11123 <conditional name="adv_opts_cond">
11124 <param name="adv_opts_selector" value="advanced"/>
11125 <param name="ignore_proteins_per_peptide" value="false"/>
11126 <param name="scan_regex" value=""/>
11127 <param name="no_spectra_data_override" value="false"/>
11128 <param name="no_spectra_references_override" value="false"/>
11129 <param name="add_ionmatch_annotation" value="0.0"/>
11130 <param name="force" value="false"/>
11131 <param name="test" value="true"/>
11132 </conditional>
11133 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11134 <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11135 <param name="out_type" value="idXML"/>
11136 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11137 <param name="mz_name" value=""/>
11138 <param name="peptideprophet_analyzed" value="false"/>
11139 <param name="score_type" value="qvalue"/>
11140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11141 <output name="ctd_out" ftype="xml">
11142 <assert_contents>
11143 <is_valid_xml/>
11144 </assert_contents>
11145 </output>
11146 </test>
11147 <test expect_num_outputs="2">
11148 <conditional name="adv_opts_cond">
11149 <param name="adv_opts_selector" value="advanced"/>
11150 <param name="ignore_proteins_per_peptide" value="false"/>
11151 <param name="scan_regex" value=""/>
11152 <param name="no_spectra_data_override" value="false"/>
11153 <param name="no_spectra_references_override" value="false"/>
11154 <param name="add_ionmatch_annotation" value="0.0"/>
11155 <param name="force" value="false"/>
11156 <param name="test" value="true"/>
11157 </conditional>
11158 <param name="in" value="PepXMLFile_test.pepxml"/>
11159 <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11160 <param name="out_type" value="idXML"/>
11161 <param name="mz_file" value="PepXMLFile_test.mzML"/>
11162 <param name="mz_name" value="PepXMLFile_test"/>
11163 <param name="peptideprophet_analyzed" value="false"/>
11164 <param name="score_type" value="qvalue"/>
11165 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11166 <output name="ctd_out" ftype="xml">
11167 <assert_contents>
11168 <is_valid_xml/>
11169 </assert_contents>
11170 </output>
11171 </test>
11172 <test expect_num_outputs="2">
11173 <conditional name="adv_opts_cond">
11174 <param name="adv_opts_selector" value="advanced"/>
11175 <param name="ignore_proteins_per_peptide" value="false"/>
11176 <param name="scan_regex" value=""/>
11177 <param name="no_spectra_data_override" value="false"/>
11178 <param name="no_spectra_references_override" value="false"/>
11179 <param name="add_ionmatch_annotation" value="0.0"/>
11180 <param name="force" value="false"/>
11181 <param name="test" value="true"/>
11182 </conditional>
11183 <param name="in" value="IDFileConverter_3_input.protXML"/>
11184 <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11185 <param name="out_type" value="idXML"/>
11186 <param name="mz_name" value=""/>
11187 <param name="peptideprophet_analyzed" value="false"/>
11188 <param name="score_type" value="qvalue"/>
11189 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11190 <output name="ctd_out" ftype="xml">
11191 <assert_contents>
11192 <is_valid_xml/>
11193 </assert_contents>
11194 </output>
11195 </test>
11196 <test expect_num_outputs="2">
11197 <conditional name="adv_opts_cond">
11198 <param name="adv_opts_selector" value="advanced"/>
11199 <param name="ignore_proteins_per_peptide" value="false"/>
11200 <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
11201 <param name="no_spectra_data_override" value="false"/>
11202 <param name="no_spectra_references_override" value="false"/>
11203 <param name="add_ionmatch_annotation" value="0.0"/>
11204 <param name="force" value="false"/>
11205 <param name="test" value="true"/>
11206 </conditional>
11207 <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
11208 <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11209 <param name="out_type" value="idXML"/>
11210 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11211 <param name="mz_name" value=""/>
11212 <param name="peptideprophet_analyzed" value="false"/>
11213 <param name="score_type" value="qvalue"/>
11214 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11215 <output name="ctd_out" ftype="xml">
11216 <assert_contents>
11217 <is_valid_xml/>
11218 </assert_contents>
11219 </output>
11220 </test>
11221 <test expect_num_outputs="2">
11222 <conditional name="adv_opts_cond">
11223 <param name="adv_opts_selector" value="advanced"/>
11224 <param name="ignore_proteins_per_peptide" value="false"/>
11225 <param name="scan_regex" value=""/>
11226 <param name="no_spectra_data_override" value="false"/>
11227 <param name="no_spectra_references_override" value="false"/>
11228 <param name="add_ionmatch_annotation" value="0.0"/>
11229 <param name="force" value="false"/>
11230 <param name="test" value="true"/>
11231 </conditional>
11232 <param name="in" value="IDFileConverter_6_input1.pepXML"/>
11233 <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11234 <param name="out_type" value="idXML"/>
11235 <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
11236 <param name="mz_name" value="F025589.dat.mzML"/>
11237 <param name="peptideprophet_analyzed" value="false"/>
11238 <param name="score_type" value="qvalue"/>
11239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11240 <output name="ctd_out" ftype="xml">
11241 <assert_contents>
11242 <is_valid_xml/>
11243 </assert_contents>
11244 </output>
11245 </test>
11246 <test expect_num_outputs="2">
11247 <conditional name="adv_opts_cond">
11248 <param name="adv_opts_selector" value="advanced"/>
11249 <param name="ignore_proteins_per_peptide" value="false"/>
11250 <param name="scan_regex" value=""/>
11251 <param name="no_spectra_data_override" value="false"/>
11252 <param name="no_spectra_references_override" value="false"/>
11253 <param name="add_ionmatch_annotation" value="0.0"/>
11254 <param name="force" value="false"/>
11255 <param name="test" value="true"/>
11256 </conditional>
11257 <param name="in" value="IDFileConverter_7_input1.xml"/>
11258 <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11259 <param name="out_type" value="idXML"/>
11260 <param name="mz_name" value=""/>
11261 <param name="peptideprophet_analyzed" value="false"/>
11262 <param name="score_type" value="qvalue"/>
11263 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11264 <output name="ctd_out" ftype="xml">
11265 <assert_contents>
11266 <is_valid_xml/>
11267 </assert_contents>
11268 </output>
11269 </test>
11270 <test expect_num_outputs="2">
11271 <conditional name="adv_opts_cond">
11272 <param name="adv_opts_selector" value="advanced"/>
11273 <param name="ignore_proteins_per_peptide" value="false"/>
11274 <param name="scan_regex" value=""/>
11275 <param name="no_spectra_data_override" value="false"/>
11276 <param name="no_spectra_references_override" value="false"/>
11277 <param name="add_ionmatch_annotation" value="0.0"/>
11278 <param name="force" value="false"/>
11279 <param name="test" value="true"/>
11280 </conditional>
11281 <param name="in" value="IDFileConverter_8_input.mzid"/>
11282 <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11283 <param name="out_type" value="idXML"/>
11284 <param name="mz_name" value=""/>
11285 <param name="peptideprophet_analyzed" value="false"/>
11286 <param name="score_type" value="qvalue"/>
11287 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11288 <output name="ctd_out" ftype="xml">
11289 <assert_contents>
11290 <is_valid_xml/>
11291 </assert_contents>
11292 </output>
11293 </test>
11294 <test expect_num_outputs="2">
11295 <conditional name="adv_opts_cond">
11296 <param name="adv_opts_selector" value="advanced"/>
11297 <param name="ignore_proteins_per_peptide" value="false"/>
11298 <param name="scan_regex" value=""/>
11299 <param name="no_spectra_data_override" value="false"/>
11300 <param name="no_spectra_references_override" value="false"/>
11301 <param name="add_ionmatch_annotation" value="0.0"/>
11302 <param name="force" value="false"/>
11303 <param name="test" value="true"/>
11304 </conditional>
11305 <param name="in" value="IDFileConverter_9_input.idXML"/>
11306 <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
11307 <param name="out_type" value="mzid"/>
11308 <param name="mz_name" value=""/>
11309 <param name="peptideprophet_analyzed" value="false"/>
11310 <param name="score_type" value="qvalue"/>
11311 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11312 <output name="ctd_out" ftype="xml">
11313 <assert_contents>
11314 <is_valid_xml/>
11315 </assert_contents>
11316 </output>
11317 </test>
11318 <test expect_num_outputs="2">
11319 <conditional name="adv_opts_cond">
11320 <param name="adv_opts_selector" value="advanced"/>
11321 <param name="ignore_proteins_per_peptide" value="false"/>
11322 <param name="scan_regex" value=""/>
11323 <param name="no_spectra_data_override" value="false"/>
11324 <param name="no_spectra_references_override" value="false"/>
11325 <param name="add_ionmatch_annotation" value="0.0"/>
11326 <param name="force" value="false"/>
11327 <param name="test" value="true"/>
11328 </conditional>
11329 <param name="in" value="IDFileConverter_10_input.pepXML"/>
11330 <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11331 <param name="out_type" value="idXML"/>
11332 <param name="mz_name" value=""/>
11333 <param name="peptideprophet_analyzed" value="false"/>
11334 <param name="score_type" value="qvalue"/>
11335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11336 <output name="ctd_out" ftype="xml">
11337 <assert_contents>
11338 <is_valid_xml/>
11339 </assert_contents>
11340 </output>
11341 </test>
11342 <test expect_num_outputs="2">
11343 <conditional name="adv_opts_cond">
11344 <param name="adv_opts_selector" value="advanced"/>
11345 <param name="ignore_proteins_per_peptide" value="false"/>
11346 <param name="scan_regex" value=""/>
11347 <param name="no_spectra_data_override" value="false"/>
11348 <param name="no_spectra_references_override" value="false"/>
11349 <param name="add_ionmatch_annotation" value="0.0"/>
11350 <param name="force" value="false"/>
11351 <param name="test" value="true"/>
11352 </conditional>
11353 <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
11354 <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11355 <param name="out_type" value="idXML"/>
11356 <param name="mz_name" value=""/>
11357 <param name="peptideprophet_analyzed" value="false"/>
11358 <param name="score_type" value="qvalue"/>
11359 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11360 <output name="ctd_out" ftype="xml">
11361 <assert_contents>
11362 <is_valid_xml/>
11363 </assert_contents>
11364 </output>
11365 </test>
11366 <test expect_num_outputs="2">
11367 <conditional name="adv_opts_cond">
11368 <param name="adv_opts_selector" value="advanced"/>
11369 <param name="ignore_proteins_per_peptide" value="false"/>
11370 <param name="scan_regex" value=""/>
11371 <param name="no_spectra_data_override" value="false"/>
11372 <param name="no_spectra_references_override" value="false"/>
11373 <param name="add_ionmatch_annotation" value="0.0"/>
11374 <param name="force" value="false"/>
11375 <param name="test" value="true"/>
11376 </conditional>
11377 <param name="in" value="IDFileConverter_12_input.psms"/>
11378 <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11379 <param name="out_type" value="idXML"/>
11380 <param name="mz_name" value=""/>
11381 <param name="peptideprophet_analyzed" value="false"/>
11382 <param name="score_type" value="qvalue"/>
11383 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11384 <output name="ctd_out" ftype="xml">
11385 <assert_contents>
11386 <is_valid_xml/>
11387 </assert_contents>
11388 </output>
11389 </test>
11390 <test expect_num_outputs="2">
11391 <conditional name="adv_opts_cond">
11392 <param name="adv_opts_selector" value="advanced"/>
11393 <param name="ignore_proteins_per_peptide" value="false"/>
11394 <param name="scan_regex" value=""/>
11395 <param name="no_spectra_data_override" value="false"/>
11396 <param name="no_spectra_references_override" value="false"/>
11397 <param name="add_ionmatch_annotation" value="0.0"/>
11398 <param name="force" value="false"/>
11399 <param name="test" value="true"/>
11400 </conditional>
11401 <param name="in" value="IDFileConverter_12_input.psms"/>
11402 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11403 <param name="out_type" value="idXML"/>
11404 <param name="mz_name" value=""/>
11405 <param name="peptideprophet_analyzed" value="false"/>
11406 <param name="score_type" value="PEP"/>
11407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11408 <output name="ctd_out" ftype="xml">
11409 <assert_contents>
11410 <is_valid_xml/>
11411 </assert_contents>
11412 </output>
11413 </test>
11414 <test expect_num_outputs="2">
11415 <conditional name="adv_opts_cond">
11416 <param name="adv_opts_selector" value="advanced"/>
11417 <param name="ignore_proteins_per_peptide" value="false"/>
11418 <param name="scan_regex" value=""/>
11419 <param name="no_spectra_data_override" value="false"/>
11420 <param name="no_spectra_references_override" value="false"/>
11421 <param name="add_ionmatch_annotation" value="0.0"/>
11422 <param name="force" value="false"/>
11423 <param name="test" value="true"/>
11424 </conditional>
11425 <param name="in" value="IDFileConverter_12_input.psms"/>
11426 <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11427 <param name="out_type" value="idXML"/>
11428 <param name="mz_name" value=""/>
11429 <param name="peptideprophet_analyzed" value="false"/>
11430 <param name="score_type" value="score"/>
11431 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11432 <output name="ctd_out" ftype="xml">
11433 <assert_contents>
11434 <is_valid_xml/>
11435 </assert_contents>
11436 </output>
11437 </test>
11438 <test expect_num_outputs="2">
11439 <conditional name="adv_opts_cond">
11440 <param name="adv_opts_selector" value="advanced"/>
11441 <param name="ignore_proteins_per_peptide" value="false"/>
11442 <param name="scan_regex" value=""/>
11443 <param name="no_spectra_data_override" value="false"/>
11444 <param name="no_spectra_references_override" value="false"/>
11445 <param name="add_ionmatch_annotation" value="0.0"/>
11446 <param name="force" value="false"/>
11447 <param name="test" value="true"/>
11448 </conditional>
11449 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11450 <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11451 <param name="out_type" value="idXML"/>
11452 <param name="mz_file" value="spectra.mzML"/>
11453 <param name="mz_name" value=""/>
11454 <param name="peptideprophet_analyzed" value="false"/>
11455 <param name="score_type" value="qvalue"/>
11456 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11457 <output name="ctd_out" ftype="xml">
11458 <assert_contents>
11459 <is_valid_xml/>
11460 </assert_contents>
11461 </output>
11462 </test>
11463 <test expect_num_outputs="2">
11464 <conditional name="adv_opts_cond">
11465 <param name="adv_opts_selector" value="advanced"/>
11466 <param name="ignore_proteins_per_peptide" value="false"/>
11467 <param name="scan_regex" value=""/>
11468 <param name="no_spectra_data_override" value="false"/>
11469 <param name="no_spectra_references_override" value="false"/>
11470 <param name="add_ionmatch_annotation" value="0.0"/>
11471 <param name="force" value="false"/>
11472 <param name="test" value="true"/>
11473 </conditional>
11474 <param name="in" value="IDFileConverter_16_input.pepXML"/>
11475 <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11476 <param name="out_type" value="idXML"/>
11477 <param name="mz_name" value=""/>
11478 <param name="peptideprophet_analyzed" value="false"/>
11479 <param name="score_type" value="qvalue"/>
11480 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11481 <output name="ctd_out" ftype="xml">
11482 <assert_contents>
11483 <is_valid_xml/>
11484 </assert_contents>
11485 </output>
11486 </test>
11487 <test expect_num_outputs="2">
11488 <conditional name="adv_opts_cond">
11489 <param name="adv_opts_selector" value="advanced"/>
11490 <param name="ignore_proteins_per_peptide" value="false"/>
11491 <param name="scan_regex" value=""/>
11492 <param name="no_spectra_data_override" value="false"/>
11493 <param name="no_spectra_references_override" value="false"/>
11494 <param name="add_ionmatch_annotation" value="0.0"/>
11495 <param name="force" value="false"/>
11496 <param name="test" value="true"/>
11497 </conditional>
11498 <param name="in" value="IDFileConverter_17_input.idXML"/>
11499 <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11500 <param name="out_type" value="pepXML"/>
11501 <param name="mz_name" value=""/>
11502 <param name="peptideprophet_analyzed" value="false"/>
11503 <param name="score_type" value="qvalue"/>
11504 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11505 <output name="ctd_out" ftype="xml">
11506 <assert_contents>
11507 <is_valid_xml/>
11508 </assert_contents>
11509 </output>
11510 </test>
11511 <test expect_num_outputs="2">
11512 <conditional name="adv_opts_cond">
11513 <param name="adv_opts_selector" value="advanced"/>
11514 <param name="ignore_proteins_per_peptide" value="false"/>
11515 <param name="scan_regex" value=""/>
11516 <param name="no_spectra_data_override" value="false"/>
11517 <param name="no_spectra_references_override" value="false"/>
11518 <param name="add_ionmatch_annotation" value="0.0"/>
11519 <param name="force" value="false"/>
11520 <param name="test" value="true"/>
11521 </conditional>
11522 <param name="in" value="IDFileConverter_18_input.idXML"/>
11523 <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11524 <param name="out_type" value="pepXML"/>
11525 <param name="mz_name" value=""/>
11526 <param name="peptideprophet_analyzed" value="false"/>
11527 <param name="score_type" value="qvalue"/>
11528 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11529 <output name="ctd_out" ftype="xml">
11530 <assert_contents>
11531 <is_valid_xml/>
11532 </assert_contents>
11533 </output>
11534 </test>
11535 <test expect_num_outputs="2">
11536 <conditional name="adv_opts_cond">
11537 <param name="adv_opts_selector" value="advanced"/>
11538 <param name="ignore_proteins_per_peptide" value="false"/>
11539 <param name="scan_regex" value=""/>
11540 <param name="no_spectra_data_override" value="false"/>
11541 <param name="no_spectra_references_override" value="false"/>
11542 <param name="add_ionmatch_annotation" value="0.0"/>
11543 <param name="force" value="false"/>
11544 <param name="test" value="true"/>
11545 </conditional>
11546 <param name="in" value="IDFileConverter_19_input.idXML"/>
11547 <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11548 <param name="out_type" value="pepXML"/>
11549 <param name="mz_name" value=""/>
11550 <param name="peptideprophet_analyzed" value="false"/>
11551 <param name="score_type" value="qvalue"/>
11552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11553 <output name="ctd_out" ftype="xml">
11554 <assert_contents>
11555 <is_valid_xml/>
11556 </assert_contents>
11557 </output>
11558 </test>
11559 <test expect_num_outputs="2">
11560 <conditional name="adv_opts_cond">
11561 <param name="adv_opts_selector" value="advanced"/>
11562 <param name="ignore_proteins_per_peptide" value="false"/>
11563 <param name="scan_regex" value=""/>
11564 <param name="no_spectra_data_override" value="false"/>
11565 <param name="no_spectra_references_override" value="false"/>
11566 <param name="add_ionmatch_annotation" value="0.0"/>
11567 <param name="force" value="false"/>
11568 <param name="test" value="true"/>
11569 </conditional>
11570 <param name="in" value="IDFileConverter_20_input.idXML"/>
11571 <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
11572 <param name="out_type" value="pepXML"/>
11573 <param name="mz_name" value=""/>
11574 <param name="peptideprophet_analyzed" value="false"/>
11575 <param name="score_type" value="qvalue"/>
11576 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11577 <output name="ctd_out" ftype="xml">
11578 <assert_contents>
11579 <is_valid_xml/>
11580 </assert_contents>
11581 </output>
11582 </test>
11583 <test expect_num_outputs="2">
11584 <conditional name="adv_opts_cond">
11585 <param name="adv_opts_selector" value="advanced"/>
11586 <param name="ignore_proteins_per_peptide" value="false"/>
11587 <param name="scan_regex" value=""/>
11588 <param name="no_spectra_data_override" value="false"/>
11589 <param name="no_spectra_references_override" value="false"/>
11590 <param name="add_ionmatch_annotation" value="0.0"/>
11591 <param name="force" value="false"/>
11592 <param name="test" value="true"/>
11593 </conditional>
11594 <param name="in" value="IDFileConverter_21_input.idXML"/>
11595 <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11596 <param name="out_type" value="idXML"/>
11597 <param name="mz_file" value="IDMapper_4_input.mzML"/>
11598 <param name="mz_name" value=""/>
11599 <param name="peptideprophet_analyzed" value="false"/>
11600 <param name="score_type" value="qvalue"/>
11601 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11602 <output name="ctd_out" ftype="xml">
11603 <assert_contents>
11604 <is_valid_xml/>
11605 </assert_contents>
11606 </output>
11607 </test>
11608 <test expect_num_outputs="2">
11609 <conditional name="adv_opts_cond">
11610 <param name="adv_opts_selector" value="advanced"/>
11611 <param name="ignore_proteins_per_peptide" value="false"/>
11612 <param name="scan_regex" value=""/>
11613 <param name="no_spectra_data_override" value="false"/>
11614 <param name="no_spectra_references_override" value="false"/>
11615 <param name="add_ionmatch_annotation" value="0.01"/>
11616 <param name="force" value="false"/>
11617 <param name="test" value="true"/>
11618 </conditional>
11619 <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
11620 <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11621 <param name="out_type" value="idXML"/>
11622 <param name="mz_file" value="spectra.mzML"/>
11623 <param name="mz_name" value=""/>
11624 <param name="peptideprophet_analyzed" value="false"/>
11625 <param name="score_type" value="qvalue"/>
11626 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11627 <output name="ctd_out" ftype="xml">
11628 <assert_contents>
11629 <is_valid_xml/>
11630 </assert_contents>
11631 </output>
11632 </test>
11633 <test expect_num_outputs="2">
11634 <conditional name="adv_opts_cond">
11635 <param name="adv_opts_selector" value="advanced"/>
11636 <param name="ignore_proteins_per_peptide" value="false"/>
11637 <param name="scan_regex" value=""/>
11638 <param name="no_spectra_data_override" value="false"/>
11639 <param name="no_spectra_references_override" value="false"/>
11640 <param name="add_ionmatch_annotation" value="0.0"/>
11641 <param name="force" value="false"/>
11642 <param name="test" value="true"/>
11643 </conditional>
11644 <param name="in" value="IDFileConverter_23_input.mzid"/>
11645 <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11646 <param name="out_type" value="idXML"/>
11647 <param name="mz_name" value=""/>
11648 <param name="peptideprophet_analyzed" value="false"/>
11649 <param name="score_type" value="qvalue"/>
11650 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11651 <output name="ctd_out" ftype="xml">
11652 <assert_contents>
11653 <is_valid_xml/>
11654 </assert_contents>
11655 </output>
11656 </test>
11657 <test expect_num_outputs="2">
11658 <conditional name="adv_opts_cond">
11659 <param name="adv_opts_selector" value="advanced"/>
11660 <param name="ignore_proteins_per_peptide" value="false"/>
11661 <param name="scan_regex" value=""/>
11662 <param name="no_spectra_data_override" value="false"/>
11663 <param name="no_spectra_references_override" value="false"/>
11664 <param name="add_ionmatch_annotation" value="0.0"/>
11665 <param name="force" value="false"/>
11666 <param name="test" value="true"/>
11667 </conditional>
11668 <param name="in" value="IDFileConverter_24_input.pep.xml"/>
11669 <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11670 <param name="out_type" value="idXML"/>
11671 <param name="mz_name" value=""/>
11672 <param name="peptideprophet_analyzed" value="false"/>
11673 <param name="score_type" value="qvalue"/>
11674 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11675 <output name="ctd_out" ftype="xml">
11676 <assert_contents>
11677 <is_valid_xml/>
11678 </assert_contents>
11679 </output>
11680 </test>
11681 <test expect_num_outputs="2">
11682 <conditional name="adv_opts_cond">
11683 <param name="adv_opts_selector" value="advanced"/>
11684 <param name="ignore_proteins_per_peptide" value="false"/>
11685 <param name="scan_regex" value=""/>
11686 <param name="no_spectra_data_override" value="false"/>
11687 <param name="no_spectra_references_override" value="false"/>
11688 <param name="add_ionmatch_annotation" value="0.0"/>
11689 <param name="force" value="false"/>
11690 <param name="test" value="true"/>
11691 </conditional>
11692 <param name="in" value="IDFileConverter_25_input.idXML"/>
11693 <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>
11694 <param name="out_type" value="pepXML"/>
11695 <param name="mz_name" value=""/>
11696 <param name="peptideprophet_analyzed" value="false"/>
11697 <param name="score_type" value="qvalue"/>
11698 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11699 <output name="ctd_out" ftype="xml">
11700 <assert_contents>
11701 <is_valid_xml/>
11702 </assert_contents>
11703 </output>
11704 </test>
11705 <test expect_num_outputs="2">
11706 <conditional name="adv_opts_cond">
11707 <param name="adv_opts_selector" value="advanced"/>
11708 <param name="ignore_proteins_per_peptide" value="false"/>
11709 <param name="scan_regex" value=""/>
11710 <param name="no_spectra_data_override" value="false"/>
11711 <param name="no_spectra_references_override" value="false"/>
11712 <param name="add_ionmatch_annotation" value="0.0"/>
11713 <param name="force" value="false"/>
11714 <param name="test" value="true"/>
11715 </conditional>
11716 <param name="in" value="IDFileConverter_26_input.mzid"/>
11717 <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11718 <param name="out_type" value="idXML"/>
11719 <param name="mz_name" value=""/>
11720 <param name="peptideprophet_analyzed" value="false"/>
11721 <param name="score_type" value="qvalue"/>
11722 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11723 <output name="ctd_out" ftype="xml">
11724 <assert_contents>
11725 <is_valid_xml/>
11726 </assert_contents>
11727 </output>
11728 </test>
11729 </xml>
11730 <xml name="autotest_IDFilter">
11731 <test expect_num_outputs="2">
11732 <conditional name="adv_opts_cond">
11733 <param name="adv_opts_selector" value="advanced"/>
11734 <param name="remove_duplicate_psm" value="false"/>
11735 <param name="remove_peptide_hits_by_metavalue" value=""/>
11736 <param name="force" value="false"/>
11737 <param name="test" value="true"/>
11738 </conditional>
11739 <param name="in" value="IDFilter_1_input.idXML"/>
11740 <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11741 <param name="var_mods" value="false"/>
11742 <param name="remove_shared_peptides" value="false"/>
11743 <param name="keep_unreferenced_protein_hits" value="false"/>
11744 <param name="remove_decoys" value="false"/>
11745 <param name="delete_unreferenced_peptide_hits" value="false"/>
11746 <section name="precursor">
11747 <param name="rt" value=":"/>
11748 <param name="mz" value=":"/>
11749 <param name="length" value=":"/>
11750 <param name="charge" value=":"/>
11751 </section>
11752 <section name="score">
11753 <param name="pep" value="0.0"/>
11754 <param name="prot" value="0.0"/>
11755 </section>
11756 <section name="whitelist">
11757 <param name="proteins" value="IDFilter_1_input.fas"/>
11758 <param name="protein_accessions" value=""/>
11759 <param name="ignore_modifications" value="false"/>
11760 <param name="modifications" value=""/>
11761 </section>
11762 <section name="blacklist">
11763 <param name="protein_accessions" value=""/>
11764 <param name="ignore_modifications" value="false"/>
11765 <param name="modifications" value=""/>
11766 </section>
11767 <section name="in_silico_digestion">
11768 <param name="enzyme" value="Trypsin"/>
11769 <param name="specificity" value="full"/>
11770 <param name="missed_cleavages" value="-1"/>
11771 <param name="methionine_cleavage" value="false"/>
11772 </section>
11773 <section name="missed_cleavages">
11774 <param name="number_of_missed_cleavages" value=":"/>
11775 <param name="enzyme" value="Trypsin"/>
11776 </section>
11777 <section name="rt">
11778 <param name="p_value" value="0.0"/>
11779 <param name="p_value_1st_dim" value="0.0"/>
11780 </section>
11781 <section name="mz">
11782 <param name="error" value="-1.0"/>
11783 <param name="unit" value="ppm"/>
11784 </section>
11785 <section name="best">
11786 <param name="n_peptide_hits" value="0"/>
11787 <param name="n_protein_hits" value="0"/>
11788 <param name="strict" value="false"/>
11789 <param name="n_to_m_peptide_hits" value=":"/>
11790 </section>
11791 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11792 <output name="ctd_out" ftype="xml">
11793 <assert_contents>
11794 <is_valid_xml/>
11795 </assert_contents>
11796 </output>
11797 </test>
11798 <test expect_num_outputs="2">
11799 <conditional name="adv_opts_cond">
11800 <param name="adv_opts_selector" value="advanced"/>
11801 <param name="remove_duplicate_psm" value="false"/>
11802 <param name="remove_peptide_hits_by_metavalue" value=""/>
11803 <param name="force" value="false"/>
11804 <param name="test" value="true"/>
11805 </conditional>
11806 <param name="in" value="IDFilter_3_input.idXML"/>
11807 <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11808 <param name="var_mods" value="false"/>
11809 <param name="remove_shared_peptides" value="false"/>
11810 <param name="keep_unreferenced_protein_hits" value="false"/>
11811 <param name="remove_decoys" value="false"/>
11812 <param name="delete_unreferenced_peptide_hits" value="false"/>
11813 <section name="precursor">
11814 <param name="rt" value=":"/>
11815 <param name="mz" value=":"/>
11816 <param name="length" value=":"/>
11817 <param name="charge" value=":"/>
11818 </section>
11819 <section name="score">
11820 <param name="pep" value="0.0"/>
11821 <param name="prot" value="0.0"/>
11822 </section>
11823 <section name="whitelist">
11824 <param name="protein_accessions" value=""/>
11825 <param name="ignore_modifications" value="false"/>
11826 <param name="modifications" value=""/>
11827 </section>
11828 <section name="blacklist">
11829 <param name="protein_accessions" value=""/>
11830 <param name="peptides" value="IDFilter_3_2_input.idXML"/>
11831 <param name="ignore_modifications" value="false"/>
11832 <param name="modifications" value=""/>
11833 </section>
11834 <section name="in_silico_digestion">
11835 <param name="enzyme" value="Trypsin"/>
11836 <param name="specificity" value="full"/>
11837 <param name="missed_cleavages" value="-1"/>
11838 <param name="methionine_cleavage" value="false"/>
11839 </section>
11840 <section name="missed_cleavages">
11841 <param name="number_of_missed_cleavages" value=":"/>
11842 <param name="enzyme" value="Trypsin"/>
11843 </section>
11844 <section name="rt">
11845 <param name="p_value" value="0.0"/>
11846 <param name="p_value_1st_dim" value="0.0"/>
11847 </section>
11848 <section name="mz">
11849 <param name="error" value="-1.0"/>
11850 <param name="unit" value="ppm"/>
11851 </section>
11852 <section name="best">
11853 <param name="n_peptide_hits" value="0"/>
11854 <param name="n_protein_hits" value="0"/>
11855 <param name="strict" value="false"/>
11856 <param name="n_to_m_peptide_hits" value=":"/>
11857 </section>
11858 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11859 <output name="ctd_out" ftype="xml">
11860 <assert_contents>
11861 <is_valid_xml/>
11862 </assert_contents>
11863 </output>
11864 </test>
11865 <test expect_num_outputs="2">
11866 <conditional name="adv_opts_cond">
11867 <param name="adv_opts_selector" value="advanced"/>
11868 <param name="remove_duplicate_psm" value="false"/>
11869 <param name="remove_peptide_hits_by_metavalue" value=""/>
11870 <param name="force" value="false"/>
11871 <param name="test" value="true"/>
11872 </conditional>
11873 <param name="in" value="IDFilter_4_input.idXML"/>
11874 <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11875 <param name="var_mods" value="false"/>
11876 <param name="remove_shared_peptides" value="false"/>
11877 <param name="keep_unreferenced_protein_hits" value="false"/>
11878 <param name="remove_decoys" value="false"/>
11879 <param name="delete_unreferenced_peptide_hits" value="false"/>
11880 <section name="precursor">
11881 <param name="rt" value=":"/>
11882 <param name="mz" value=":"/>
11883 <param name="length" value=":"/>
11884 <param name="charge" value=":"/>
11885 </section>
11886 <section name="score">
11887 <param name="pep" value="0.0"/>
11888 <param name="prot" value="0.0"/>
11889 </section>
11890 <section name="whitelist">
11891 <param name="protein_accessions" value=""/>
11892 <param name="ignore_modifications" value="false"/>
11893 <param name="modifications" value=""/>
11894 </section>
11895 <section name="blacklist">
11896 <param name="protein_accessions" value=""/>
11897 <param name="ignore_modifications" value="false"/>
11898 <param name="modifications" value=""/>
11899 </section>
11900 <section name="in_silico_digestion">
11901 <param name="enzyme" value="Trypsin"/>
11902 <param name="specificity" value="full"/>
11903 <param name="missed_cleavages" value="-1"/>
11904 <param name="methionine_cleavage" value="false"/>
11905 </section>
11906 <section name="missed_cleavages">
11907 <param name="number_of_missed_cleavages" value=":"/>
11908 <param name="enzyme" value="Trypsin"/>
11909 </section>
11910 <section name="rt">
11911 <param name="p_value" value="0.08"/>
11912 <param name="p_value_1st_dim" value="0.0"/>
11913 </section>
11914 <section name="mz">
11915 <param name="error" value="-1.0"/>
11916 <param name="unit" value="ppm"/>
11917 </section>
11918 <section name="best">
11919 <param name="n_peptide_hits" value="0"/>
11920 <param name="n_protein_hits" value="0"/>
11921 <param name="strict" value="false"/>
11922 <param name="n_to_m_peptide_hits" value=":"/>
11923 </section>
11924 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11925 <output name="ctd_out" ftype="xml">
11926 <assert_contents>
11927 <is_valid_xml/>
11928 </assert_contents>
11929 </output>
11930 </test>
11931 <test expect_num_outputs="2">
11932 <conditional name="adv_opts_cond">
11933 <param name="adv_opts_selector" value="advanced"/>
11934 <param name="remove_duplicate_psm" value="false"/>
11935 <param name="remove_peptide_hits_by_metavalue" value=""/>
11936 <param name="force" value="false"/>
11937 <param name="test" value="true"/>
11938 </conditional>
11939 <param name="in" value="IDFilter_5_input.idXML"/>
11940 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
11941 <param name="var_mods" value="false"/>
11942 <param name="remove_shared_peptides" value="false"/>
11943 <param name="keep_unreferenced_protein_hits" value="false"/>
11944 <param name="remove_decoys" value="false"/>
11945 <param name="delete_unreferenced_peptide_hits" value="false"/>
11946 <section name="precursor">
11947 <param name="rt" value=":"/>
11948 <param name="mz" value=":"/>
11949 <param name="length" value=":"/>
11950 <param name="charge" value=":"/>
11951 </section>
11952 <section name="score">
11953 <param name="pep" value="32.0"/>
11954 <param name="prot" value="25.0"/>
11955 </section>
11956 <section name="whitelist">
11957 <param name="protein_accessions" value=""/>
11958 <param name="ignore_modifications" value="false"/>
11959 <param name="modifications" value=""/>
11960 </section>
11961 <section name="blacklist">
11962 <param name="protein_accessions" value=""/>
11963 <param name="ignore_modifications" value="false"/>
11964 <param name="modifications" value=""/>
11965 </section>
11966 <section name="in_silico_digestion">
11967 <param name="enzyme" value="Trypsin"/>
11968 <param name="specificity" value="full"/>
11969 <param name="missed_cleavages" value="-1"/>
11970 <param name="methionine_cleavage" value="false"/>
11971 </section>
11972 <section name="missed_cleavages">
11973 <param name="number_of_missed_cleavages" value=":"/>
11974 <param name="enzyme" value="Trypsin"/>
11975 </section>
11976 <section name="rt">
11977 <param name="p_value" value="0.0"/>
11978 <param name="p_value_1st_dim" value="0.0"/>
11979 </section>
11980 <section name="mz">
11981 <param name="error" value="-1.0"/>
11982 <param name="unit" value="ppm"/>
11983 </section>
11984 <section name="best">
11985 <param name="n_peptide_hits" value="0"/>
11986 <param name="n_protein_hits" value="0"/>
11987 <param name="strict" value="false"/>
11988 <param name="n_to_m_peptide_hits" value=":"/>
11989 </section>
11990 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
11991 <output name="ctd_out" ftype="xml">
11992 <assert_contents>
11993 <is_valid_xml/>
11994 </assert_contents>
11995 </output>
11996 </test>
11997 <test expect_num_outputs="2">
11998 <conditional name="adv_opts_cond">
11999 <param name="adv_opts_selector" value="advanced"/>
12000 <param name="remove_duplicate_psm" value="false"/>
12001 <param name="remove_peptide_hits_by_metavalue" value=""/>
12002 <param name="force" value="false"/>
12003 <param name="test" value="true"/>
12004 </conditional>
12005 <param name="in" value="IDFilter_5_input.idXML"/>
12006 <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12007 <param name="var_mods" value="false"/>
12008 <param name="remove_shared_peptides" value="false"/>
12009 <param name="keep_unreferenced_protein_hits" value="false"/>
12010 <param name="remove_decoys" value="false"/>
12011 <param name="delete_unreferenced_peptide_hits" value="false"/>
12012 <section name="precursor">
12013 <param name="rt" value=":"/>
12014 <param name="mz" value=":"/>
12015 <param name="length" value=":"/>
12016 <param name="charge" value=":"/>
12017 </section>
12018 <section name="score">
12019 <param name="pep" value="32.0"/>
12020 <param name="prot" value="0.0"/>
12021 </section>
12022 <section name="whitelist">
12023 <param name="protein_accessions" value=""/>
12024 <param name="ignore_modifications" value="false"/>
12025 <param name="modifications" value=""/>
12026 </section>
12027 <section name="blacklist">
12028 <param name="protein_accessions" value=""/>
12029 <param name="ignore_modifications" value="false"/>
12030 <param name="modifications" value=""/>
12031 </section>
12032 <section name="in_silico_digestion">
12033 <param name="enzyme" value="Trypsin"/>
12034 <param name="specificity" value="full"/>
12035 <param name="missed_cleavages" value="-1"/>
12036 <param name="methionine_cleavage" value="false"/>
12037 </section>
12038 <section name="missed_cleavages">
12039 <param name="number_of_missed_cleavages" value=":"/>
12040 <param name="enzyme" value="Trypsin"/>
12041 </section>
12042 <section name="rt">
12043 <param name="p_value" value="0.0"/>
12044 <param name="p_value_1st_dim" value="0.0"/>
12045 </section>
12046 <section name="mz">
12047 <param name="error" value="-1.0"/>
12048 <param name="unit" value="ppm"/>
12049 </section>
12050 <section name="best">
12051 <param name="n_peptide_hits" value="0"/>
12052 <param name="n_protein_hits" value="0"/>
12053 <param name="strict" value="false"/>
12054 <param name="n_to_m_peptide_hits" value=":"/>
12055 </section>
12056 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12057 <output name="ctd_out" ftype="xml">
12058 <assert_contents>
12059 <is_valid_xml/>
12060 </assert_contents>
12061 </output>
12062 </test>
12063 <test expect_num_outputs="2">
12064 <conditional name="adv_opts_cond">
12065 <param name="adv_opts_selector" value="advanced"/>
12066 <param name="remove_duplicate_psm" value="false"/>
12067 <param name="remove_peptide_hits_by_metavalue" value=""/>
12068 <param name="force" value="false"/>
12069 <param name="test" value="true"/>
12070 </conditional>
12071 <param name="in" value="IDFilter_5_input.idXML"/>
12072 <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12073 <param name="var_mods" value="false"/>
12074 <param name="remove_shared_peptides" value="false"/>
12075 <param name="keep_unreferenced_protein_hits" value="false"/>
12076 <param name="remove_decoys" value="false"/>
12077 <param name="delete_unreferenced_peptide_hits" value="false"/>
12078 <section name="precursor">
12079 <param name="rt" value=":"/>
12080 <param name="mz" value=":"/>
12081 <param name="length" value=":"/>
12082 <param name="charge" value=":"/>
12083 </section>
12084 <section name="score">
12085 <param name="pep" value="0.0"/>
12086 <param name="prot" value="25.0"/>
12087 </section>
12088 <section name="whitelist">
12089 <param name="protein_accessions" value=""/>
12090 <param name="ignore_modifications" value="false"/>
12091 <param name="modifications" value=""/>
12092 </section>
12093 <section name="blacklist">
12094 <param name="protein_accessions" value=""/>
12095 <param name="ignore_modifications" value="false"/>
12096 <param name="modifications" value=""/>
12097 </section>
12098 <section name="in_silico_digestion">
12099 <param name="enzyme" value="Trypsin"/>
12100 <param name="specificity" value="full"/>
12101 <param name="missed_cleavages" value="-1"/>
12102 <param name="methionine_cleavage" value="false"/>
12103 </section>
12104 <section name="missed_cleavages">
12105 <param name="number_of_missed_cleavages" value=":"/>
12106 <param name="enzyme" value="Trypsin"/>
12107 </section>
12108 <section name="rt">
12109 <param name="p_value" value="0.0"/>
12110 <param name="p_value_1st_dim" value="0.0"/>
12111 </section>
12112 <section name="mz">
12113 <param name="error" value="-1.0"/>
12114 <param name="unit" value="ppm"/>
12115 </section>
12116 <section name="best">
12117 <param name="n_peptide_hits" value="0"/>
12118 <param name="n_protein_hits" value="0"/>
12119 <param name="strict" value="false"/>
12120 <param name="n_to_m_peptide_hits" value=":"/>
12121 </section>
12122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12123 <output name="ctd_out" ftype="xml">
12124 <assert_contents>
12125 <is_valid_xml/>
12126 </assert_contents>
12127 </output>
12128 </test>
12129 <test expect_num_outputs="2">
12130 <conditional name="adv_opts_cond">
12131 <param name="adv_opts_selector" value="advanced"/>
12132 <param name="remove_duplicate_psm" value="false"/>
12133 <param name="remove_peptide_hits_by_metavalue" value=""/>
12134 <param name="force" value="false"/>
12135 <param name="test" value="true"/>
12136 </conditional>
12137 <param name="in" value="IDFilter_5_input.idXML"/>
12138 <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12139 <param name="var_mods" value="false"/>
12140 <param name="remove_shared_peptides" value="false"/>
12141 <param name="keep_unreferenced_protein_hits" value="false"/>
12142 <param name="remove_decoys" value="false"/>
12143 <param name="delete_unreferenced_peptide_hits" value="true"/>
12144 <section name="precursor">
12145 <param name="rt" value=":"/>
12146 <param name="mz" value=":"/>
12147 <param name="length" value=":"/>
12148 <param name="charge" value=":"/>
12149 </section>
12150 <section name="score">
12151 <param name="pep" value="0.0"/>
12152 <param name="prot" value="25.0"/>
12153 </section>
12154 <section name="whitelist">
12155 <param name="protein_accessions" value=""/>
12156 <param name="ignore_modifications" value="false"/>
12157 <param name="modifications" value=""/>
12158 </section>
12159 <section name="blacklist">
12160 <param name="protein_accessions" value=""/>
12161 <param name="ignore_modifications" value="false"/>
12162 <param name="modifications" value=""/>
12163 </section>
12164 <section name="in_silico_digestion">
12165 <param name="enzyme" value="Trypsin"/>
12166 <param name="specificity" value="full"/>
12167 <param name="missed_cleavages" value="-1"/>
12168 <param name="methionine_cleavage" value="false"/>
12169 </section>
12170 <section name="missed_cleavages">
12171 <param name="number_of_missed_cleavages" value=":"/>
12172 <param name="enzyme" value="Trypsin"/>
12173 </section>
12174 <section name="rt">
12175 <param name="p_value" value="0.0"/>
12176 <param name="p_value_1st_dim" value="0.0"/>
12177 </section>
12178 <section name="mz">
12179 <param name="error" value="-1.0"/>
12180 <param name="unit" value="ppm"/>
12181 </section>
12182 <section name="best">
12183 <param name="n_peptide_hits" value="0"/>
12184 <param name="n_protein_hits" value="0"/>
12185 <param name="strict" value="false"/>
12186 <param name="n_to_m_peptide_hits" value=":"/>
12187 </section>
12188 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12189 <output name="ctd_out" ftype="xml">
12190 <assert_contents>
12191 <is_valid_xml/>
12192 </assert_contents>
12193 </output>
12194 </test>
12195 <test expect_num_outputs="2">
12196 <conditional name="adv_opts_cond">
12197 <param name="adv_opts_selector" value="advanced"/>
12198 <param name="remove_duplicate_psm" value="false"/>
12199 <param name="remove_peptide_hits_by_metavalue" value=""/>
12200 <param name="force" value="false"/>
12201 <param name="test" value="true"/>
12202 </conditional>
12203 <param name="in" value="IDFilter_6_input.idXML"/>
12204 <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12205 <param name="var_mods" value="false"/>
12206 <param name="remove_shared_peptides" value="false"/>
12207 <param name="keep_unreferenced_protein_hits" value="false"/>
12208 <param name="remove_decoys" value="false"/>
12209 <param name="delete_unreferenced_peptide_hits" value="false"/>
12210 <section name="precursor">
12211 <param name="rt" value=":"/>
12212 <param name="mz" value=":"/>
12213 <param name="length" value=":"/>
12214 <param name="charge" value=":"/>
12215 </section>
12216 <section name="score">
12217 <param name="pep" value="0.0"/>
12218 <param name="prot" value="0.0"/>
12219 </section>
12220 <section name="whitelist">
12221 <param name="protein_accessions" value=""/>
12222 <param name="ignore_modifications" value="false"/>
12223 <param name="modifications" value=""/>
12224 </section>
12225 <section name="blacklist">
12226 <param name="protein_accessions" value=""/>
12227 <param name="ignore_modifications" value="false"/>
12228 <param name="modifications" value=""/>
12229 </section>
12230 <section name="in_silico_digestion">
12231 <param name="enzyme" value="Trypsin"/>
12232 <param name="specificity" value="full"/>
12233 <param name="missed_cleavages" value="-1"/>
12234 <param name="methionine_cleavage" value="false"/>
12235 </section>
12236 <section name="missed_cleavages">
12237 <param name="number_of_missed_cleavages" value=":"/>
12238 <param name="enzyme" value="Trypsin"/>
12239 </section>
12240 <section name="rt">
12241 <param name="p_value" value="0.0"/>
12242 <param name="p_value_1st_dim" value="0.0"/>
12243 </section>
12244 <section name="mz">
12245 <param name="error" value="-1.0"/>
12246 <param name="unit" value="ppm"/>
12247 </section>
12248 <section name="best">
12249 <param name="n_peptide_hits" value="2"/>
12250 <param name="n_protein_hits" value="10"/>
12251 <param name="strict" value="false"/>
12252 <param name="n_to_m_peptide_hits" value=":"/>
12253 </section>
12254 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12255 <output name="ctd_out" ftype="xml">
12256 <assert_contents>
12257 <is_valid_xml/>
12258 </assert_contents>
12259 </output>
12260 </test>
12261 <test expect_num_outputs="2">
12262 <conditional name="adv_opts_cond">
12263 <param name="adv_opts_selector" value="advanced"/>
12264 <param name="remove_duplicate_psm" value="true"/>
12265 <param name="remove_peptide_hits_by_metavalue" value=""/>
12266 <param name="force" value="false"/>
12267 <param name="test" value="true"/>
12268 </conditional>
12269 <param name="in" value="IDFilter_7_input.idXML"/>
12270 <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12271 <param name="var_mods" value="false"/>
12272 <param name="remove_shared_peptides" value="false"/>
12273 <param name="keep_unreferenced_protein_hits" value="false"/>
12274 <param name="remove_decoys" value="false"/>
12275 <param name="delete_unreferenced_peptide_hits" value="false"/>
12276 <section name="precursor">
12277 <param name="rt" value=":"/>
12278 <param name="mz" value=":"/>
12279 <param name="length" value=":"/>
12280 <param name="charge" value=":"/>
12281 </section>
12282 <section name="score">
12283 <param name="pep" value="0.0"/>
12284 <param name="prot" value="0.0"/>
12285 </section>
12286 <section name="whitelist">
12287 <param name="protein_accessions" value=""/>
12288 <param name="ignore_modifications" value="false"/>
12289 <param name="modifications" value=""/>
12290 </section>
12291 <section name="blacklist">
12292 <param name="protein_accessions" value=""/>
12293 <param name="ignore_modifications" value="false"/>
12294 <param name="modifications" value=""/>
12295 </section>
12296 <section name="in_silico_digestion">
12297 <param name="enzyme" value="Trypsin"/>
12298 <param name="specificity" value="full"/>
12299 <param name="missed_cleavages" value="-1"/>
12300 <param name="methionine_cleavage" value="false"/>
12301 </section>
12302 <section name="missed_cleavages">
12303 <param name="number_of_missed_cleavages" value=":"/>
12304 <param name="enzyme" value="Trypsin"/>
12305 </section>
12306 <section name="rt">
12307 <param name="p_value" value="0.0"/>
12308 <param name="p_value_1st_dim" value="0.0"/>
12309 </section>
12310 <section name="mz">
12311 <param name="error" value="-1.0"/>
12312 <param name="unit" value="ppm"/>
12313 </section>
12314 <section name="best">
12315 <param name="n_peptide_hits" value="0"/>
12316 <param name="n_protein_hits" value="0"/>
12317 <param name="strict" value="false"/>
12318 <param name="n_to_m_peptide_hits" value=":"/>
12319 </section>
12320 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12321 <output name="ctd_out" ftype="xml">
12322 <assert_contents>
12323 <is_valid_xml/>
12324 </assert_contents>
12325 </output>
12326 </test>
12327 <test expect_num_outputs="2">
12328 <conditional name="adv_opts_cond">
12329 <param name="adv_opts_selector" value="advanced"/>
12330 <param name="remove_duplicate_psm" value="false"/>
12331 <param name="remove_peptide_hits_by_metavalue" value=""/>
12332 <param name="force" value="false"/>
12333 <param name="test" value="true"/>
12334 </conditional>
12335 <param name="in" value="IDFilter_8_input.idXML"/>
12336 <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12337 <param name="var_mods" value="false"/>
12338 <param name="remove_shared_peptides" value="false"/>
12339 <param name="keep_unreferenced_protein_hits" value="false"/>
12340 <param name="remove_decoys" value="false"/>
12341 <param name="delete_unreferenced_peptide_hits" value="false"/>
12342 <section name="precursor">
12343 <param name="rt" value="200:350"/>
12344 <param name="mz" value="999:1000"/>
12345 <param name="length" value=":"/>
12346 <param name="charge" value=":"/>
12347 </section>
12348 <section name="score">
12349 <param name="pep" value="0.0"/>
12350 <param name="prot" value="0.0"/>
12351 </section>
12352 <section name="whitelist">
12353 <param name="protein_accessions" value=""/>
12354 <param name="ignore_modifications" value="false"/>
12355 <param name="modifications" value=""/>
12356 </section>
12357 <section name="blacklist">
12358 <param name="protein_accessions" value=""/>
12359 <param name="ignore_modifications" value="false"/>
12360 <param name="modifications" value=""/>
12361 </section>
12362 <section name="in_silico_digestion">
12363 <param name="enzyme" value="Trypsin"/>
12364 <param name="specificity" value="full"/>
12365 <param name="missed_cleavages" value="-1"/>
12366 <param name="methionine_cleavage" value="false"/>
12367 </section>
12368 <section name="missed_cleavages">
12369 <param name="number_of_missed_cleavages" value=":"/>
12370 <param name="enzyme" value="Trypsin"/>
12371 </section>
12372 <section name="rt">
12373 <param name="p_value" value="0.0"/>
12374 <param name="p_value_1st_dim" value="0.0"/>
12375 </section>
12376 <section name="mz">
12377 <param name="error" value="-1.0"/>
12378 <param name="unit" value="ppm"/>
12379 </section>
12380 <section name="best">
12381 <param name="n_peptide_hits" value="0"/>
12382 <param name="n_protein_hits" value="0"/>
12383 <param name="strict" value="false"/>
12384 <param name="n_to_m_peptide_hits" value=":"/>
12385 </section>
12386 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12387 <output name="ctd_out" ftype="xml">
12388 <assert_contents>
12389 <is_valid_xml/>
12390 </assert_contents>
12391 </output>
12392 </test>
12393 <test expect_num_outputs="2">
12394 <conditional name="adv_opts_cond">
12395 <param name="adv_opts_selector" value="advanced"/>
12396 <param name="remove_duplicate_psm" value="false"/>
12397 <param name="remove_peptide_hits_by_metavalue" value=""/>
12398 <param name="force" value="false"/>
12399 <param name="test" value="true"/>
12400 </conditional>
12401 <param name="in" value="IDFilter_9_input.idXML"/>
12402 <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12403 <param name="var_mods" value="false"/>
12404 <param name="remove_shared_peptides" value="false"/>
12405 <param name="keep_unreferenced_protein_hits" value="false"/>
12406 <param name="remove_decoys" value="false"/>
12407 <param name="delete_unreferenced_peptide_hits" value="false"/>
12408 <section name="precursor">
12409 <param name="rt" value=":"/>
12410 <param name="mz" value=":"/>
12411 <param name="length" value=":"/>
12412 <param name="charge" value=":"/>
12413 </section>
12414 <section name="score">
12415 <param name="pep" value="0.05"/>
12416 <param name="prot" value="0.0"/>
12417 </section>
12418 <section name="whitelist">
12419 <param name="protein_accessions" value=""/>
12420 <param name="ignore_modifications" value="false"/>
12421 <param name="modifications" value=""/>
12422 </section>
12423 <section name="blacklist">
12424 <param name="protein_accessions" value=""/>
12425 <param name="ignore_modifications" value="false"/>
12426 <param name="modifications" value=""/>
12427 </section>
12428 <section name="in_silico_digestion">
12429 <param name="enzyme" value="Trypsin"/>
12430 <param name="specificity" value="full"/>
12431 <param name="missed_cleavages" value="-1"/>
12432 <param name="methionine_cleavage" value="false"/>
12433 </section>
12434 <section name="missed_cleavages">
12435 <param name="number_of_missed_cleavages" value=":"/>
12436 <param name="enzyme" value="Trypsin"/>
12437 </section>
12438 <section name="rt">
12439 <param name="p_value" value="0.0"/>
12440 <param name="p_value_1st_dim" value="0.0"/>
12441 </section>
12442 <section name="mz">
12443 <param name="error" value="-1.0"/>
12444 <param name="unit" value="ppm"/>
12445 </section>
12446 <section name="best">
12447 <param name="n_peptide_hits" value="0"/>
12448 <param name="n_protein_hits" value="0"/>
12449 <param name="strict" value="false"/>
12450 <param name="n_to_m_peptide_hits" value=":"/>
12451 </section>
12452 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12453 <output name="ctd_out" ftype="xml">
12454 <assert_contents>
12455 <is_valid_xml/>
12456 </assert_contents>
12457 </output>
12458 </test>
12459 <test expect_num_outputs="2">
12460 <conditional name="adv_opts_cond">
12461 <param name="adv_opts_selector" value="advanced"/>
12462 <param name="remove_duplicate_psm" value="false"/>
12463 <param name="remove_peptide_hits_by_metavalue" value=""/>
12464 <param name="force" value="false"/>
12465 <param name="test" value="true"/>
12466 </conditional>
12467 <param name="in" value="IDFilter_10_input.idXML"/>
12468 <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12469 <param name="var_mods" value="false"/>
12470 <param name="remove_shared_peptides" value="false"/>
12471 <param name="keep_unreferenced_protein_hits" value="false"/>
12472 <param name="remove_decoys" value="false"/>
12473 <param name="delete_unreferenced_peptide_hits" value="true"/>
12474 <section name="precursor">
12475 <param name="rt" value=":"/>
12476 <param name="mz" value=":"/>
12477 <param name="length" value=":"/>
12478 <param name="charge" value=":"/>
12479 </section>
12480 <section name="score">
12481 <param name="pep" value="0.0"/>
12482 <param name="prot" value="0.3"/>
12483 </section>
12484 <section name="whitelist">
12485 <param name="protein_accessions" value=""/>
12486 <param name="ignore_modifications" value="false"/>
12487 <param name="modifications" value=""/>
12488 </section>
12489 <section name="blacklist">
12490 <param name="protein_accessions" value=""/>
12491 <param name="ignore_modifications" value="false"/>
12492 <param name="modifications" value=""/>
12493 </section>
12494 <section name="in_silico_digestion">
12495 <param name="enzyme" value="Trypsin"/>
12496 <param name="specificity" value="full"/>
12497 <param name="missed_cleavages" value="-1"/>
12498 <param name="methionine_cleavage" value="false"/>
12499 </section>
12500 <section name="missed_cleavages">
12501 <param name="number_of_missed_cleavages" value=":"/>
12502 <param name="enzyme" value="Trypsin"/>
12503 </section>
12504 <section name="rt">
12505 <param name="p_value" value="0.0"/>
12506 <param name="p_value_1st_dim" value="0.0"/>
12507 </section>
12508 <section name="mz">
12509 <param name="error" value="-1.0"/>
12510 <param name="unit" value="ppm"/>
12511 </section>
12512 <section name="best">
12513 <param name="n_peptide_hits" value="0"/>
12514 <param name="n_protein_hits" value="0"/>
12515 <param name="strict" value="false"/>
12516 <param name="n_to_m_peptide_hits" value=":"/>
12517 </section>
12518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12519 <output name="ctd_out" ftype="xml">
12520 <assert_contents>
12521 <is_valid_xml/>
12522 </assert_contents>
12523 </output>
12524 </test>
12525 <test expect_num_outputs="2">
12526 <conditional name="adv_opts_cond">
12527 <param name="adv_opts_selector" value="advanced"/>
12528 <param name="remove_duplicate_psm" value="false"/>
12529 <param name="remove_peptide_hits_by_metavalue" value=""/>
12530 <param name="force" value="false"/>
12531 <param name="test" value="true"/>
12532 </conditional>
12533 <param name="in" value="IDFilter_11_input.idXML"/>
12534 <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12535 <param name="var_mods" value="false"/>
12536 <param name="remove_shared_peptides" value="false"/>
12537 <param name="keep_unreferenced_protein_hits" value="false"/>
12538 <param name="remove_decoys" value="true"/>
12539 <param name="delete_unreferenced_peptide_hits" value="true"/>
12540 <section name="precursor">
12541 <param name="rt" value=":"/>
12542 <param name="mz" value=":"/>
12543 <param name="length" value=":"/>
12544 <param name="charge" value=":"/>
12545 </section>
12546 <section name="score">
12547 <param name="pep" value="0.0"/>
12548 <param name="prot" value="0.0"/>
12549 </section>
12550 <section name="whitelist">
12551 <param name="protein_accessions" value=""/>
12552 <param name="ignore_modifications" value="false"/>
12553 <param name="modifications" value=""/>
12554 </section>
12555 <section name="blacklist">
12556 <param name="protein_accessions" value=""/>
12557 <param name="ignore_modifications" value="false"/>
12558 <param name="modifications" value=""/>
12559 </section>
12560 <section name="in_silico_digestion">
12561 <param name="enzyme" value="Trypsin"/>
12562 <param name="specificity" value="full"/>
12563 <param name="missed_cleavages" value="-1"/>
12564 <param name="methionine_cleavage" value="false"/>
12565 </section>
12566 <section name="missed_cleavages">
12567 <param name="number_of_missed_cleavages" value=":"/>
12568 <param name="enzyme" value="Trypsin"/>
12569 </section>
12570 <section name="rt">
12571 <param name="p_value" value="0.0"/>
12572 <param name="p_value_1st_dim" value="0.0"/>
12573 </section>
12574 <section name="mz">
12575 <param name="error" value="-1.0"/>
12576 <param name="unit" value="ppm"/>
12577 </section>
12578 <section name="best">
12579 <param name="n_peptide_hits" value="0"/>
12580 <param name="n_protein_hits" value="0"/>
12581 <param name="strict" value="false"/>
12582 <param name="n_to_m_peptide_hits" value=":"/>
12583 </section>
12584 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12585 <output name="ctd_out" ftype="xml">
12586 <assert_contents>
12587 <is_valid_xml/>
12588 </assert_contents>
12589 </output>
12590 </test>
12591 <test expect_num_outputs="2">
12592 <conditional name="adv_opts_cond">
12593 <param name="adv_opts_selector" value="advanced"/>
12594 <param name="remove_duplicate_psm" value="false"/>
12595 <param name="remove_peptide_hits_by_metavalue" value=""/>
12596 <param name="force" value="false"/>
12597 <param name="test" value="true"/>
12598 </conditional>
12599 <param name="in" value="IDFilter_12_input.idXML"/>
12600 <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12601 <param name="var_mods" value="false"/>
12602 <param name="remove_shared_peptides" value="false"/>
12603 <param name="keep_unreferenced_protein_hits" value="false"/>
12604 <param name="remove_decoys" value="false"/>
12605 <param name="delete_unreferenced_peptide_hits" value="false"/>
12606 <section name="precursor">
12607 <param name="rt" value=":"/>
12608 <param name="mz" value=":"/>
12609 <param name="length" value=":"/>
12610 <param name="charge" value=":"/>
12611 </section>
12612 <section name="score">
12613 <param name="pep" value="0.0"/>
12614 <param name="prot" value="0.0"/>
12615 </section>
12616 <section name="whitelist">
12617 <param name="protein_accessions" value=""/>
12618 <param name="ignore_modifications" value="false"/>
12619 <param name="modifications" value=""/>
12620 </section>
12621 <section name="blacklist">
12622 <param name="protein_accessions" value=""/>
12623 <param name="ignore_modifications" value="false"/>
12624 <param name="modifications" value=""/>
12625 </section>
12626 <section name="in_silico_digestion">
12627 <param name="fasta" value="IDFilter_12_input.fasta"/>
12628 <param name="enzyme" value="Trypsin"/>
12629 <param name="specificity" value="full"/>
12630 <param name="missed_cleavages" value="-1"/>
12631 <param name="methionine_cleavage" value="false"/>
12632 </section>
12633 <section name="missed_cleavages">
12634 <param name="number_of_missed_cleavages" value=":"/>
12635 <param name="enzyme" value="Trypsin"/>
12636 </section>
12637 <section name="rt">
12638 <param name="p_value" value="0.0"/>
12639 <param name="p_value_1st_dim" value="0.0"/>
12640 </section>
12641 <section name="mz">
12642 <param name="error" value="-1.0"/>
12643 <param name="unit" value="ppm"/>
12644 </section>
12645 <section name="best">
12646 <param name="n_peptide_hits" value="0"/>
12647 <param name="n_protein_hits" value="0"/>
12648 <param name="strict" value="false"/>
12649 <param name="n_to_m_peptide_hits" value=":"/>
12650 </section>
12651 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12652 <output name="ctd_out" ftype="xml">
12653 <assert_contents>
12654 <is_valid_xml/>
12655 </assert_contents>
12656 </output>
12657 </test>
12658 <test expect_num_outputs="2">
12659 <conditional name="adv_opts_cond">
12660 <param name="adv_opts_selector" value="advanced"/>
12661 <param name="remove_duplicate_psm" value="false"/>
12662 <param name="remove_peptide_hits_by_metavalue" value=""/>
12663 <param name="force" value="false"/>
12664 <param name="test" value="true"/>
12665 </conditional>
12666 <param name="in" value="IDFilter_13_input.idXML"/>
12667 <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12668 <param name="var_mods" value="false"/>
12669 <param name="remove_shared_peptides" value="false"/>
12670 <param name="keep_unreferenced_protein_hits" value="false"/>
12671 <param name="remove_decoys" value="false"/>
12672 <param name="delete_unreferenced_peptide_hits" value="false"/>
12673 <section name="precursor">
12674 <param name="rt" value=":"/>
12675 <param name="mz" value=":"/>
12676 <param name="length" value=":"/>
12677 <param name="charge" value=":"/>
12678 </section>
12679 <section name="score">
12680 <param name="pep" value="0.0"/>
12681 <param name="prot" value="0.0"/>
12682 </section>
12683 <section name="whitelist">
12684 <param name="protein_accessions" value=""/>
12685 <param name="ignore_modifications" value="false"/>
12686 <param name="modifications" value=""/>
12687 </section>
12688 <section name="blacklist">
12689 <param name="protein_accessions" value=""/>
12690 <param name="ignore_modifications" value="false"/>
12691 <param name="modifications" value=""/>
12692 </section>
12693 <section name="in_silico_digestion">
12694 <param name="fasta" value="IDFilter_13_input.fasta"/>
12695 <param name="enzyme" value="Trypsin"/>
12696 <param name="specificity" value="full"/>
12697 <param name="missed_cleavages" value="1"/>
12698 <param name="methionine_cleavage" value="false"/>
12699 </section>
12700 <section name="missed_cleavages">
12701 <param name="number_of_missed_cleavages" value=":"/>
12702 <param name="enzyme" value="Trypsin"/>
12703 </section>
12704 <section name="rt">
12705 <param name="p_value" value="0.0"/>
12706 <param name="p_value_1st_dim" value="0.0"/>
12707 </section>
12708 <section name="mz">
12709 <param name="error" value="-1.0"/>
12710 <param name="unit" value="ppm"/>
12711 </section>
12712 <section name="best">
12713 <param name="n_peptide_hits" value="0"/>
12714 <param name="n_protein_hits" value="0"/>
12715 <param name="strict" value="false"/>
12716 <param name="n_to_m_peptide_hits" value=":"/>
12717 </section>
12718 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12719 <output name="ctd_out" ftype="xml">
12720 <assert_contents>
12721 <is_valid_xml/>
12722 </assert_contents>
12723 </output>
12724 </test>
12725 <test expect_num_outputs="2">
12726 <conditional name="adv_opts_cond">
12727 <param name="adv_opts_selector" value="advanced"/>
12728 <param name="remove_duplicate_psm" value="false"/>
12729 <param name="remove_peptide_hits_by_metavalue" value=""/>
12730 <param name="force" value="false"/>
12731 <param name="test" value="true"/>
12732 </conditional>
12733 <param name="in" value="IDFilter_14_input.idXML"/>
12734 <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12735 <param name="var_mods" value="false"/>
12736 <param name="remove_shared_peptides" value="false"/>
12737 <param name="keep_unreferenced_protein_hits" value="false"/>
12738 <param name="remove_decoys" value="false"/>
12739 <param name="delete_unreferenced_peptide_hits" value="false"/>
12740 <section name="precursor">
12741 <param name="rt" value=":"/>
12742 <param name="mz" value=":"/>
12743 <param name="length" value=":"/>
12744 <param name="charge" value=":"/>
12745 </section>
12746 <section name="score">
12747 <param name="pep" value="0.0"/>
12748 <param name="prot" value="0.0"/>
12749 </section>
12750 <section name="whitelist">
12751 <param name="protein_accessions" value=""/>
12752 <param name="ignore_modifications" value="false"/>
12753 <param name="modifications" value=""/>
12754 </section>
12755 <section name="blacklist">
12756 <param name="protein_accessions" value=""/>
12757 <param name="ignore_modifications" value="false"/>
12758 <param name="modifications" value=""/>
12759 </section>
12760 <section name="in_silico_digestion">
12761 <param name="fasta" value="IDFilter_14_input.fasta"/>
12762 <param name="enzyme" value="Trypsin/P"/>
12763 <param name="specificity" value="full"/>
12764 <param name="missed_cleavages" value="1"/>
12765 <param name="methionine_cleavage" value="false"/>
12766 </section>
12767 <section name="missed_cleavages">
12768 <param name="number_of_missed_cleavages" value=":"/>
12769 <param name="enzyme" value="Trypsin"/>
12770 </section>
12771 <section name="rt">
12772 <param name="p_value" value="0.0"/>
12773 <param name="p_value_1st_dim" value="0.0"/>
12774 </section>
12775 <section name="mz">
12776 <param name="error" value="-1.0"/>
12777 <param name="unit" value="ppm"/>
12778 </section>
12779 <section name="best">
12780 <param name="n_peptide_hits" value="0"/>
12781 <param name="n_protein_hits" value="0"/>
12782 <param name="strict" value="false"/>
12783 <param name="n_to_m_peptide_hits" value=":"/>
12784 </section>
12785 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12786 <output name="ctd_out" ftype="xml">
12787 <assert_contents>
12788 <is_valid_xml/>
12789 </assert_contents>
12790 </output>
12791 </test>
12792 <test expect_num_outputs="2">
12793 <conditional name="adv_opts_cond">
12794 <param name="adv_opts_selector" value="advanced"/>
12795 <param name="remove_duplicate_psm" value="false"/>
12796 <param name="remove_peptide_hits_by_metavalue" value=""/>
12797 <param name="force" value="false"/>
12798 <param name="test" value="true"/>
12799 </conditional>
12800 <param name="in" value="IDFilter_15_input.idXML"/>
12801 <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12802 <param name="var_mods" value="false"/>
12803 <param name="remove_shared_peptides" value="false"/>
12804 <param name="keep_unreferenced_protein_hits" value="false"/>
12805 <param name="remove_decoys" value="false"/>
12806 <param name="delete_unreferenced_peptide_hits" value="false"/>
12807 <section name="precursor">
12808 <param name="rt" value=":"/>
12809 <param name="mz" value=":"/>
12810 <param name="length" value=":"/>
12811 <param name="charge" value=":"/>
12812 </section>
12813 <section name="score">
12814 <param name="pep" value="0.0"/>
12815 <param name="prot" value="0.0"/>
12816 </section>
12817 <section name="whitelist">
12818 <param name="protein_accessions" value=""/>
12819 <param name="ignore_modifications" value="false"/>
12820 <param name="modifications" value=""/>
12821 </section>
12822 <section name="blacklist">
12823 <param name="protein_accessions" value=""/>
12824 <param name="ignore_modifications" value="false"/>
12825 <param name="modifications" value=""/>
12826 </section>
12827 <section name="in_silico_digestion">
12828 <param name="fasta" value="IDFilter_15_input.fasta"/>
12829 <param name="enzyme" value="Trypsin/P"/>
12830 <param name="specificity" value="semi"/>
12831 <param name="missed_cleavages" value="1"/>
12832 <param name="methionine_cleavage" value="false"/>
12833 </section>
12834 <section name="missed_cleavages">
12835 <param name="number_of_missed_cleavages" value=":"/>
12836 <param name="enzyme" value="Trypsin"/>
12837 </section>
12838 <section name="rt">
12839 <param name="p_value" value="0.0"/>
12840 <param name="p_value_1st_dim" value="0.0"/>
12841 </section>
12842 <section name="mz">
12843 <param name="error" value="-1.0"/>
12844 <param name="unit" value="ppm"/>
12845 </section>
12846 <section name="best">
12847 <param name="n_peptide_hits" value="0"/>
12848 <param name="n_protein_hits" value="0"/>
12849 <param name="strict" value="false"/>
12850 <param name="n_to_m_peptide_hits" value=":"/>
12851 </section>
12852 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12853 <output name="ctd_out" ftype="xml">
12854 <assert_contents>
12855 <is_valid_xml/>
12856 </assert_contents>
12857 </output>
12858 </test>
12859 <test expect_num_outputs="2">
12860 <conditional name="adv_opts_cond">
12861 <param name="adv_opts_selector" value="advanced"/>
12862 <param name="remove_duplicate_psm" value="false"/>
12863 <param name="remove_peptide_hits_by_metavalue" value=""/>
12864 <param name="force" value="false"/>
12865 <param name="test" value="true"/>
12866 </conditional>
12867 <param name="in" value="IDFilter_16_input.idXML"/>
12868 <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12869 <param name="var_mods" value="false"/>
12870 <param name="remove_shared_peptides" value="false"/>
12871 <param name="keep_unreferenced_protein_hits" value="false"/>
12872 <param name="remove_decoys" value="false"/>
12873 <param name="delete_unreferenced_peptide_hits" value="false"/>
12874 <section name="precursor">
12875 <param name="rt" value=":"/>
12876 <param name="mz" value=":"/>
12877 <param name="length" value=":"/>
12878 <param name="charge" value=":"/>
12879 </section>
12880 <section name="score">
12881 <param name="pep" value="0.0"/>
12882 <param name="prot" value="0.0"/>
12883 </section>
12884 <section name="whitelist">
12885 <param name="protein_accessions" value=""/>
12886 <param name="ignore_modifications" value="false"/>
12887 <param name="modifications" value=""/>
12888 </section>
12889 <section name="blacklist">
12890 <param name="protein_accessions" value=""/>
12891 <param name="ignore_modifications" value="false"/>
12892 <param name="modifications" value=""/>
12893 </section>
12894 <section name="in_silico_digestion">
12895 <param name="fasta" value="IDFilter_16_input.fasta"/>
12896 <param name="enzyme" value="Trypsin/P"/>
12897 <param name="specificity" value="full"/>
12898 <param name="missed_cleavages" value="1"/>
12899 <param name="methionine_cleavage" value="true"/>
12900 </section>
12901 <section name="missed_cleavages">
12902 <param name="number_of_missed_cleavages" value=":"/>
12903 <param name="enzyme" value="Trypsin"/>
12904 </section>
12905 <section name="rt">
12906 <param name="p_value" value="0.0"/>
12907 <param name="p_value_1st_dim" value="0.0"/>
12908 </section>
12909 <section name="mz">
12910 <param name="error" value="-1.0"/>
12911 <param name="unit" value="ppm"/>
12912 </section>
12913 <section name="best">
12914 <param name="n_peptide_hits" value="0"/>
12915 <param name="n_protein_hits" value="0"/>
12916 <param name="strict" value="false"/>
12917 <param name="n_to_m_peptide_hits" value=":"/>
12918 </section>
12919 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12920 <output name="ctd_out" ftype="xml">
12921 <assert_contents>
12922 <is_valid_xml/>
12923 </assert_contents>
12924 </output>
12925 </test>
12926 <test expect_num_outputs="2">
12927 <conditional name="adv_opts_cond">
12928 <param name="adv_opts_selector" value="advanced"/>
12929 <param name="remove_duplicate_psm" value="false"/>
12930 <param name="remove_peptide_hits_by_metavalue" value=""/>
12931 <param name="force" value="false"/>
12932 <param name="test" value="true"/>
12933 </conditional>
12934 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
12935 <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
12936 <param name="var_mods" value="false"/>
12937 <param name="remove_shared_peptides" value="false"/>
12938 <param name="keep_unreferenced_protein_hits" value="false"/>
12939 <param name="remove_decoys" value="false"/>
12940 <param name="delete_unreferenced_peptide_hits" value="false"/>
12941 <section name="precursor">
12942 <param name="rt" value=":"/>
12943 <param name="mz" value=":"/>
12944 <param name="length" value=":"/>
12945 <param name="charge" value=":"/>
12946 </section>
12947 <section name="score">
12948 <param name="pep" value="0.0"/>
12949 <param name="prot" value="0.0"/>
12950 </section>
12951 <section name="whitelist">
12952 <param name="protein_accessions" value=""/>
12953 <param name="ignore_modifications" value="false"/>
12954 <param name="modifications" value=""/>
12955 </section>
12956 <section name="blacklist">
12957 <param name="protein_accessions" value=""/>
12958 <param name="ignore_modifications" value="false"/>
12959 <param name="modifications" value=""/>
12960 </section>
12961 <section name="in_silico_digestion">
12962 <param name="enzyme" value="Trypsin"/>
12963 <param name="specificity" value="full"/>
12964 <param name="missed_cleavages" value="-1"/>
12965 <param name="methionine_cleavage" value="false"/>
12966 </section>
12967 <section name="missed_cleavages">
12968 <param name="number_of_missed_cleavages" value=":2"/>
12969 <param name="enzyme" value="Lys-N"/>
12970 </section>
12971 <section name="rt">
12972 <param name="p_value" value="0.0"/>
12973 <param name="p_value_1st_dim" value="0.0"/>
12974 </section>
12975 <section name="mz">
12976 <param name="error" value="-1.0"/>
12977 <param name="unit" value="ppm"/>
12978 </section>
12979 <section name="best">
12980 <param name="n_peptide_hits" value="0"/>
12981 <param name="n_protein_hits" value="0"/>
12982 <param name="strict" value="false"/>
12983 <param name="n_to_m_peptide_hits" value=":"/>
12984 </section>
12985 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
12986 <output name="ctd_out" ftype="xml">
12987 <assert_contents>
12988 <is_valid_xml/>
12989 </assert_contents>
12990 </output>
12991 </test>
12992 <test expect_num_outputs="2">
12993 <conditional name="adv_opts_cond">
12994 <param name="adv_opts_selector" value="advanced"/>
12995 <param name="remove_duplicate_psm" value="false"/>
12996 <param name="remove_peptide_hits_by_metavalue" value=""/>
12997 <param name="force" value="false"/>
12998 <param name="test" value="true"/>
12999 </conditional>
13000 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13001 <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13002 <param name="var_mods" value="false"/>
13003 <param name="remove_shared_peptides" value="false"/>
13004 <param name="keep_unreferenced_protein_hits" value="false"/>
13005 <param name="remove_decoys" value="false"/>
13006 <param name="delete_unreferenced_peptide_hits" value="false"/>
13007 <section name="precursor">
13008 <param name="rt" value=":"/>
13009 <param name="mz" value=":"/>
13010 <param name="length" value=":"/>
13011 <param name="charge" value=":"/>
13012 </section>
13013 <section name="score">
13014 <param name="pep" value="0.0"/>
13015 <param name="prot" value="0.0"/>
13016 </section>
13017 <section name="whitelist">
13018 <param name="protein_accessions" value=""/>
13019 <param name="ignore_modifications" value="false"/>
13020 <param name="modifications" value=""/>
13021 </section>
13022 <section name="blacklist">
13023 <param name="protein_accessions" value=""/>
13024 <param name="ignore_modifications" value="false"/>
13025 <param name="modifications" value=""/>
13026 </section>
13027 <section name="in_silico_digestion">
13028 <param name="enzyme" value="Trypsin"/>
13029 <param name="specificity" value="full"/>
13030 <param name="missed_cleavages" value="-1"/>
13031 <param name="methionine_cleavage" value="false"/>
13032 </section>
13033 <section name="missed_cleavages">
13034 <param name="number_of_missed_cleavages" value="2:"/>
13035 <param name="enzyme" value="Lys-N"/>
13036 </section>
13037 <section name="rt">
13038 <param name="p_value" value="0.0"/>
13039 <param name="p_value_1st_dim" value="0.0"/>
13040 </section>
13041 <section name="mz">
13042 <param name="error" value="-1.0"/>
13043 <param name="unit" value="ppm"/>
13044 </section>
13045 <section name="best">
13046 <param name="n_peptide_hits" value="0"/>
13047 <param name="n_protein_hits" value="0"/>
13048 <param name="strict" value="false"/>
13049 <param name="n_to_m_peptide_hits" value=":"/>
13050 </section>
13051 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13052 <output name="ctd_out" ftype="xml">
13053 <assert_contents>
13054 <is_valid_xml/>
13055 </assert_contents>
13056 </output>
13057 </test>
13058 <test expect_num_outputs="2">
13059 <conditional name="adv_opts_cond">
13060 <param name="adv_opts_selector" value="advanced"/>
13061 <param name="remove_duplicate_psm" value="false"/>
13062 <param name="remove_peptide_hits_by_metavalue" value=""/>
13063 <param name="force" value="false"/>
13064 <param name="test" value="true"/>
13065 </conditional>
13066 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13067 <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13068 <param name="var_mods" value="false"/>
13069 <param name="remove_shared_peptides" value="false"/>
13070 <param name="keep_unreferenced_protein_hits" value="false"/>
13071 <param name="remove_decoys" value="false"/>
13072 <param name="delete_unreferenced_peptide_hits" value="false"/>
13073 <section name="precursor">
13074 <param name="rt" value=":"/>
13075 <param name="mz" value=":"/>
13076 <param name="length" value=":"/>
13077 <param name="charge" value=":"/>
13078 </section>
13079 <section name="score">
13080 <param name="pep" value="0.0"/>
13081 <param name="prot" value="0.0"/>
13082 </section>
13083 <section name="whitelist">
13084 <param name="protein_accessions" value=""/>
13085 <param name="ignore_modifications" value="false"/>
13086 <param name="modifications" value=""/>
13087 </section>
13088 <section name="blacklist">
13089 <param name="protein_accessions" value=""/>
13090 <param name="ignore_modifications" value="false"/>
13091 <param name="modifications" value=""/>
13092 </section>
13093 <section name="in_silico_digestion">
13094 <param name="enzyme" value="Trypsin"/>
13095 <param name="specificity" value="full"/>
13096 <param name="missed_cleavages" value="-1"/>
13097 <param name="methionine_cleavage" value="false"/>
13098 </section>
13099 <section name="missed_cleavages">
13100 <param name="number_of_missed_cleavages" value="1:3"/>
13101 <param name="enzyme" value="Lys-N"/>
13102 </section>
13103 <section name="rt">
13104 <param name="p_value" value="0.0"/>
13105 <param name="p_value_1st_dim" value="0.0"/>
13106 </section>
13107 <section name="mz">
13108 <param name="error" value="-1.0"/>
13109 <param name="unit" value="ppm"/>
13110 </section>
13111 <section name="best">
13112 <param name="n_peptide_hits" value="0"/>
13113 <param name="n_protein_hits" value="0"/>
13114 <param name="strict" value="false"/>
13115 <param name="n_to_m_peptide_hits" value=":"/>
13116 </section>
13117 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13118 <output name="ctd_out" ftype="xml">
13119 <assert_contents>
13120 <is_valid_xml/>
13121 </assert_contents>
13122 </output>
13123 </test>
13124 <test expect_num_outputs="2">
13125 <conditional name="adv_opts_cond">
13126 <param name="adv_opts_selector" value="advanced"/>
13127 <param name="remove_duplicate_psm" value="false"/>
13128 <param name="remove_peptide_hits_by_metavalue" value=""/>
13129 <param name="force" value="false"/>
13130 <param name="test" value="true"/>
13131 </conditional>
13132 <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
13133 <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13134 <param name="var_mods" value="false"/>
13135 <param name="remove_shared_peptides" value="false"/>
13136 <param name="keep_unreferenced_protein_hits" value="false"/>
13137 <param name="remove_decoys" value="false"/>
13138 <param name="delete_unreferenced_peptide_hits" value="false"/>
13139 <section name="precursor">
13140 <param name="rt" value=":"/>
13141 <param name="mz" value=":"/>
13142 <param name="length" value=":"/>
13143 <param name="charge" value=":"/>
13144 </section>
13145 <section name="score">
13146 <param name="pep" value="0.0"/>
13147 <param name="prot" value="0.0"/>
13148 </section>
13149 <section name="whitelist">
13150 <param name="protein_accessions" value=""/>
13151 <param name="ignore_modifications" value="false"/>
13152 <param name="modifications" value=""/>
13153 </section>
13154 <section name="blacklist">
13155 <param name="protein_accessions" value=""/>
13156 <param name="ignore_modifications" value="false"/>
13157 <param name="modifications" value=""/>
13158 </section>
13159 <section name="in_silico_digestion">
13160 <param name="enzyme" value="Trypsin"/>
13161 <param name="specificity" value="full"/>
13162 <param name="missed_cleavages" value="-1"/>
13163 <param name="methionine_cleavage" value="false"/>
13164 </section>
13165 <section name="missed_cleavages">
13166 <param name="number_of_missed_cleavages" value="1:0"/>
13167 <param name="enzyme" value="Trypsin"/>
13168 </section>
13169 <section name="rt">
13170 <param name="p_value" value="0.0"/>
13171 <param name="p_value_1st_dim" value="0.0"/>
13172 </section>
13173 <section name="mz">
13174 <param name="error" value="-1.0"/>
13175 <param name="unit" value="ppm"/>
13176 </section>
13177 <section name="best">
13178 <param name="n_peptide_hits" value="0"/>
13179 <param name="n_protein_hits" value="0"/>
13180 <param name="strict" value="false"/>
13181 <param name="n_to_m_peptide_hits" value=":"/>
13182 </section>
13183 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13184 <output name="ctd_out" ftype="xml">
13185 <assert_contents>
13186 <is_valid_xml/>
13187 </assert_contents>
13188 </output>
13189 </test>
13190 <test expect_num_outputs="2">
13191 <conditional name="adv_opts_cond">
13192 <param name="adv_opts_selector" value="advanced"/>
13193 <param name="remove_duplicate_psm" value="false"/>
13194 <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/>
13195 <param name="force" value="false"/>
13196 <param name="test" value="true"/>
13197 </conditional>
13198 <param name="in" value="IDFilter_16_input.idXML"/>
13199 <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13200 <param name="var_mods" value="false"/>
13201 <param name="remove_shared_peptides" value="false"/>
13202 <param name="keep_unreferenced_protein_hits" value="false"/>
13203 <param name="remove_decoys" value="false"/>
13204 <param name="delete_unreferenced_peptide_hits" value="false"/>
13205 <section name="precursor">
13206 <param name="rt" value=":"/>
13207 <param name="mz" value=":"/>
13208 <param name="length" value=":"/>
13209 <param name="charge" value=":"/>
13210 </section>
13211 <section name="score">
13212 <param name="pep" value="0.0"/>
13213 <param name="prot" value="0.0"/>
13214 </section>
13215 <section name="whitelist">
13216 <param name="protein_accessions" value=""/>
13217 <param name="ignore_modifications" value="false"/>
13218 <param name="modifications" value=""/>
13219 </section>
13220 <section name="blacklist">
13221 <param name="protein_accessions" value=""/>
13222 <param name="ignore_modifications" value="false"/>
13223 <param name="modifications" value=""/>
13224 </section>
13225 <section name="in_silico_digestion">
13226 <param name="enzyme" value="Trypsin"/>
13227 <param name="specificity" value="full"/>
13228 <param name="missed_cleavages" value="-1"/>
13229 <param name="methionine_cleavage" value="false"/>
13230 </section>
13231 <section name="missed_cleavages">
13232 <param name="number_of_missed_cleavages" value=":"/>
13233 <param name="enzyme" value="Trypsin"/>
13234 </section>
13235 <section name="rt">
13236 <param name="p_value" value="0.0"/>
13237 <param name="p_value_1st_dim" value="0.0"/>
13238 </section>
13239 <section name="mz">
13240 <param name="error" value="-1.0"/>
13241 <param name="unit" value="ppm"/>
13242 </section>
13243 <section name="best">
13244 <param name="n_peptide_hits" value="0"/>
13245 <param name="n_protein_hits" value="0"/>
13246 <param name="strict" value="false"/>
13247 <param name="n_to_m_peptide_hits" value=":"/>
13248 </section>
13249 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13250 <output name="ctd_out" ftype="xml">
13251 <assert_contents>
13252 <is_valid_xml/>
13253 </assert_contents>
13254 </output>
13255 </test>
13256 <test expect_num_outputs="2">
13257 <conditional name="adv_opts_cond">
13258 <param name="adv_opts_selector" value="advanced"/>
13259 <param name="remove_duplicate_psm" value="false"/>
13260 <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/>
13261 <param name="force" value="false"/>
13262 <param name="test" value="true"/>
13263 </conditional>
13264 <param name="in" value="IDFilter_16_input.idXML"/>
13265 <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13266 <param name="var_mods" value="false"/>
13267 <param name="remove_shared_peptides" value="false"/>
13268 <param name="keep_unreferenced_protein_hits" value="false"/>
13269 <param name="remove_decoys" value="false"/>
13270 <param name="delete_unreferenced_peptide_hits" value="false"/>
13271 <section name="precursor">
13272 <param name="rt" value=":"/>
13273 <param name="mz" value=":"/>
13274 <param name="length" value=":"/>
13275 <param name="charge" value=":"/>
13276 </section>
13277 <section name="score">
13278 <param name="pep" value="0.0"/>
13279 <param name="prot" value="0.0"/>
13280 </section>
13281 <section name="whitelist">
13282 <param name="protein_accessions" value=""/>
13283 <param name="ignore_modifications" value="false"/>
13284 <param name="modifications" value=""/>
13285 </section>
13286 <section name="blacklist">
13287 <param name="protein_accessions" value=""/>
13288 <param name="ignore_modifications" value="false"/>
13289 <param name="modifications" value=""/>
13290 </section>
13291 <section name="in_silico_digestion">
13292 <param name="enzyme" value="Trypsin"/>
13293 <param name="specificity" value="full"/>
13294 <param name="missed_cleavages" value="-1"/>
13295 <param name="methionine_cleavage" value="false"/>
13296 </section>
13297 <section name="missed_cleavages">
13298 <param name="number_of_missed_cleavages" value=":"/>
13299 <param name="enzyme" value="Trypsin"/>
13300 </section>
13301 <section name="rt">
13302 <param name="p_value" value="0.0"/>
13303 <param name="p_value_1st_dim" value="0.0"/>
13304 </section>
13305 <section name="mz">
13306 <param name="error" value="-1.0"/>
13307 <param name="unit" value="ppm"/>
13308 </section>
13309 <section name="best">
13310 <param name="n_peptide_hits" value="0"/>
13311 <param name="n_protein_hits" value="0"/>
13312 <param name="strict" value="false"/>
13313 <param name="n_to_m_peptide_hits" value=":"/>
13314 </section>
13315 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13316 <output name="ctd_out" ftype="xml">
13317 <assert_contents>
13318 <is_valid_xml/>
13319 </assert_contents>
13320 </output>
13321 </test>
13322 </xml>
13323 <xml name="autotest_IDMapper">
13324 <test expect_num_outputs="2">
13325 <conditional name="adv_opts_cond">
13326 <param name="adv_opts_selector" value="advanced"/>
13327 <param name="ignore_charge" value="true"/>
13328 <param name="force" value="false"/>
13329 <param name="test" value="true"/>
13330 </conditional>
13331 <param name="id" value="IDMapper_1_input.idXML"/>
13332 <param name="in" value="IDMapper_1_input.featureXML"/>
13333 <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13334 <param name="rt_tolerance" value="5.0"/>
13335 <param name="mz_tolerance" value="1.0"/>
13336 <param name="mz_measure" value="Da"/>
13337 <param name="mz_reference" value="precursor"/>
13338 <section name="feature">
13339 <param name="use_centroid_rt" value="false"/>
13340 <param name="use_centroid_mz" value="false"/>
13341 </section>
13342 <section name="consensus">
13343 <param name="use_subelements" value="false"/>
13344 <param name="annotate_ids_with_subelements" value="false"/>
13345 </section>
13346 <section name="spectra"/>
13347 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13348 <output name="ctd_out" ftype="xml">
13349 <assert_contents>
13350 <is_valid_xml/>
13351 </assert_contents>
13352 </output>
13353 </test>
13354 <test expect_num_outputs="2">
13355 <conditional name="adv_opts_cond">
13356 <param name="adv_opts_selector" value="advanced"/>
13357 <param name="ignore_charge" value="false"/>
13358 <param name="force" value="false"/>
13359 <param name="test" value="true"/>
13360 </conditional>
13361 <param name="id" value="IDMapper_2_input.idXML"/>
13362 <param name="in" value="IDMapper_2_input.consensusXML"/>
13363 <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
13364 <param name="rt_tolerance" value="5.0"/>
13365 <param name="mz_tolerance" value="1.0"/>
13366 <param name="mz_measure" value="Da"/>
13367 <param name="mz_reference" value="precursor"/>
13368 <section name="feature">
13369 <param name="use_centroid_rt" value="false"/>
13370 <param name="use_centroid_mz" value="true"/>
13371 </section>
13372 <section name="consensus">
13373 <param name="use_subelements" value="false"/>
13374 <param name="annotate_ids_with_subelements" value="false"/>
13375 </section>
13376 <section name="spectra"/>
13377 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13378 <output name="ctd_out" ftype="xml">
13379 <assert_contents>
13380 <is_valid_xml/>
13381 </assert_contents>
13382 </output>
13383 </test>
13384 <test expect_num_outputs="2">
13385 <conditional name="adv_opts_cond">
13386 <param name="adv_opts_selector" value="advanced"/>
13387 <param name="ignore_charge" value="true"/>
13388 <param name="force" value="false"/>
13389 <param name="test" value="true"/>
13390 </conditional>
13391 <param name="id" value="IDMapper_3_input.idXML"/>
13392 <param name="in" value="IDMapper_3_input.featureXML"/>
13393 <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13394 <param name="rt_tolerance" value="4.0"/>
13395 <param name="mz_tolerance" value="3.0"/>
13396 <param name="mz_measure" value="ppm"/>
13397 <param name="mz_reference" value="precursor"/>
13398 <section name="feature">
13399 <param name="use_centroid_rt" value="false"/>
13400 <param name="use_centroid_mz" value="true"/>
13401 </section>
13402 <section name="consensus">
13403 <param name="use_subelements" value="false"/>
13404 <param name="annotate_ids_with_subelements" value="false"/>
13405 </section>
13406 <section name="spectra"/>
13407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13408 <output name="ctd_out" ftype="xml">
13409 <assert_contents>
13410 <is_valid_xml/>
13411 </assert_contents>
13412 </output>
13413 </test>
13414 <test expect_num_outputs="2">
13415 <conditional name="adv_opts_cond">
13416 <param name="adv_opts_selector" value="advanced"/>
13417 <param name="ignore_charge" value="false"/>
13418 <param name="force" value="false"/>
13419 <param name="test" value="true"/>
13420 </conditional>
13421 <param name="id" value="IDMapper_4_input.idXML"/>
13422 <param name="in" value="IDMapper_4_input.featureXML"/>
13423 <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13424 <param name="rt_tolerance" value="10.0"/>
13425 <param name="mz_tolerance" value="20.0"/>
13426 <param name="mz_measure" value="ppm"/>
13427 <param name="mz_reference" value="peptide"/>
13428 <section name="feature">
13429 <param name="use_centroid_rt" value="false"/>
13430 <param name="use_centroid_mz" value="true"/>
13431 </section>
13432 <section name="consensus">
13433 <param name="use_subelements" value="false"/>
13434 <param name="annotate_ids_with_subelements" value="false"/>
13435 </section>
13436 <section name="spectra">
13437 <param name="_in" value="IDMapper_4_input.mzML"/>
13438 </section>
13439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13440 <output name="ctd_out" ftype="xml">
13441 <assert_contents>
13442 <is_valid_xml/>
13443 </assert_contents>
13444 </output>
13445 </test>
13446 <test expect_num_outputs="2">
13447 <conditional name="adv_opts_cond">
13448 <param name="adv_opts_selector" value="advanced"/>
13449 <param name="ignore_charge" value="false"/>
13450 <param name="force" value="false"/>
13451 <param name="test" value="true"/>
13452 </conditional>
13453 <param name="id" value="IDMapper_5_input.idXML"/>
13454 <param name="in" value="IDMapper_5_input.featureXML"/>
13455 <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13456 <param name="rt_tolerance" value="20.0"/>
13457 <param name="mz_tolerance" value="10.0"/>
13458 <param name="mz_measure" value="ppm"/>
13459 <param name="mz_reference" value="peptide"/>
13460 <section name="feature">
13461 <param name="use_centroid_rt" value="false"/>
13462 <param name="use_centroid_mz" value="false"/>
13463 </section>
13464 <section name="consensus">
13465 <param name="use_subelements" value="false"/>
13466 <param name="annotate_ids_with_subelements" value="false"/>
13467 </section>
13468 <section name="spectra">
13469 <param name="_in" value="IDMapper_5_input.mzML"/>
13470 </section>
13471 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13472 <output name="ctd_out" ftype="xml">
13473 <assert_contents>
13474 <is_valid_xml/>
13475 </assert_contents>
13476 </output>
13477 </test>
13478 </xml>
13479 <xml name="autotest_IDMassAccuracy">
13480 <test expect_num_outputs="5">
13481 <conditional name="adv_opts_cond">
13482 <param name="adv_opts_selector" value="advanced"/>
13483 <param name="number_of_bins" value="10"/>
13484 <param name="force" value="false"/>
13485 <param name="test" value="true"/>
13486 </conditional>
13487 <param name="in" value="spectra.mzML"/>
13488 <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
13489 <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
13490 <param name="precursor_error_ppm" value="false"/>
13491 <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
13492 <param name="fragment_error_ppm" value="false"/>
13493 <param name="fragment_mass_tolerance" value="0.5"/>
13494 <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
13495 <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
13496 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
13497 <output name="ctd_out" ftype="xml">
13498 <assert_contents>
13499 <is_valid_xml/>
13500 </assert_contents>
13501 </output>
13502 </test>
13503 </xml>
13504 <xml name="autotest_IDMerger">
13505 <test expect_num_outputs="2">
13506 <conditional name="adv_opts_cond">
13507 <param name="adv_opts_selector" value="advanced"/>
13508 <param name="force" value="false"/>
13509 <param name="test" value="true"/>
13510 </conditional>
13511 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
13512 <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13513 <param name="annotate_file_origin" value="true"/>
13514 <param name="pepxml_protxml" value="false"/>
13515 <param name="merge_proteins_add_PSMs" value="false"/>
13516 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13517 <output name="ctd_out" ftype="xml">
13518 <assert_contents>
13519 <is_valid_xml/>
13520 </assert_contents>
13521 </output>
13522 </test>
13523 <test expect_num_outputs="2">
13524 <conditional name="adv_opts_cond">
13525 <param name="adv_opts_selector" value="advanced"/>
13526 <param name="force" value="false"/>
13527 <param name="test" value="true"/>
13528 </conditional>
13529 <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
13530 <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13531 <param name="annotate_file_origin" value="false"/>
13532 <param name="pepxml_protxml" value="true"/>
13533 <param name="merge_proteins_add_PSMs" value="false"/>
13534 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13535 <output name="ctd_out" ftype="xml">
13536 <assert_contents>
13537 <is_valid_xml/>
13538 </assert_contents>
13539 </output>
13540 </test>
13541 <test expect_num_outputs="2">
13542 <conditional name="adv_opts_cond">
13543 <param name="adv_opts_selector" value="advanced"/>
13544 <param name="force" value="false"/>
13545 <param name="test" value="true"/>
13546 </conditional>
13547 <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
13548 <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13549 <param name="annotate_file_origin" value="false"/>
13550 <param name="pepxml_protxml" value="false"/>
13551 <param name="merge_proteins_add_PSMs" value="false"/>
13552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13553 <output name="ctd_out" ftype="xml">
13554 <assert_contents>
13555 <is_valid_xml/>
13556 </assert_contents>
13557 </output>
13558 </test>
13559 <test expect_num_outputs="2">
13560 <conditional name="adv_opts_cond">
13561 <param name="adv_opts_selector" value="advanced"/>
13562 <param name="force" value="false"/>
13563 <param name="test" value="true"/>
13564 </conditional>
13565 <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
13566 <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13567 <param name="annotate_file_origin" value="false"/>
13568 <param name="pepxml_protxml" value="false"/>
13569 <param name="merge_proteins_add_PSMs" value="false"/>
13570 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13571 <output name="ctd_out" ftype="xml">
13572 <assert_contents>
13573 <is_valid_xml/>
13574 </assert_contents>
13575 </output>
13576 </test>
13577 <test expect_num_outputs="2">
13578 <conditional name="adv_opts_cond">
13579 <param name="adv_opts_selector" value="advanced"/>
13580 <param name="force" value="false"/>
13581 <param name="test" value="true"/>
13582 </conditional>
13583 <param name="in" value="IDMerger_2_input1.idXML"/>
13584 <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13585 <param name="add_to" value="IDMerger_5_input1.idXML"/>
13586 <param name="annotate_file_origin" value="false"/>
13587 <param name="pepxml_protxml" value="false"/>
13588 <param name="merge_proteins_add_PSMs" value="false"/>
13589 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13590 <output name="ctd_out" ftype="xml">
13591 <assert_contents>
13592 <is_valid_xml/>
13593 </assert_contents>
13594 </output>
13595 </test>
13596 <test expect_num_outputs="2">
13597 <conditional name="adv_opts_cond">
13598 <param name="adv_opts_selector" value="advanced"/>
13599 <param name="force" value="false"/>
13600 <param name="test" value="true"/>
13601 </conditional>
13602 <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
13603 <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13604 <param name="annotate_file_origin" value="true"/>
13605 <param name="pepxml_protxml" value="false"/>
13606 <param name="merge_proteins_add_PSMs" value="false"/>
13607 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13608 <output name="ctd_out" ftype="xml">
13609 <assert_contents>
13610 <is_valid_xml/>
13611 </assert_contents>
13612 </output>
13613 </test>
13614 </xml>
13615 <xml name="autotest_IDPosteriorErrorProbability">
13616 <test expect_num_outputs="2">
13617 <conditional name="adv_opts_cond">
13618 <param name="adv_opts_selector" value="advanced"/>
13619 <param name="fdr_for_targets_smaller" value="0.05"/>
13620 <param name="force" value="false"/>
13621 <param name="test" value="true"/>
13622 </conditional>
13623 <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
13624 <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13625 <param name="split_charge" value="false"/>
13626 <param name="top_hits_only" value="false"/>
13627 <param name="ignore_bad_data" value="false"/>
13628 <param name="prob_correct" value="false"/>
13629 <section name="fit_algorithm">
13630 <param name="number_of_bins" value="100"/>
13631 <param name="incorrectly_assigned" value="Gumbel"/>
13632 <param name="max_nr_iterations" value="1000"/>
13633 <param name="neg_log_delta" value="6"/>
13634 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13635 </section>
13636 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13637 <output name="ctd_out" ftype="xml">
13638 <assert_contents>
13639 <is_valid_xml/>
13640 </assert_contents>
13641 </output>
13642 </test>
13643 <test expect_num_outputs="2">
13644 <conditional name="adv_opts_cond">
13645 <param name="adv_opts_selector" value="advanced"/>
13646 <param name="fdr_for_targets_smaller" value="0.05"/>
13647 <param name="force" value="false"/>
13648 <param name="test" value="true"/>
13649 </conditional>
13650 <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
13651 <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13652 <param name="split_charge" value="false"/>
13653 <param name="top_hits_only" value="false"/>
13654 <param name="ignore_bad_data" value="false"/>
13655 <param name="prob_correct" value="false"/>
13656 <section name="fit_algorithm">
13657 <param name="number_of_bins" value="100"/>
13658 <param name="incorrectly_assigned" value="Gumbel"/>
13659 <param name="max_nr_iterations" value="1000"/>
13660 <param name="neg_log_delta" value="6"/>
13661 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13662 </section>
13663 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13664 <output name="ctd_out" ftype="xml">
13665 <assert_contents>
13666 <is_valid_xml/>
13667 </assert_contents>
13668 </output>
13669 </test>
13670 <test expect_num_outputs="2">
13671 <conditional name="adv_opts_cond">
13672 <param name="adv_opts_selector" value="advanced"/>
13673 <param name="fdr_for_targets_smaller" value="0.05"/>
13674 <param name="force" value="false"/>
13675 <param name="test" value="true"/>
13676 </conditional>
13677 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
13678 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13679 <param name="split_charge" value="false"/>
13680 <param name="top_hits_only" value="false"/>
13681 <param name="ignore_bad_data" value="false"/>
13682 <param name="prob_correct" value="false"/>
13683 <section name="fit_algorithm">
13684 <param name="number_of_bins" value="100"/>
13685 <param name="incorrectly_assigned" value="Gumbel"/>
13686 <param name="max_nr_iterations" value="1000"/>
13687 <param name="neg_log_delta" value="6"/>
13688 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13689 </section>
13690 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13691 <output name="ctd_out" ftype="xml">
13692 <assert_contents>
13693 <is_valid_xml/>
13694 </assert_contents>
13695 </output>
13696 </test>
13697 <test expect_num_outputs="2">
13698 <conditional name="adv_opts_cond">
13699 <param name="adv_opts_selector" value="advanced"/>
13700 <param name="fdr_for_targets_smaller" value="0.05"/>
13701 <param name="force" value="false"/>
13702 <param name="test" value="true"/>
13703 </conditional>
13704 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
13705 <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13706 <param name="split_charge" value="true"/>
13707 <param name="top_hits_only" value="false"/>
13708 <param name="ignore_bad_data" value="false"/>
13709 <param name="prob_correct" value="false"/>
13710 <section name="fit_algorithm">
13711 <param name="number_of_bins" value="100"/>
13712 <param name="incorrectly_assigned" value="Gumbel"/>
13713 <param name="max_nr_iterations" value="1000"/>
13714 <param name="neg_log_delta" value="6"/>
13715 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13716 </section>
13717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13718 <output name="ctd_out" ftype="xml">
13719 <assert_contents>
13720 <is_valid_xml/>
13721 </assert_contents>
13722 </output>
13723 </test>
13724 <test expect_num_outputs="2">
13725 <conditional name="adv_opts_cond">
13726 <param name="adv_opts_selector" value="advanced"/>
13727 <param name="fdr_for_targets_smaller" value="0.05"/>
13728 <param name="force" value="false"/>
13729 <param name="test" value="true"/>
13730 </conditional>
13731 <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
13732 <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13733 <param name="split_charge" value="true"/>
13734 <param name="top_hits_only" value="false"/>
13735 <param name="ignore_bad_data" value="false"/>
13736 <param name="prob_correct" value="false"/>
13737 <section name="fit_algorithm">
13738 <param name="number_of_bins" value="100"/>
13739 <param name="incorrectly_assigned" value="Gumbel"/>
13740 <param name="max_nr_iterations" value="1000"/>
13741 <param name="neg_log_delta" value="6"/>
13742 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13743 </section>
13744 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13745 <output name="ctd_out" ftype="xml">
13746 <assert_contents>
13747 <is_valid_xml/>
13748 </assert_contents>
13749 </output>
13750 </test>
13751 <test expect_num_outputs="2">
13752 <conditional name="adv_opts_cond">
13753 <param name="adv_opts_selector" value="advanced"/>
13754 <param name="fdr_for_targets_smaller" value="0.05"/>
13755 <param name="force" value="false"/>
13756 <param name="test" value="true"/>
13757 </conditional>
13758 <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
13759 <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13760 <param name="split_charge" value="true"/>
13761 <param name="top_hits_only" value="false"/>
13762 <param name="ignore_bad_data" value="false"/>
13763 <param name="prob_correct" value="false"/>
13764 <section name="fit_algorithm">
13765 <param name="number_of_bins" value="100"/>
13766 <param name="incorrectly_assigned" value="Gumbel"/>
13767 <param name="max_nr_iterations" value="1000"/>
13768 <param name="neg_log_delta" value="6"/>
13769 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13770 </section>
13771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13772 <output name="ctd_out" ftype="xml">
13773 <assert_contents>
13774 <is_valid_xml/>
13775 </assert_contents>
13776 </output>
13777 </test>
13778 <test expect_num_outputs="2">
13779 <conditional name="adv_opts_cond">
13780 <param name="adv_opts_selector" value="advanced"/>
13781 <param name="fdr_for_targets_smaller" value="0.05"/>
13782 <param name="force" value="false"/>
13783 <param name="test" value="true"/>
13784 </conditional>
13785 <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
13786 <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13787 <param name="split_charge" value="false"/>
13788 <param name="top_hits_only" value="false"/>
13789 <param name="ignore_bad_data" value="true"/>
13790 <param name="prob_correct" value="false"/>
13791 <section name="fit_algorithm">
13792 <param name="number_of_bins" value="100"/>
13793 <param name="incorrectly_assigned" value="Gumbel"/>
13794 <param name="max_nr_iterations" value="1000"/>
13795 <param name="neg_log_delta" value="6"/>
13796 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13797 </section>
13798 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13799 <output name="ctd_out" ftype="xml">
13800 <assert_contents>
13801 <is_valid_xml/>
13802 </assert_contents>
13803 </output>
13804 </test>
13805 <test expect_num_outputs="2">
13806 <conditional name="adv_opts_cond">
13807 <param name="adv_opts_selector" value="advanced"/>
13808 <param name="fdr_for_targets_smaller" value="0.05"/>
13809 <param name="force" value="false"/>
13810 <param name="test" value="true"/>
13811 </conditional>
13812 <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
13813 <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13814 <param name="split_charge" value="false"/>
13815 <param name="top_hits_only" value="false"/>
13816 <param name="ignore_bad_data" value="false"/>
13817 <param name="prob_correct" value="true"/>
13818 <section name="fit_algorithm">
13819 <param name="number_of_bins" value="100"/>
13820 <param name="incorrectly_assigned" value="Gumbel"/>
13821 <param name="max_nr_iterations" value="1000"/>
13822 <param name="neg_log_delta" value="6"/>
13823 <param name="outlier_handling" value="ignore_iqr_outliers"/>
13824 </section>
13825 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13826 <output name="ctd_out" ftype="xml">
13827 <assert_contents>
13828 <is_valid_xml/>
13829 </assert_contents>
13830 </output>
13831 </test>
13832 </xml>
13833 <xml name="autotest_IDRipper"/>
13834 <xml name="autotest_IDRTCalibration">
13835 <test expect_num_outputs="2">
13836 <conditional name="adv_opts_cond">
13837 <param name="adv_opts_selector" value="advanced"/>
13838 <param name="force" value="false"/>
13839 <param name="test" value="true"/>
13840 </conditional>
13841 <param name="in" value="IDRTCalibration_1_input.idXML"/>
13842 <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13843 <param name="calibrant_1_reference" value="0.1"/>
13844 <param name="calibrant_2_reference" value="0.9"/>
13845 <param name="calibrant_1_input" value="10.0"/>
13846 <param name="calibrant_2_input" value="90.0"/>
13847 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13848 <output name="ctd_out" ftype="xml">
13849 <assert_contents>
13850 <is_valid_xml/>
13851 </assert_contents>
13852 </output>
13853 </test>
13854 <test expect_num_outputs="2">
13855 <conditional name="adv_opts_cond">
13856 <param name="adv_opts_selector" value="advanced"/>
13857 <param name="force" value="false"/>
13858 <param name="test" value="true"/>
13859 </conditional>
13860 <param name="in" value="degenerated_empty.idXML"/>
13861 <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13862 <param name="calibrant_1_reference" value="0.1"/>
13863 <param name="calibrant_2_reference" value="0.9"/>
13864 <param name="calibrant_1_input" value="10.0"/>
13865 <param name="calibrant_2_input" value="90.0"/>
13866 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13867 <output name="ctd_out" ftype="xml">
13868 <assert_contents>
13869 <is_valid_xml/>
13870 </assert_contents>
13871 </output>
13872 </test>
13873 </xml>
13874 <xml name="autotest_IDScoreSwitcher">
13875 <test expect_num_outputs="2">
13876 <conditional name="adv_opts_cond">
13877 <param name="adv_opts_selector" value="advanced"/>
13878 <param name="force" value="false"/>
13879 <param name="test" value="true"/>
13880 </conditional>
13881 <param name="in" value="IDFileConverter_12_output.idXML"/>
13882 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13883 <param name="new_score" value="Percolator_PEP"/>
13884 <param name="new_score_orientation" value="lower_better"/>
13885 <param name="new_score_type" value="Posterior Error Probability"/>
13886 <param name="old_score" value="Percolator_qvalue"/>
13887 <param name="proteins" value="false"/>
13888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13889 <output name="ctd_out" ftype="xml">
13890 <assert_contents>
13891 <is_valid_xml/>
13892 </assert_contents>
13893 </output>
13894 </test>
13895 <test expect_num_outputs="2">
13896 <conditional name="adv_opts_cond">
13897 <param name="adv_opts_selector" value="advanced"/>
13898 <param name="force" value="false"/>
13899 <param name="test" value="true"/>
13900 </conditional>
13901 <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
13902 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13903 <param name="new_score" value="Posterior Probability_score"/>
13904 <param name="new_score_orientation" value="higher_better"/>
13905 <param name="new_score_type" value="Posterior Probability"/>
13906 <param name="old_score" value=""/>
13907 <param name="proteins" value="true"/>
13908 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
13909 <output name="ctd_out" ftype="xml">
13910 <assert_contents>
13911 <is_valid_xml/>
13912 </assert_contents>
13913 </output>
13914 </test>
13915 </xml>
13916 <xml name="autotest_IDSplitter">
13917 <test expect_num_outputs="3">
13918 <conditional name="adv_opts_cond">
13919 <param name="adv_opts_selector" value="advanced"/>
13920 <param name="force" value="false"/>
13921 <param name="test" value="true"/>
13922 </conditional>
13923 <param name="in" value="IDMapper_1_output.featureXML"/>
13924 <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
13925 <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
13926 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
13927 <output name="ctd_out" ftype="xml">
13928 <assert_contents>
13929 <is_valid_xml/>
13930 </assert_contents>
13931 </output>
13932 </test>
13933 </xml>
13934 <xml name="autotest_InternalCalibration">
13935 <test expect_num_outputs="4">
13936 <conditional name="adv_opts_cond">
13937 <param name="adv_opts_selector" value="advanced"/>
13938 <param name="force" value="false"/>
13939 <param name="test" value="true"/>
13940 </conditional>
13941 <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
13942 <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
13943 <param name="ppm_match_tolerance" value="25.0"/>
13944 <param name="ms_level" value="1"/>
13945 <param name="RT_chunking" value="-1.0"/>
13946 <section name="cal">
13947 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
13948 <param name="lock_require_mono" value="false"/>
13949 <param name="lock_require_iso" value="false"/>
13950 <param name="model_type" value="linear"/>
13951 </section>
13952 <section name="RANSAC">
13953 <param name="enabled" value="true"/>
13954 <param name="threshold" value="1.0"/>
13955 <param name="pc_inliers" value="30"/>
13956 <param name="iter" value="500"/>
13957 </section>
13958 <section name="goodness">
13959 <param name="median" value="4.0"/>
13960 <param name="MAD" value="2.0"/>
13961 </section>
13962 <section name="quality_control"/>
13963 <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
13964 <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
13965 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
13966 <output name="ctd_out" ftype="xml">
13967 <assert_contents>
13968 <is_valid_xml/>
13969 </assert_contents>
13970 </output>
13971 </test>
13972 <test expect_num_outputs="4">
13973 <conditional name="adv_opts_cond">
13974 <param name="adv_opts_selector" value="advanced"/>
13975 <param name="force" value="false"/>
13976 <param name="test" value="true"/>
13977 </conditional>
13978 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
13979 <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
13980 <param name="ppm_match_tolerance" value="25.0"/>
13981 <param name="ms_level" value="1 2 3"/>
13982 <param name="RT_chunking" value="60.0"/>
13983 <section name="cal">
13984 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
13985 <param name="lock_require_mono" value="true"/>
13986 <param name="lock_require_iso" value="false"/>
13987 <param name="model_type" value="linear"/>
13988 </section>
13989 <section name="RANSAC">
13990 <param name="enabled" value="false"/>
13991 <param name="threshold" value="10.0"/>
13992 <param name="pc_inliers" value="30"/>
13993 <param name="iter" value="70"/>
13994 </section>
13995 <section name="goodness">
13996 <param name="median" value="4.0"/>
13997 <param name="MAD" value="2.0"/>
13998 </section>
13999 <section name="quality_control"/>
14000 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
14001 <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
14002 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
14003 <output name="ctd_out" ftype="xml">
14004 <assert_contents>
14005 <is_valid_xml/>
14006 </assert_contents>
14007 </output>
14008 </test>
14009 </xml>
14010 <xml name="autotest_IsobaricAnalyzer">
14011 <test expect_num_outputs="2">
14012 <conditional name="adv_opts_cond">
14013 <param name="adv_opts_selector" value="advanced"/>
14014 <param name="force" value="false"/>
14015 <param name="test" value="true"/>
14016 </conditional>
14017 <param name="type" value="itraq4plex"/>
14018 <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
14019 <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14020 <section name="extraction">
14021 <param name="select_activation" value=""/>
14022 <param name="reporter_mass_shift" value="0.1"/>
14023 <param name="min_precursor_intensity" value="1.0"/>
14024 <param name="keep_unannotated_precursor" value="true"/>
14025 <param name="min_reporter_intensity" value="0.0"/>
14026 <param name="discard_low_intensity_quantifications" value="false"/>
14027 <param name="min_precursor_purity" value="0.0"/>
14028 <param name="precursor_isotope_deviation" value="10.0"/>
14029 <param name="purity_interpolation" value="true"/>
14030 </section>
14031 <section name="itraq4plex">
14032 <param name="channel_114_description" value="l1"/>
14033 <param name="channel_115_description" value="l2"/>
14034 <param name="channel_116_description" value="l3"/>
14035 <param name="channel_117_description" value="lung"/>
14036 <param name="reference_channel" value="114"/>
14037 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14038 </section>
14039 <section name="itraq8plex">
14040 <param name="channel_113_description" value=""/>
14041 <param name="channel_114_description" value=""/>
14042 <param name="channel_115_description" value=""/>
14043 <param name="channel_116_description" value=""/>
14044 <param name="channel_117_description" value=""/>
14045 <param name="channel_118_description" value=""/>
14046 <param name="channel_119_description" value=""/>
14047 <param name="channel_121_description" value=""/>
14048 <param name="reference_channel" value="113"/>
14049 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14050 </section>
14051 <section name="quantification">
14052 <param name="isotope_correction" value="true"/>
14053 <param name="normalization" value="false"/>
14054 </section>
14055 <section name="tmt10plex">
14056 <param name="channel_126_description" value=""/>
14057 <param name="channel_127N_description" value=""/>
14058 <param name="channel_127C_description" value=""/>
14059 <param name="channel_128N_description" value=""/>
14060 <param name="channel_128C_description" value=""/>
14061 <param name="channel_129N_description" value=""/>
14062 <param name="channel_129C_description" value=""/>
14063 <param name="channel_130N_description" value=""/>
14064 <param name="channel_130C_description" value=""/>
14065 <param name="channel_131_description" value=""/>
14066 <param name="reference_channel" value="126"/>
14067 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14068 </section>
14069 <section name="tmt11plex">
14070 <param name="channel_126_description" value=""/>
14071 <param name="channel_127N_description" value=""/>
14072 <param name="channel_127C_description" value=""/>
14073 <param name="channel_128N_description" value=""/>
14074 <param name="channel_128C_description" value=""/>
14075 <param name="channel_129N_description" value=""/>
14076 <param name="channel_129C_description" value=""/>
14077 <param name="channel_130N_description" value=""/>
14078 <param name="channel_130C_description" value=""/>
14079 <param name="channel_131N_description" value=""/>
14080 <param name="channel_131C_description" value=""/>
14081 <param name="reference_channel" value="126"/>
14082 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14083 </section>
14084 <section name="tmt16plex">
14085 <param name="channel_126_description" value=""/>
14086 <param name="channel_127N_description" value=""/>
14087 <param name="channel_127C_description" value=""/>
14088 <param name="channel_128N_description" value=""/>
14089 <param name="channel_128C_description" value=""/>
14090 <param name="channel_129N_description" value=""/>
14091 <param name="channel_129C_description" value=""/>
14092 <param name="channel_130N_description" value=""/>
14093 <param name="channel_130C_description" value=""/>
14094 <param name="channel_131N_description" value=""/>
14095 <param name="channel_131C_description" value=""/>
14096 <param name="channel_132N_description" value=""/>
14097 <param name="channel_132C_description" value=""/>
14098 <param name="channel_133N_description" value=""/>
14099 <param name="channel_133C_description" value=""/>
14100 <param name="channel_134N_description" value=""/>
14101 <param name="reference_channel" value="126"/>
14102 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14103 </section>
14104 <section name="tmt6plex">
14105 <param name="channel_126_description" value=""/>
14106 <param name="channel_127_description" value=""/>
14107 <param name="channel_128_description" value=""/>
14108 <param name="channel_129_description" value=""/>
14109 <param name="channel_130_description" value=""/>
14110 <param name="channel_131_description" value=""/>
14111 <param name="reference_channel" value="126"/>
14112 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14113 </section>
14114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14115 <output name="ctd_out" ftype="xml">
14116 <assert_contents>
14117 <is_valid_xml/>
14118 </assert_contents>
14119 </output>
14120 </test>
14121 <test expect_num_outputs="2">
14122 <conditional name="adv_opts_cond">
14123 <param name="adv_opts_selector" value="advanced"/>
14124 <param name="force" value="false"/>
14125 <param name="test" value="true"/>
14126 </conditional>
14127 <param name="type" value="itraq4plex"/>
14128 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
14129 <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14130 <section name="extraction">
14131 <param name="select_activation" value="High-energy collision-induced dissociation"/>
14132 <param name="reporter_mass_shift" value="0.002"/>
14133 <param name="min_precursor_intensity" value="1.0"/>
14134 <param name="keep_unannotated_precursor" value="true"/>
14135 <param name="min_reporter_intensity" value="0.0"/>
14136 <param name="discard_low_intensity_quantifications" value="false"/>
14137 <param name="min_precursor_purity" value="0.0"/>
14138 <param name="precursor_isotope_deviation" value="10.0"/>
14139 <param name="purity_interpolation" value="true"/>
14140 </section>
14141 <section name="itraq4plex">
14142 <param name="channel_114_description" value=""/>
14143 <param name="channel_115_description" value=""/>
14144 <param name="channel_116_description" value=""/>
14145 <param name="channel_117_description" value=""/>
14146 <param name="reference_channel" value="114"/>
14147 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14148 </section>
14149 <section name="itraq8plex">
14150 <param name="channel_113_description" value=""/>
14151 <param name="channel_114_description" value=""/>
14152 <param name="channel_115_description" value=""/>
14153 <param name="channel_116_description" value=""/>
14154 <param name="channel_117_description" value=""/>
14155 <param name="channel_118_description" value=""/>
14156 <param name="channel_119_description" value=""/>
14157 <param name="channel_121_description" value=""/>
14158 <param name="reference_channel" value="113"/>
14159 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14160 </section>
14161 <section name="quantification">
14162 <param name="isotope_correction" value="true"/>
14163 <param name="normalization" value="false"/>
14164 </section>
14165 <section name="tmt10plex">
14166 <param name="channel_126_description" value=""/>
14167 <param name="channel_127N_description" value=""/>
14168 <param name="channel_127C_description" value=""/>
14169 <param name="channel_128N_description" value=""/>
14170 <param name="channel_128C_description" value=""/>
14171 <param name="channel_129N_description" value=""/>
14172 <param name="channel_129C_description" value=""/>
14173 <param name="channel_130N_description" value=""/>
14174 <param name="channel_130C_description" value=""/>
14175 <param name="channel_131_description" value=""/>
14176 <param name="reference_channel" value="126"/>
14177 <param name="correction_matrix" value="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
14178 </section>
14179 <section name="tmt11plex">
14180 <param name="channel_126_description" value=""/>
14181 <param name="channel_127N_description" value=""/>
14182 <param name="channel_127C_description" value=""/>
14183 <param name="channel_128N_description" value=""/>
14184 <param name="channel_128C_description" value=""/>
14185 <param name="channel_129N_description" value=""/>
14186 <param name="channel_129C_description" value=""/>
14187 <param name="channel_130N_description" value=""/>
14188 <param name="channel_130C_description" value=""/>
14189 <param name="channel_131N_description" value=""/>
14190 <param name="channel_131C_description" value=""/>
14191 <param name="reference_channel" value="126"/>
14192 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14193 </section>
14194 <section name="tmt16plex">
14195 <param name="channel_126_description" value=""/>
14196 <param name="channel_127N_description" value=""/>
14197 <param name="channel_127C_description" value=""/>
14198 <param name="channel_128N_description" value=""/>
14199 <param name="channel_128C_description" value=""/>
14200 <param name="channel_129N_description" value=""/>
14201 <param name="channel_129C_description" value=""/>
14202 <param name="channel_130N_description" value=""/>
14203 <param name="channel_130C_description" value=""/>
14204 <param name="channel_131N_description" value=""/>
14205 <param name="channel_131C_description" value=""/>
14206 <param name="channel_132N_description" value=""/>
14207 <param name="channel_132C_description" value=""/>
14208 <param name="channel_133N_description" value=""/>
14209 <param name="channel_133C_description" value=""/>
14210 <param name="channel_134N_description" value=""/>
14211 <param name="reference_channel" value="126"/>
14212 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14213 </section>
14214 <section name="tmt6plex">
14215 <param name="channel_126_description" value=""/>
14216 <param name="channel_127_description" value=""/>
14217 <param name="channel_128_description" value=""/>
14218 <param name="channel_129_description" value=""/>
14219 <param name="channel_130_description" value=""/>
14220 <param name="channel_131_description" value=""/>
14221 <param name="reference_channel" value="126"/>
14222 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14223 </section>
14224 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14225 <output name="ctd_out" ftype="xml">
14226 <assert_contents>
14227 <is_valid_xml/>
14228 </assert_contents>
14229 </output>
14230 </test>
14231 <test expect_num_outputs="2">
14232 <conditional name="adv_opts_cond">
14233 <param name="adv_opts_selector" value="advanced"/>
14234 <param name="force" value="false"/>
14235 <param name="test" value="true"/>
14236 </conditional>
14237 <param name="type" value="itraq4plex"/>
14238 <param name="in" value="TMTTenPlexMethod_test.mzML"/>
14239 <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14240 <section name="extraction">
14241 <param name="select_activation" value="High-energy collision-induced dissociation"/>
14242 <param name="reporter_mass_shift" value="0.002"/>
14243 <param name="min_precursor_intensity" value="1.0"/>
14244 <param name="keep_unannotated_precursor" value="true"/>
14245 <param name="min_reporter_intensity" value="0.0"/>
14246 <param name="discard_low_intensity_quantifications" value="false"/>
14247 <param name="min_precursor_purity" value="0.0"/>
14248 <param name="precursor_isotope_deviation" value="10.0"/>
14249 <param name="purity_interpolation" value="true"/>
14250 </section>
14251 <section name="itraq4plex">
14252 <param name="channel_114_description" value=""/>
14253 <param name="channel_115_description" value=""/>
14254 <param name="channel_116_description" value=""/>
14255 <param name="channel_117_description" value=""/>
14256 <param name="reference_channel" value="114"/>
14257 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14258 </section>
14259 <section name="itraq8plex">
14260 <param name="channel_113_description" value=""/>
14261 <param name="channel_114_description" value=""/>
14262 <param name="channel_115_description" value=""/>
14263 <param name="channel_116_description" value=""/>
14264 <param name="channel_117_description" value=""/>
14265 <param name="channel_118_description" value=""/>
14266 <param name="channel_119_description" value=""/>
14267 <param name="channel_121_description" value=""/>
14268 <param name="reference_channel" value="113"/>
14269 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14270 </section>
14271 <section name="quantification">
14272 <param name="isotope_correction" value="true"/>
14273 <param name="normalization" value="false"/>
14274 </section>
14275 <section name="tmt10plex">
14276 <param name="channel_126_description" value=""/>
14277 <param name="channel_127N_description" value=""/>
14278 <param name="channel_127C_description" value=""/>
14279 <param name="channel_128N_description" value=""/>
14280 <param name="channel_128C_description" value=""/>
14281 <param name="channel_129N_description" value=""/>
14282 <param name="channel_129C_description" value=""/>
14283 <param name="channel_130N_description" value=""/>
14284 <param name="channel_130C_description" value=""/>
14285 <param name="channel_131_description" value=""/>
14286 <param name="reference_channel" value="126"/>
14287 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14288 </section>
14289 <section name="tmt11plex">
14290 <param name="channel_126_description" value=""/>
14291 <param name="channel_127N_description" value=""/>
14292 <param name="channel_127C_description" value=""/>
14293 <param name="channel_128N_description" value=""/>
14294 <param name="channel_128C_description" value=""/>
14295 <param name="channel_129N_description" value=""/>
14296 <param name="channel_129C_description" value=""/>
14297 <param name="channel_130N_description" value=""/>
14298 <param name="channel_130C_description" value=""/>
14299 <param name="channel_131N_description" value=""/>
14300 <param name="channel_131C_description" value=""/>
14301 <param name="reference_channel" value="126"/>
14302 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14303 </section>
14304 <section name="tmt16plex">
14305 <param name="channel_126_description" value=""/>
14306 <param name="channel_127N_description" value=""/>
14307 <param name="channel_127C_description" value=""/>
14308 <param name="channel_128N_description" value=""/>
14309 <param name="channel_128C_description" value=""/>
14310 <param name="channel_129N_description" value=""/>
14311 <param name="channel_129C_description" value=""/>
14312 <param name="channel_130N_description" value=""/>
14313 <param name="channel_130C_description" value=""/>
14314 <param name="channel_131N_description" value=""/>
14315 <param name="channel_131C_description" value=""/>
14316 <param name="channel_132N_description" value=""/>
14317 <param name="channel_132C_description" value=""/>
14318 <param name="channel_133N_description" value=""/>
14319 <param name="channel_133C_description" value=""/>
14320 <param name="channel_134N_description" value=""/>
14321 <param name="reference_channel" value="126"/>
14322 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14323 </section>
14324 <section name="tmt6plex">
14325 <param name="channel_126_description" value=""/>
14326 <param name="channel_127_description" value=""/>
14327 <param name="channel_128_description" value=""/>
14328 <param name="channel_129_description" value=""/>
14329 <param name="channel_130_description" value=""/>
14330 <param name="channel_131_description" value=""/>
14331 <param name="reference_channel" value="126"/>
14332 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14333 </section>
14334 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14335 <output name="ctd_out" ftype="xml">
14336 <assert_contents>
14337 <is_valid_xml/>
14338 </assert_contents>
14339 </output>
14340 </test>
14341 <test expect_num_outputs="2">
14342 <conditional name="adv_opts_cond">
14343 <param name="adv_opts_selector" value="advanced"/>
14344 <param name="force" value="false"/>
14345 <param name="test" value="true"/>
14346 </conditional>
14347 <param name="type" value="tmt10plex"/>
14348 <param name="in" value="MS3_nonHierarchical.mzML"/>
14349 <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
14350 <section name="extraction">
14351 <param name="select_activation" value="Collision-induced dissociation"/>
14352 <param name="reporter_mass_shift" value="0.002"/>
14353 <param name="min_precursor_intensity" value="1.0"/>
14354 <param name="keep_unannotated_precursor" value="true"/>
14355 <param name="min_reporter_intensity" value="0.0"/>
14356 <param name="discard_low_intensity_quantifications" value="false"/>
14357 <param name="min_precursor_purity" value="0.0"/>
14358 <param name="precursor_isotope_deviation" value="10.0"/>
14359 <param name="purity_interpolation" value="true"/>
14360 </section>
14361 <section name="itraq4plex">
14362 <param name="channel_114_description" value=""/>
14363 <param name="channel_115_description" value=""/>
14364 <param name="channel_116_description" value=""/>
14365 <param name="channel_117_description" value=""/>
14366 <param name="reference_channel" value="114"/>
14367 <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
14368 </section>
14369 <section name="itraq8plex">
14370 <param name="channel_113_description" value=""/>
14371 <param name="channel_114_description" value=""/>
14372 <param name="channel_115_description" value=""/>
14373 <param name="channel_116_description" value=""/>
14374 <param name="channel_117_description" value=""/>
14375 <param name="channel_118_description" value=""/>
14376 <param name="channel_119_description" value=""/>
14377 <param name="channel_121_description" value=""/>
14378 <param name="reference_channel" value="113"/>
14379 <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
14380 </section>
14381 <section name="quantification">
14382 <param name="isotope_correction" value="true"/>
14383 <param name="normalization" value="false"/>
14384 </section>
14385 <section name="tmt10plex">
14386 <param name="channel_126_description" value=""/>
14387 <param name="channel_127N_description" value=""/>
14388 <param name="channel_127C_description" value=""/>
14389 <param name="channel_128N_description" value=""/>
14390 <param name="channel_128C_description" value=""/>
14391 <param name="channel_129N_description" value=""/>
14392 <param name="channel_129C_description" value=""/>
14393 <param name="channel_130N_description" value=""/>
14394 <param name="channel_130C_description" value=""/>
14395 <param name="channel_131_description" value=""/>
14396 <param name="reference_channel" value="126"/>
14397 <param name="correction_matrix" value="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
14398 </section>
14399 <section name="tmt11plex">
14400 <param name="channel_126_description" value=""/>
14401 <param name="channel_127N_description" value=""/>
14402 <param name="channel_127C_description" value=""/>
14403 <param name="channel_128N_description" value=""/>
14404 <param name="channel_128C_description" value=""/>
14405 <param name="channel_129N_description" value=""/>
14406 <param name="channel_129C_description" value=""/>
14407 <param name="channel_130N_description" value=""/>
14408 <param name="channel_130C_description" value=""/>
14409 <param name="channel_131N_description" value=""/>
14410 <param name="channel_131C_description" value=""/>
14411 <param name="reference_channel" value="126"/>
14412 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14413 </section>
14414 <section name="tmt16plex">
14415 <param name="channel_126_description" value=""/>
14416 <param name="channel_127N_description" value=""/>
14417 <param name="channel_127C_description" value=""/>
14418 <param name="channel_128N_description" value=""/>
14419 <param name="channel_128C_description" value=""/>
14420 <param name="channel_129N_description" value=""/>
14421 <param name="channel_129C_description" value=""/>
14422 <param name="channel_130N_description" value=""/>
14423 <param name="channel_130C_description" value=""/>
14424 <param name="channel_131N_description" value=""/>
14425 <param name="channel_131C_description" value=""/>
14426 <param name="channel_132N_description" value=""/>
14427 <param name="channel_132C_description" value=""/>
14428 <param name="channel_133N_description" value=""/>
14429 <param name="channel_133C_description" value=""/>
14430 <param name="channel_134N_description" value=""/>
14431 <param name="reference_channel" value="126"/>
14432 <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
14433 </section>
14434 <section name="tmt6plex">
14435 <param name="channel_126_description" value=""/>
14436 <param name="channel_127_description" value=""/>
14437 <param name="channel_128_description" value=""/>
14438 <param name="channel_129_description" value=""/>
14439 <param name="channel_130_description" value=""/>
14440 <param name="channel_131_description" value=""/>
14441 <param name="reference_channel" value="126"/>
14442 <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
14443 </section>
14444 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14445 <output name="ctd_out" ftype="xml">
14446 <assert_contents>
14447 <is_valid_xml/>
14448 </assert_contents>
14449 </output>
14450 </test>
14451 </xml>
14452 <xml name="autotest_LabeledEval">
14453 </xml>
14454 <xml name="autotest_LowMemPeakPickerHiResRandomAccess">
14455 <test expect_num_outputs="2">
14456 <conditional name="adv_opts_cond">
14457 <param name="adv_opts_selector" value="advanced"/>
14458 <param name="force" value="false"/>
14459 <param name="test" value="true"/>
14460 </conditional>
14461 <param name="in" value="PeakPickerHiRes_RandomAccess_input.mzML"/>
14462 <output name="out" file="LowMemPeakPickerHiRes_RandomAccess_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
14463 <section name="algorithm">
14464 <param name="signal_to_noise" value="1.0"/>
14465 <param name="spacing_difference_gap" value="4.0"/>
14466 <param name="spacing_difference" value="1.5"/>
14467 <param name="missing" value="1"/>
14468 <param name="ms_levels" value="1"/>
14469 <param name="report_FWHM" value="false"/>
14470 <param name="report_FWHM_unit" value="relative"/>
14471 <section name="SignalToNoise">
14472 <param name="max_intensity" value="-1"/>
14473 <param name="auto_max_stdev_factor" value="3.0"/>
14474 <param name="auto_max_percentile" value="95"/>
14475 <param name="auto_mode" value="0"/>
14476 <param name="win_len" value="200.0"/>
14477 <param name="bin_count" value="30"/>
14478 <param name="min_required_elements" value="10"/>
14479 <param name="noise_for_empty_window" value="1e+20"/>
14480 <param name="write_log_messages" value="true"/>
14481 </section>
14482 </section>
14483 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14484 <output name="ctd_out" ftype="xml">
14485 <assert_contents>
14486 <is_valid_xml/>
14487 </assert_contents>
14488 </output>
14489 </test>
14490 </xml>
14491 <xml name="autotest_LowMemPeakPickerHiRes">
14492 <test expect_num_outputs="2">
14493 <conditional name="adv_opts_cond">
14494 <param name="adv_opts_selector" value="advanced"/>
14495 <param name="force" value="false"/>
14496 <param name="test" value="true"/>
14497 </conditional>
14498 <param name="in" value="PeakPickerHiRes_input.mzML"/>
14499 <output name="out" file="LowMemPeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
14500 <section name="algorithm">
14501 <param name="signal_to_noise" value="1.0"/>
14502 <param name="spacing_difference_gap" value="4.0"/>
14503 <param name="spacing_difference" value="1.5"/>
14504 <param name="missing" value="1"/>
14505 <param name="ms_levels" value="1"/>
14506 <param name="report_FWHM" value="false"/>
14507 <param name="report_FWHM_unit" value="relative"/>
14508 <section name="SignalToNoise">
14509 <param name="max_intensity" value="-1"/>
14510 <param name="auto_max_stdev_factor" value="3.0"/>
14511 <param name="auto_max_percentile" value="95"/>
14512 <param name="auto_mode" value="0"/>
14513 <param name="win_len" value="200.0"/>
14514 <param name="bin_count" value="30"/>
14515 <param name="min_required_elements" value="10"/>
14516 <param name="noise_for_empty_window" value="1e+20"/>
14517 <param name="write_log_messages" value="true"/>
14518 </section>
14519 </section>
14520 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14521 <output name="ctd_out" ftype="xml">
14522 <assert_contents>
14523 <is_valid_xml/>
14524 </assert_contents>
14525 </output>
14526 </test>
14527 </xml>
14528 <xml name="autotest_LuciphorAdapter">
14529 <test expect_num_outputs="2">
14530 <conditional name="adv_opts_cond">
14531 <param name="adv_opts_selector" value="advanced"/>
14532 <param name="force" value="false"/>
14533 <param name="test" value="true"/>
14534 </conditional>
14535 <param name="in" value="LuciphorAdapter_1_input.mzML"/>
14536 <param name="id" value="LuciphorAdapter_1_input.idXML"/>
14537 <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
14538 <param name="fragment_method" value="CID"/>
14539 <param name="fragment_mass_tolerance" value="0.5"/>
14540 <param name="fragment_error_units" value="Da"/>
14541 <param name="min_mz" value="150.0"/>
14542 <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
14543 <param name="neutral_losses" value="&quot;sty -H3PO4 -97.97690&quot;"/>
14544 <param name="decoy_mass" value="79.966331"/>
14545 <param name="decoy_neutral_losses" value="&quot;X -H3PO4 -97.97690&quot;"/>
14546 <param name="max_charge_state" value="5"/>
14547 <param name="max_peptide_length" value="40"/>
14548 <param name="max_num_perm" value="16384"/>
14549 <param name="modeling_score_threshold" value="0.95"/>
14550 <param name="scoring_threshold" value="0.0"/>
14551 <param name="min_num_psms_model" value="1"/>
14552 <param name="run_mode" value="0"/>
14553 <param name="rt_tolerance" value="0.01"/>
14554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
14555 <output name="ctd_out" ftype="xml">
14556 <assert_contents>
14557 <is_valid_xml/>
14558 </assert_contents>
14559 </output>
14560 </test>
14561 </xml>
14562 <xml name="autotest_MapAlignerIdentification">
14563 <test expect_num_outputs="2">
14564 <conditional name="adv_opts_cond">
14565 <param name="adv_opts_selector" value="advanced"/>
14566 <param name="force" value="false"/>
14567 <param name="test" value="true"/>
14568 </conditional>
14569 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
14570 <output_collection name="out" count="2"/>
14571 <section name="reference">
14572 <param name="index" value="0"/>
14573 </section>
14574 <section name="algorithm">
14575 <param name="score_cutoff" value="false"/>
14576 <param name="min_score" value="0.05"/>
14577 <param name="min_run_occur" value="2"/>
14578 <param name="max_rt_shift" value="0.0"/>
14579 <param name="use_unassigned_peptides" value="true"/>
14580 <param name="use_feature_rt" value="false"/>
14581 </section>
14582 <section name="model">
14583 <param name="type" value="b_spline"/>
14584 <section name="linear">
14585 <param name="symmetric_regression" value="false"/>
14586 <param name="x_weight" value=""/>
14587 <param name="y_weight" value=""/>
14588 <param name="x_datum_min" value="1e-15"/>
14589 <param name="x_datum_max" value="1000000000000000.0"/>
14590 <param name="y_datum_min" value="1e-15"/>
14591 <param name="y_datum_max" value="1000000000000000.0"/>
14592 </section>
14593 <section name="b_spline">
14594 <param name="wavelength" value="0.0"/>
14595 <param name="num_nodes" value="5"/>
14596 <param name="extrapolate" value="linear"/>
14597 <param name="boundary_condition" value="2"/>
14598 </section>
14599 <section name="lowess">
14600 <param name="span" value="0.666666666666667"/>
14601 <param name="num_iterations" value="3"/>
14602 <param name="delta" value="-1.0"/>
14603 <param name="interpolation_type" value="cspline"/>
14604 <param name="extrapolation_type" value="four-point-linear"/>
14605 </section>
14606 <section name="interpolated">
14607 <param name="interpolation_type" value="cspline"/>
14608 <param name="extrapolation_type" value="two-point-linear"/>
14609 </section>
14610 </section>
14611 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
14612 <output name="ctd_out" ftype="xml">
14613 <assert_contents>
14614 <is_valid_xml/>
14615 </assert_contents>
14616 </output>
14617 </test>
14618 <test expect_num_outputs="2">
14619 <conditional name="adv_opts_cond">
14620 <param name="adv_opts_selector" value="advanced"/>
14621 <param name="force" value="false"/>
14622 <param name="test" value="true"/>
14623 </conditional>
14624 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
14625 <output_collection name="out" count="1"/>
14626 <section name="reference">
14627 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
14628 <param name="index" value="0"/>
14629 </section>
14630 <section name="algorithm">
14631 <param name="score_cutoff" value="false"/>
14632 <param name="min_score" value="0.05"/>
14633 <param name="min_run_occur" value="2"/>
14634 <param name="max_rt_shift" value="0.0"/>
14635 <param name="use_unassigned_peptides" value="true"/>
14636 <param name="use_feature_rt" value="false"/>
14637 </section>
14638 <section name="model">
14639 <param name="type" value="b_spline"/>
14640 <section name="linear">
14641 <param name="symmetric_regression" value="false"/>
14642 <param name="x_weight" value=""/>
14643 <param name="y_weight" value=""/>
14644 <param name="x_datum_min" value="1e-15"/>
14645 <param name="x_datum_max" value="1000000000000000.0"/>
14646 <param name="y_datum_min" value="1e-15"/>
14647 <param name="y_datum_max" value="1000000000000000.0"/>
14648 </section>
14649 <section name="b_spline">
14650 <param name="wavelength" value="0.0"/>
14651 <param name="num_nodes" value="5"/>
14652 <param name="extrapolate" value="linear"/>
14653 <param name="boundary_condition" value="2"/>
14654 </section>
14655 <section name="lowess">
14656 <param name="span" value="0.666666666666667"/>
14657 <param name="num_iterations" value="3"/>
14658 <param name="delta" value="-1.0"/>
14659 <param name="interpolation_type" value="cspline"/>
14660 <param name="extrapolation_type" value="four-point-linear"/>
14661 </section>
14662 <section name="interpolated">
14663 <param name="interpolation_type" value="cspline"/>
14664 <param name="extrapolation_type" value="two-point-linear"/>
14665 </section>
14666 </section>
14667 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
14668 <output name="ctd_out" ftype="xml">
14669 <assert_contents>
14670 <is_valid_xml/>
14671 </assert_contents>
14672 </output>
14673 </test>
14674 <test expect_num_outputs="2">
14675 <conditional name="adv_opts_cond">
14676 <param name="adv_opts_selector" value="advanced"/>
14677 <param name="force" value="false"/>
14678 <param name="test" value="true"/>
14679 </conditional>
14680 <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
14681 <output_collection name="out" count="2"/>
14682 <section name="reference">
14683 <param name="index" value="1"/>
14684 </section>
14685 <section name="algorithm">
14686 <param name="score_cutoff" value="false"/>
14687 <param name="min_score" value="0.05"/>
14688 <param name="min_run_occur" value="2"/>
14689 <param name="max_rt_shift" value="0.0"/>
14690 <param name="use_unassigned_peptides" value="true"/>
14691 <param name="use_feature_rt" value="false"/>
14692 </section>
14693 <section name="model">
14694 <param name="type" value="b_spline"/>
14695 <section name="linear">
14696 <param name="symmetric_regression" value="false"/>
14697 <param name="x_weight" value=""/>
14698 <param name="y_weight" value=""/>
14699 <param name="x_datum_min" value="1e-15"/>
14700 <param name="x_datum_max" value="1000000000000000.0"/>
14701 <param name="y_datum_min" value="1e-15"/>
14702 <param name="y_datum_max" value="1000000000000000.0"/>
14703 </section>
14704 <section name="b_spline">
14705 <param name="wavelength" value="0.0"/>
14706 <param name="num_nodes" value="5"/>
14707 <param name="extrapolate" value="linear"/>
14708 <param name="boundary_condition" value="2"/>
14709 </section>
14710 <section name="lowess">
14711 <param name="span" value="0.666666666666667"/>
14712 <param name="num_iterations" value="3"/>
14713 <param name="delta" value="-1.0"/>
14714 <param name="interpolation_type" value="cspline"/>
14715 <param name="extrapolation_type" value="four-point-linear"/>
14716 </section>
14717 <section name="interpolated">
14718 <param name="interpolation_type" value="cspline"/>
14719 <param name="extrapolation_type" value="two-point-linear"/>
14720 </section>
14721 </section>
14722 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
14723 <output name="ctd_out" ftype="xml">
14724 <assert_contents>
14725 <is_valid_xml/>
14726 </assert_contents>
14727 </output>
14728 </test>
14729 <test expect_num_outputs="2">
14730 <conditional name="adv_opts_cond">
14731 <param name="adv_opts_selector" value="advanced"/>
14732 <param name="force" value="false"/>
14733 <param name="test" value="true"/>
14734 </conditional>
14735 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
14736 <output_collection name="out" count="2"/>
14737 <section name="reference">
14738 <param name="index" value="2"/>
14739 </section>
14740 <section name="algorithm">
14741 <param name="score_cutoff" value="false"/>
14742 <param name="min_score" value="0.05"/>
14743 <param name="min_run_occur" value="2"/>
14744 <param name="max_rt_shift" value="0.0"/>
14745 <param name="use_unassigned_peptides" value="true"/>
14746 <param name="use_feature_rt" value="false"/>
14747 </section>
14748 <section name="model">
14749 <param name="type" value="b_spline"/>
14750 <section name="linear">
14751 <param name="symmetric_regression" value="false"/>
14752 <param name="x_weight" value=""/>
14753 <param name="y_weight" value=""/>
14754 <param name="x_datum_min" value="1e-15"/>
14755 <param name="x_datum_max" value="1000000000000000.0"/>
14756 <param name="y_datum_min" value="1e-15"/>
14757 <param name="y_datum_max" value="1000000000000000.0"/>
14758 </section>
14759 <section name="b_spline">
14760 <param name="wavelength" value="0.0"/>
14761 <param name="num_nodes" value="5"/>
14762 <param name="extrapolate" value="linear"/>
14763 <param name="boundary_condition" value="2"/>
14764 </section>
14765 <section name="lowess">
14766 <param name="span" value="0.666666666666667"/>
14767 <param name="num_iterations" value="3"/>
14768 <param name="delta" value="-1.0"/>
14769 <param name="interpolation_type" value="cspline"/>
14770 <param name="extrapolation_type" value="four-point-linear"/>
14771 </section>
14772 <section name="interpolated">
14773 <param name="interpolation_type" value="cspline"/>
14774 <param name="extrapolation_type" value="two-point-linear"/>
14775 </section>
14776 </section>
14777 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
14778 <output name="ctd_out" ftype="xml">
14779 <assert_contents>
14780 <is_valid_xml/>
14781 </assert_contents>
14782 </output>
14783 </test>
14784 <test expect_num_outputs="2">
14785 <conditional name="adv_opts_cond">
14786 <param name="adv_opts_selector" value="advanced"/>
14787 <param name="force" value="false"/>
14788 <param name="test" value="true"/>
14789 </conditional>
14790 <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
14791 <output_collection name="out" count="2"/>
14792 <section name="reference">
14793 <param name="index" value="0"/>
14794 </section>
14795 <section name="algorithm">
14796 <param name="score_cutoff" value="false"/>
14797 <param name="min_score" value="0.05"/>
14798 <param name="min_run_occur" value="2"/>
14799 <param name="max_rt_shift" value="0.0"/>
14800 <param name="use_unassigned_peptides" value="true"/>
14801 <param name="use_feature_rt" value="false"/>
14802 </section>
14803 <section name="model">
14804 <param name="type" value="b_spline"/>
14805 <section name="linear">
14806 <param name="symmetric_regression" value="false"/>
14807 <param name="x_weight" value=""/>
14808 <param name="y_weight" value=""/>
14809 <param name="x_datum_min" value="1e-15"/>
14810 <param name="x_datum_max" value="1000000000000000.0"/>
14811 <param name="y_datum_min" value="1e-15"/>
14812 <param name="y_datum_max" value="1000000000000000.0"/>
14813 </section>
14814 <section name="b_spline">
14815 <param name="wavelength" value="0.0"/>
14816 <param name="num_nodes" value="5"/>
14817 <param name="extrapolate" value="linear"/>
14818 <param name="boundary_condition" value="2"/>
14819 </section>
14820 <section name="lowess">
14821 <param name="span" value="0.666666666666667"/>
14822 <param name="num_iterations" value="3"/>
14823 <param name="delta" value="-1.0"/>
14824 <param name="interpolation_type" value="cspline"/>
14825 <param name="extrapolation_type" value="four-point-linear"/>
14826 </section>
14827 <section name="interpolated">
14828 <param name="interpolation_type" value="cspline"/>
14829 <param name="extrapolation_type" value="two-point-linear"/>
14830 </section>
14831 </section>
14832 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
14833 <output name="ctd_out" ftype="xml">
14834 <assert_contents>
14835 <is_valid_xml/>
14836 </assert_contents>
14837 </output>
14838 </test>
14839 <test expect_num_outputs="2">
14840 <conditional name="adv_opts_cond">
14841 <param name="adv_opts_selector" value="advanced"/>
14842 <param name="force" value="false"/>
14843 <param name="test" value="true"/>
14844 </conditional>
14845 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
14846 <output_collection name="trafo_out" count="1"/>
14847 <section name="reference">
14848 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
14849 <param name="index" value="0"/>
14850 </section>
14851 <section name="algorithm">
14852 <param name="score_cutoff" value="false"/>
14853 <param name="min_score" value="0.05"/>
14854 <param name="min_run_occur" value="2"/>
14855 <param name="max_rt_shift" value="0.0"/>
14856 <param name="use_unassigned_peptides" value="true"/>
14857 <param name="use_feature_rt" value="false"/>
14858 </section>
14859 <section name="model">
14860 <param name="type" value="b_spline"/>
14861 <section name="linear">
14862 <param name="symmetric_regression" value="false"/>
14863 <param name="x_weight" value=""/>
14864 <param name="y_weight" value=""/>
14865 <param name="x_datum_min" value="1e-15"/>
14866 <param name="x_datum_max" value="1000000000000000.0"/>
14867 <param name="y_datum_min" value="1e-15"/>
14868 <param name="y_datum_max" value="1000000000000000.0"/>
14869 </section>
14870 <section name="b_spline">
14871 <param name="wavelength" value="0.0"/>
14872 <param name="num_nodes" value="5"/>
14873 <param name="extrapolate" value="linear"/>
14874 <param name="boundary_condition" value="2"/>
14875 </section>
14876 <section name="lowess">
14877 <param name="span" value="0.666666666666667"/>
14878 <param name="num_iterations" value="3"/>
14879 <param name="delta" value="-1.0"/>
14880 <param name="interpolation_type" value="cspline"/>
14881 <param name="extrapolation_type" value="four-point-linear"/>
14882 </section>
14883 <section name="interpolated">
14884 <param name="interpolation_type" value="cspline"/>
14885 <param name="extrapolation_type" value="two-point-linear"/>
14886 </section>
14887 </section>
14888 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
14889 <output name="ctd_out" ftype="xml">
14890 <assert_contents>
14891 <is_valid_xml/>
14892 </assert_contents>
14893 </output>
14894 </test>
14895 </xml>
14896 <xml name="autotest_MapAlignerPoseClustering">
14897 <test expect_num_outputs="3">
14898 <conditional name="adv_opts_cond">
14899 <param name="adv_opts_selector" value="advanced"/>
14900 <param name="force" value="false"/>
14901 <param name="test" value="true"/>
14902 </conditional>
14903 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
14904 <output_collection name="out" count="3"/>
14905 <output_collection name="trafo_out" count="3"/>
14906 <section name="reference">
14907 <param name="index" value="0"/>
14908 </section>
14909 <section name="algorithm">
14910 <param name="max_num_peaks_considered" value="400"/>
14911 <section name="superimposer">
14912 <param name="mz_pair_max_distance" value="0.5"/>
14913 <param name="rt_pair_distance_fraction" value="0.1"/>
14914 <param name="num_used_points" value="2000"/>
14915 <param name="scaling_bucket_size" value="0.005"/>
14916 <param name="shift_bucket_size" value="3.0"/>
14917 <param name="max_shift" value="1000.0"/>
14918 <param name="max_scaling" value="2.0"/>
14919 <param name="dump_buckets" value=""/>
14920 <param name="dump_pairs" value=""/>
14921 </section>
14922 <section name="pairfinder">
14923 <param name="second_nearest_gap" value="2.0"/>
14924 <param name="use_identifications" value="false"/>
14925 <param name="ignore_charge" value="true"/>
14926 <param name="ignore_adduct" value="true"/>
14927 <section name="distance_RT">
14928 <param name="max_difference" value="30.0"/>
14929 <param name="exponent" value="1.0"/>
14930 <param name="weight" value="1.0"/>
14931 </section>
14932 <section name="distance_MZ">
14933 <param name="max_difference" value="0.3"/>
14934 <param name="unit" value="Da"/>
14935 <param name="exponent" value="2.0"/>
14936 <param name="weight" value="1.0"/>
14937 </section>
14938 <section name="distance_intensity">
14939 <param name="exponent" value="1.0"/>
14940 <param name="weight" value="0.0"/>
14941 <param name="log_transform" value="disabled"/>
14942 </section>
14943 </section>
14944 </section>
14945 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
14946 <output name="ctd_out" ftype="xml">
14947 <assert_contents>
14948 <is_valid_xml/>
14949 </assert_contents>
14950 </output>
14951 </test>
14952 <test expect_num_outputs="2">
14953 <conditional name="adv_opts_cond">
14954 <param name="adv_opts_selector" value="advanced"/>
14955 <param name="force" value="false"/>
14956 <param name="test" value="true"/>
14957 </conditional>
14958 <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
14959 <output_collection name="out" count="3"/>
14960 <section name="reference">
14961 <param name="index" value="0"/>
14962 </section>
14963 <section name="algorithm">
14964 <param name="max_num_peaks_considered" value="400"/>
14965 <section name="superimposer">
14966 <param name="mz_pair_max_distance" value="0.5"/>
14967 <param name="rt_pair_distance_fraction" value="0.1"/>
14968 <param name="num_used_points" value="2000"/>
14969 <param name="scaling_bucket_size" value="0.005"/>
14970 <param name="shift_bucket_size" value="3.0"/>
14971 <param name="max_shift" value="1000.0"/>
14972 <param name="max_scaling" value="2.0"/>
14973 <param name="dump_buckets" value=""/>
14974 <param name="dump_pairs" value=""/>
14975 </section>
14976 <section name="pairfinder">
14977 <param name="second_nearest_gap" value="2.0"/>
14978 <param name="use_identifications" value="false"/>
14979 <param name="ignore_charge" value="false"/>
14980 <param name="ignore_adduct" value="true"/>
14981 <section name="distance_RT">
14982 <param name="max_difference" value="100.0"/>
14983 <param name="exponent" value="1.0"/>
14984 <param name="weight" value="1.0"/>
14985 </section>
14986 <section name="distance_MZ">
14987 <param name="max_difference" value="0.3"/>
14988 <param name="unit" value="Da"/>
14989 <param name="exponent" value="2.0"/>
14990 <param name="weight" value="1.0"/>
14991 </section>
14992 <section name="distance_intensity">
14993 <param name="exponent" value="1.0"/>
14994 <param name="weight" value="0.0"/>
14995 <param name="log_transform" value="disabled"/>
14996 </section>
14997 </section>
14998 </section>
14999 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15000 <output name="ctd_out" ftype="xml">
15001 <assert_contents>
15002 <is_valid_xml/>
15003 </assert_contents>
15004 </output>
15005 </test>
15006 <test expect_num_outputs="2">
15007 <conditional name="adv_opts_cond">
15008 <param name="adv_opts_selector" value="advanced"/>
15009 <param name="force" value="false"/>
15010 <param name="test" value="true"/>
15011 </conditional>
15012 <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
15013 <output_collection name="out" count="2"/>
15014 <section name="reference">
15015 <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
15016 <param name="index" value="0"/>
15017 </section>
15018 <section name="algorithm">
15019 <param name="max_num_peaks_considered" value="400"/>
15020 <section name="superimposer">
15021 <param name="mz_pair_max_distance" value="0.5"/>
15022 <param name="rt_pair_distance_fraction" value="0.1"/>
15023 <param name="num_used_points" value="2000"/>
15024 <param name="scaling_bucket_size" value="0.005"/>
15025 <param name="shift_bucket_size" value="3.0"/>
15026 <param name="max_shift" value="1000.0"/>
15027 <param name="max_scaling" value="2.0"/>
15028 <param name="dump_buckets" value=""/>
15029 <param name="dump_pairs" value=""/>
15030 </section>
15031 <section name="pairfinder">
15032 <param name="second_nearest_gap" value="2.0"/>
15033 <param name="use_identifications" value="false"/>
15034 <param name="ignore_charge" value="true"/>
15035 <param name="ignore_adduct" value="true"/>
15036 <section name="distance_RT">
15037 <param name="max_difference" value="30.0"/>
15038 <param name="exponent" value="1.0"/>
15039 <param name="weight" value="1.0"/>
15040 </section>
15041 <section name="distance_MZ">
15042 <param name="max_difference" value="0.3"/>
15043 <param name="unit" value="Da"/>
15044 <param name="exponent" value="2.0"/>
15045 <param name="weight" value="1.0"/>
15046 </section>
15047 <section name="distance_intensity">
15048 <param name="exponent" value="1.0"/>
15049 <param name="weight" value="0.0"/>
15050 <param name="log_transform" value="disabled"/>
15051 </section>
15052 </section>
15053 </section>
15054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15055 <output name="ctd_out" ftype="xml">
15056 <assert_contents>
15057 <is_valid_xml/>
15058 </assert_contents>
15059 </output>
15060 </test>
15061 <test expect_num_outputs="2">
15062 <conditional name="adv_opts_cond">
15063 <param name="adv_opts_selector" value="advanced"/>
15064 <param name="force" value="false"/>
15065 <param name="test" value="true"/>
15066 </conditional>
15067 <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
15068 <output_collection name="trafo_out" count="2"/>
15069 <section name="reference">
15070 <param name="index" value="2"/>
15071 </section>
15072 <section name="algorithm">
15073 <param name="max_num_peaks_considered" value="400"/>
15074 <section name="superimposer">
15075 <param name="mz_pair_max_distance" value="0.5"/>
15076 <param name="rt_pair_distance_fraction" value="0.1"/>
15077 <param name="num_used_points" value="2000"/>
15078 <param name="scaling_bucket_size" value="0.005"/>
15079 <param name="shift_bucket_size" value="3.0"/>
15080 <param name="max_shift" value="1000.0"/>
15081 <param name="max_scaling" value="2.0"/>
15082 <param name="dump_buckets" value=""/>
15083 <param name="dump_pairs" value=""/>
15084 </section>
15085 <section name="pairfinder">
15086 <param name="second_nearest_gap" value="2.0"/>
15087 <param name="use_identifications" value="false"/>
15088 <param name="ignore_charge" value="true"/>
15089 <param name="ignore_adduct" value="true"/>
15090 <section name="distance_RT">
15091 <param name="max_difference" value="30.0"/>
15092 <param name="exponent" value="1.0"/>
15093 <param name="weight" value="1.0"/>
15094 </section>
15095 <section name="distance_MZ">
15096 <param name="max_difference" value="0.3"/>
15097 <param name="unit" value="Da"/>
15098 <param name="exponent" value="2.0"/>
15099 <param name="weight" value="1.0"/>
15100 </section>
15101 <section name="distance_intensity">
15102 <param name="exponent" value="1.0"/>
15103 <param name="weight" value="0.0"/>
15104 <param name="log_transform" value="disabled"/>
15105 </section>
15106 </section>
15107 </section>
15108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15109 <output name="ctd_out" ftype="xml">
15110 <assert_contents>
15111 <is_valid_xml/>
15112 </assert_contents>
15113 </output>
15114 </test>
15115 </xml>
15116 <xml name="autotest_MapAlignerSpectrum">
15117 <test expect_num_outputs="2">
15118 <conditional name="adv_opts_cond">
15119 <param name="adv_opts_selector" value="advanced"/>
15120 <param name="force" value="false"/>
15121 <param name="test" value="true"/>
15122 </conditional>
15123 <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/>
15124 <output_collection name="out" count="3"/>
15125 <section name="algorithm">
15126 <param name="gapcost" value="1.0"/>
15127 <param name="affinegapcost" value="0.5"/>
15128 <param name="cutoff_score" value="0.7"/>
15129 <param name="bucketsize" value="100"/>
15130 <param name="anchorpoints" value="100"/>
15131 <param name="mismatchscore" value="-5.0"/>
15132 <param name="scorefunction" value="SteinScottImproveScore"/>
15133 </section>
15134 <section name="model">
15135 <param name="type" value="interpolated"/>
15136 <section name="linear">
15137 <param name="symmetric_regression" value="false"/>
15138 <param name="x_weight" value=""/>
15139 <param name="y_weight" value=""/>
15140 <param name="x_datum_min" value="1e-15"/>
15141 <param name="x_datum_max" value="1000000000000000.0"/>
15142 <param name="y_datum_min" value="1e-15"/>
15143 <param name="y_datum_max" value="1000000000000000.0"/>
15144 </section>
15145 <section name="b_spline">
15146 <param name="wavelength" value="0.0"/>
15147 <param name="num_nodes" value="5"/>
15148 <param name="extrapolate" value="linear"/>
15149 <param name="boundary_condition" value="2"/>
15150 </section>
15151 <section name="lowess">
15152 <param name="span" value="0.666666666666667"/>
15153 <param name="num_iterations" value="3"/>
15154 <param name="delta" value="-1.0"/>
15155 <param name="interpolation_type" value="cspline"/>
15156 <param name="extrapolation_type" value="four-point-linear"/>
15157 </section>
15158 <section name="interpolated">
15159 <param name="interpolation_type" value="cspline"/>
15160 <param name="extrapolation_type" value="two-point-linear"/>
15161 </section>
15162 </section>
15163 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15164 <output name="ctd_out" ftype="xml">
15165 <assert_contents>
15166 <is_valid_xml/>
15167 </assert_contents>
15168 </output>
15169 </test>
15170 </xml>
15171 <xml name="autotest_MapAlignerTreeGuided">
15172 <test expect_num_outputs="2">
15173 <conditional name="adv_opts_cond">
15174 <param name="adv_opts_selector" value="advanced"/>
15175 <param name="force" value="false"/>
15176 <param name="test" value="true"/>
15177 </conditional>
15178 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15179 <output_collection name="out" count="3"/>
15180 <section name="algorithm">
15181 <param name="model_type" value="b_spline"/>
15182 <section name="model">
15183 <param name="type" value="b_spline"/>
15184 <section name="linear">
15185 <param name="symmetric_regression" value="false"/>
15186 <param name="x_weight" value=""/>
15187 <param name="y_weight" value=""/>
15188 <param name="x_datum_min" value="1e-15"/>
15189 <param name="x_datum_max" value="1000000000000000.0"/>
15190 <param name="y_datum_min" value="1e-15"/>
15191 <param name="y_datum_max" value="1000000000000000.0"/>
15192 </section>
15193 <section name="b_spline">
15194 <param name="wavelength" value="0.0"/>
15195 <param name="num_nodes" value="5"/>
15196 <param name="extrapolate" value="linear"/>
15197 <param name="boundary_condition" value="2"/>
15198 </section>
15199 <section name="lowess">
15200 <param name="span" value="0.666666666666667"/>
15201 <param name="num_iterations" value="3"/>
15202 <param name="delta" value="-1.0"/>
15203 <param name="interpolation_type" value="cspline"/>
15204 <param name="extrapolation_type" value="four-point-linear"/>
15205 </section>
15206 <section name="interpolated">
15207 <param name="interpolation_type" value="cspline"/>
15208 <param name="extrapolation_type" value="two-point-linear"/>
15209 </section>
15210 </section>
15211 <section name="align_algorithm">
15212 <param name="score_cutoff" value="false"/>
15213 <param name="min_score" value="0.05"/>
15214 <param name="min_run_occur" value="2"/>
15215 <param name="max_rt_shift" value="0.5"/>
15216 <param name="use_unassigned_peptides" value="true"/>
15217 <param name="use_feature_rt" value="true"/>
15218 </section>
15219 </section>
15220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15221 <output name="ctd_out" ftype="xml">
15222 <assert_contents>
15223 <is_valid_xml/>
15224 </assert_contents>
15225 </output>
15226 </test>
15227 <test expect_num_outputs="2">
15228 <conditional name="adv_opts_cond">
15229 <param name="adv_opts_selector" value="advanced"/>
15230 <param name="force" value="false"/>
15231 <param name="test" value="true"/>
15232 </conditional>
15233 <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
15234 <output_collection name="trafo_out" count="3"/>
15235 <section name="algorithm">
15236 <param name="model_type" value="b_spline"/>
15237 <section name="model">
15238 <param name="type" value="b_spline"/>
15239 <section name="linear">
15240 <param name="symmetric_regression" value="false"/>
15241 <param name="x_weight" value=""/>
15242 <param name="y_weight" value=""/>
15243 <param name="x_datum_min" value="1e-15"/>
15244 <param name="x_datum_max" value="1000000000000000.0"/>
15245 <param name="y_datum_min" value="1e-15"/>
15246 <param name="y_datum_max" value="1000000000000000.0"/>
15247 </section>
15248 <section name="b_spline">
15249 <param name="wavelength" value="0.0"/>
15250 <param name="num_nodes" value="5"/>
15251 <param name="extrapolate" value="linear"/>
15252 <param name="boundary_condition" value="2"/>
15253 </section>
15254 <section name="lowess">
15255 <param name="span" value="0.666666666666667"/>
15256 <param name="num_iterations" value="3"/>
15257 <param name="delta" value="-1.0"/>
15258 <param name="interpolation_type" value="cspline"/>
15259 <param name="extrapolation_type" value="four-point-linear"/>
15260 </section>
15261 <section name="interpolated">
15262 <param name="interpolation_type" value="cspline"/>
15263 <param name="extrapolation_type" value="two-point-linear"/>
15264 </section>
15265 </section>
15266 <section name="align_algorithm">
15267 <param name="score_cutoff" value="false"/>
15268 <param name="min_score" value="0.05"/>
15269 <param name="min_run_occur" value="2"/>
15270 <param name="max_rt_shift" value="0.5"/>
15271 <param name="use_unassigned_peptides" value="true"/>
15272 <param name="use_feature_rt" value="true"/>
15273 </section>
15274 </section>
15275 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15276 <output name="ctd_out" ftype="xml">
15277 <assert_contents>
15278 <is_valid_xml/>
15279 </assert_contents>
15280 </output>
15281 </test>
15282 </xml>
15283 <xml name="autotest_MapNormalizer">
15284 <test expect_num_outputs="2">
15285 <conditional name="adv_opts_cond">
15286 <param name="adv_opts_selector" value="advanced"/>
15287 <param name="force" value="false"/>
15288 <param name="test" value="true"/>
15289 </conditional>
15290 <param name="in" value="MapNormalizer_input.mzML"/>
15291 <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
15292 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15293 <output name="ctd_out" ftype="xml">
15294 <assert_contents>
15295 <is_valid_xml/>
15296 </assert_contents>
15297 </output>
15298 </test>
15299 </xml>
15300 <xml name="autotest_MapRTTransformer">
15301 <test expect_num_outputs="2">
15302 <conditional name="adv_opts_cond">
15303 <param name="adv_opts_selector" value="advanced"/>
15304 <param name="force" value="false"/>
15305 <param name="test" value="true"/>
15306 </conditional>
15307 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
15308 <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15309 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
15310 <param name="invert" value="false"/>
15311 <param name="store_original_rt" value="false"/>
15312 <section name="model">
15313 <param name="type" value="none"/>
15314 <section name="linear">
15315 <param name="symmetric_regression" value="false"/>
15316 <param name="x_weight" value=""/>
15317 <param name="y_weight" value=""/>
15318 <param name="x_datum_min" value="1e-15"/>
15319 <param name="x_datum_max" value="1000000000000000.0"/>
15320 <param name="y_datum_min" value="1e-15"/>
15321 <param name="y_datum_max" value="1000000000000000.0"/>
15322 </section>
15323 <section name="b_spline">
15324 <param name="wavelength" value="0.0"/>
15325 <param name="num_nodes" value="5"/>
15326 <param name="extrapolate" value="linear"/>
15327 <param name="boundary_condition" value="2"/>
15328 </section>
15329 <section name="lowess">
15330 <param name="span" value="0.666666666666667"/>
15331 <param name="num_iterations" value="3"/>
15332 <param name="delta" value="-1.0"/>
15333 <param name="interpolation_type" value="cspline"/>
15334 <param name="extrapolation_type" value="four-point-linear"/>
15335 </section>
15336 <section name="interpolated">
15337 <param name="interpolation_type" value="cspline"/>
15338 <param name="extrapolation_type" value="two-point-linear"/>
15339 </section>
15340 </section>
15341 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15342 <output name="ctd_out" ftype="xml">
15343 <assert_contents>
15344 <is_valid_xml/>
15345 </assert_contents>
15346 </output>
15347 </test>
15348 <test expect_num_outputs="2">
15349 <conditional name="adv_opts_cond">
15350 <param name="adv_opts_selector" value="advanced"/>
15351 <param name="force" value="false"/>
15352 <param name="test" value="true"/>
15353 </conditional>
15354 <param name="in" value="MapRTTransformer_2_input.mzML"/>
15355 <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
15356 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
15357 <param name="invert" value="false"/>
15358 <param name="store_original_rt" value="false"/>
15359 <section name="model">
15360 <param name="type" value="none"/>
15361 <section name="linear">
15362 <param name="symmetric_regression" value="false"/>
15363 <param name="x_weight" value=""/>
15364 <param name="y_weight" value=""/>
15365 <param name="x_datum_min" value="1e-15"/>
15366 <param name="x_datum_max" value="1000000000000000.0"/>
15367 <param name="y_datum_min" value="1e-15"/>
15368 <param name="y_datum_max" value="1000000000000000.0"/>
15369 </section>
15370 <section name="b_spline">
15371 <param name="wavelength" value="0.0"/>
15372 <param name="num_nodes" value="5"/>
15373 <param name="extrapolate" value="linear"/>
15374 <param name="boundary_condition" value="2"/>
15375 </section>
15376 <section name="lowess">
15377 <param name="span" value="0.666666666666667"/>
15378 <param name="num_iterations" value="3"/>
15379 <param name="delta" value="-1.0"/>
15380 <param name="interpolation_type" value="cspline"/>
15381 <param name="extrapolation_type" value="four-point-linear"/>
15382 </section>
15383 <section name="interpolated">
15384 <param name="interpolation_type" value="cspline"/>
15385 <param name="extrapolation_type" value="two-point-linear"/>
15386 </section>
15387 </section>
15388 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15389 <output name="ctd_out" ftype="xml">
15390 <assert_contents>
15391 <is_valid_xml/>
15392 </assert_contents>
15393 </output>
15394 </test>
15395 <test expect_num_outputs="2">
15396 <conditional name="adv_opts_cond">
15397 <param name="adv_opts_selector" value="advanced"/>
15398 <param name="force" value="false"/>
15399 <param name="test" value="true"/>
15400 </conditional>
15401 <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
15402 <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
15403 <param name="invert" value="true"/>
15404 <param name="store_original_rt" value="false"/>
15405 <section name="model">
15406 <param name="type" value="none"/>
15407 <section name="linear">
15408 <param name="symmetric_regression" value="false"/>
15409 <param name="x_weight" value=""/>
15410 <param name="y_weight" value=""/>
15411 <param name="x_datum_min" value="1e-15"/>
15412 <param name="x_datum_max" value="1000000000000000.0"/>
15413 <param name="y_datum_min" value="1e-15"/>
15414 <param name="y_datum_max" value="1000000000000000.0"/>
15415 </section>
15416 <section name="b_spline">
15417 <param name="wavelength" value="0.0"/>
15418 <param name="num_nodes" value="5"/>
15419 <param name="extrapolate" value="linear"/>
15420 <param name="boundary_condition" value="2"/>
15421 </section>
15422 <section name="lowess">
15423 <param name="span" value="0.666666666666667"/>
15424 <param name="num_iterations" value="3"/>
15425 <param name="delta" value="-1.0"/>
15426 <param name="interpolation_type" value="cspline"/>
15427 <param name="extrapolation_type" value="four-point-linear"/>
15428 </section>
15429 <section name="interpolated">
15430 <param name="interpolation_type" value="cspline"/>
15431 <param name="extrapolation_type" value="two-point-linear"/>
15432 </section>
15433 </section>
15434 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
15435 <output name="ctd_out" ftype="xml">
15436 <assert_contents>
15437 <is_valid_xml/>
15438 </assert_contents>
15439 </output>
15440 </test>
15441 <test expect_num_outputs="2">
15442 <conditional name="adv_opts_cond">
15443 <param name="adv_opts_selector" value="advanced"/>
15444 <param name="force" value="false"/>
15445 <param name="test" value="true"/>
15446 </conditional>
15447 <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
15448 <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
15449 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
15450 <param name="invert" value="false"/>
15451 <param name="store_original_rt" value="false"/>
15452 <section name="model">
15453 <param name="type" value="none"/>
15454 <section name="linear">
15455 <param name="symmetric_regression" value="false"/>
15456 <param name="x_weight" value=""/>
15457 <param name="y_weight" value=""/>
15458 <param name="x_datum_min" value="1e-15"/>
15459 <param name="x_datum_max" value="1000000000000000.0"/>
15460 <param name="y_datum_min" value="1e-15"/>
15461 <param name="y_datum_max" value="1000000000000000.0"/>
15462 </section>
15463 <section name="b_spline">
15464 <param name="wavelength" value="0.0"/>
15465 <param name="num_nodes" value="5"/>
15466 <param name="extrapolate" value="linear"/>
15467 <param name="boundary_condition" value="2"/>
15468 </section>
15469 <section name="lowess">
15470 <param name="span" value="0.666666666666667"/>
15471 <param name="num_iterations" value="3"/>
15472 <param name="delta" value="-1.0"/>
15473 <param name="interpolation_type" value="cspline"/>
15474 <param name="extrapolation_type" value="four-point-linear"/>
15475 </section>
15476 <section name="interpolated">
15477 <param name="interpolation_type" value="cspline"/>
15478 <param name="extrapolation_type" value="two-point-linear"/>
15479 </section>
15480 </section>
15481 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15482 <output name="ctd_out" ftype="xml">
15483 <assert_contents>
15484 <is_valid_xml/>
15485 </assert_contents>
15486 </output>
15487 </test>
15488 <test expect_num_outputs="2">
15489 <conditional name="adv_opts_cond">
15490 <param name="adv_opts_selector" value="advanced"/>
15491 <param name="force" value="false"/>
15492 <param name="test" value="true"/>
15493 </conditional>
15494 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
15495 <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15496 <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
15497 <param name="invert" value="false"/>
15498 <param name="store_original_rt" value="false"/>
15499 <section name="model">
15500 <param name="type" value="none"/>
15501 <section name="linear">
15502 <param name="symmetric_regression" value="false"/>
15503 <param name="x_weight" value=""/>
15504 <param name="y_weight" value=""/>
15505 <param name="x_datum_min" value="1e-15"/>
15506 <param name="x_datum_max" value="1000000000000000.0"/>
15507 <param name="y_datum_min" value="1e-15"/>
15508 <param name="y_datum_max" value="1000000000000000.0"/>
15509 </section>
15510 <section name="b_spline">
15511 <param name="wavelength" value="0.0"/>
15512 <param name="num_nodes" value="5"/>
15513 <param name="extrapolate" value="linear"/>
15514 <param name="boundary_condition" value="2"/>
15515 </section>
15516 <section name="lowess">
15517 <param name="span" value="0.666666666666667"/>
15518 <param name="num_iterations" value="3"/>
15519 <param name="delta" value="-1.0"/>
15520 <param name="interpolation_type" value="cspline"/>
15521 <param name="extrapolation_type" value="four-point-linear"/>
15522 </section>
15523 <section name="interpolated">
15524 <param name="interpolation_type" value="cspline"/>
15525 <param name="extrapolation_type" value="two-point-linear"/>
15526 </section>
15527 </section>
15528 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15529 <output name="ctd_out" ftype="xml">
15530 <assert_contents>
15531 <is_valid_xml/>
15532 </assert_contents>
15533 </output>
15534 </test>
15535 <test expect_num_outputs="2">
15536 <conditional name="adv_opts_cond">
15537 <param name="adv_opts_selector" value="advanced"/>
15538 <param name="force" value="false"/>
15539 <param name="test" value="true"/>
15540 </conditional>
15541 <param name="in" value="MapRTTransformer_1_input.featureXML"/>
15542 <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15543 <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
15544 <param name="invert" value="false"/>
15545 <param name="store_original_rt" value="true"/>
15546 <section name="model">
15547 <param name="type" value="none"/>
15548 <section name="linear">
15549 <param name="symmetric_regression" value="false"/>
15550 <param name="x_weight" value=""/>
15551 <param name="y_weight" value=""/>
15552 <param name="x_datum_min" value="1e-15"/>
15553 <param name="x_datum_max" value="1000000000000000.0"/>
15554 <param name="y_datum_min" value="1e-15"/>
15555 <param name="y_datum_max" value="1000000000000000.0"/>
15556 </section>
15557 <section name="b_spline">
15558 <param name="wavelength" value="0.0"/>
15559 <param name="num_nodes" value="5"/>
15560 <param name="extrapolate" value="linear"/>
15561 <param name="boundary_condition" value="2"/>
15562 </section>
15563 <section name="lowess">
15564 <param name="span" value="0.666666666666667"/>
15565 <param name="num_iterations" value="3"/>
15566 <param name="delta" value="-1.0"/>
15567 <param name="interpolation_type" value="cspline"/>
15568 <param name="extrapolation_type" value="four-point-linear"/>
15569 </section>
15570 <section name="interpolated">
15571 <param name="interpolation_type" value="cspline"/>
15572 <param name="extrapolation_type" value="two-point-linear"/>
15573 </section>
15574 </section>
15575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15576 <output name="ctd_out" ftype="xml">
15577 <assert_contents>
15578 <is_valid_xml/>
15579 </assert_contents>
15580 </output>
15581 </test>
15582 </xml>
15583 <xml name="autotest_MapStatistics">
15584 </xml>
15585 <xml name="autotest_MaRaClusterAdapter"/>
15586 <xml name="autotest_MascotAdapterOnline">
15587 <test expect_num_outputs="2">
15588 <conditional name="adv_opts_cond">
15589 <param name="adv_opts_selector" value="advanced"/>
15590 <param name="keep_protein_links" value="true"/>
15591 <param name="force" value="false"/>
15592 <param name="test" value="true"/>
15593 </conditional>
15594 <param name="in" value="spectra_comet.mzML"/>
15595 <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
15596 <section name="Mascot_parameters">
15597 <param name="database" value="SwissProt"/>
15598 <param name="search_type" value="MIS"/>
15599 <param name="enzyme" value="Trypsin"/>
15600 <param name="instrument" value="Default"/>
15601 <param name="missed_cleavages" value="1"/>
15602 <param name="precursor_mass_tolerance" value="3.0"/>
15603 <param name="precursor_error_units" value="Da"/>
15604 <param name="fragment_mass_tolerance" value="0.3"/>
15605 <param name="fragment_error_units" value="Da"/>
15606 <param name="charges" value="1,2,3"/>
15607 <param name="taxonomy" value="All entries"/>
15608 <param name="fixed_modifications" value=""/>
15609 <param name="variable_modifications" value=""/>
15610 <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
15611 <param name="mass_type" value="monoisotopic"/>
15612 <param name="number_of_hits" value="0"/>
15613 <param name="skip_spectrum_charges" value="false"/>
15614 <param name="search_title" value="OpenMS_search"/>
15615 <param name="username" value="OpenMS"/>
15616 <param name="email" value="openmsjenkins@gmail.com"/>
15617 </section>
15618 <section name="Mascot_server">
15619 <param name="hostname" value="www.matrixscience.com"/>
15620 <param name="host_port" value="80"/>
15621 <param name="server_path" value=""/>
15622 <param name="timeout" value="1500"/>
15623 <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/>
15624 <param name="use_proxy" value="false"/>
15625 <param name="proxy_host" value=""/>
15626 <param name="proxy_port" value="0"/>
15627 <param name="proxy_username" value=""/>
15628 <param name="proxy_password" value=""/>
15629 <param name="login" value="false"/>
15630 <param name="username" value=""/>
15631 <param name="password" value=""/>
15632 <param name="use_ssl" value="false"/>
15633 <param name="export_params" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0"/>
15634 <param name="skip_export" value="false"/>
15635 </section>
15636 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15637 <output name="ctd_out" ftype="xml">
15638 <assert_contents>
15639 <is_valid_xml/>
15640 </assert_contents>
15641 </output>
15642 </test>
15643 </xml>
15644 <xml name="autotest_MascotAdapter">
15645 <test expect_num_outputs="2">
15646 <conditional name="adv_opts_cond">
15647 <param name="adv_opts_selector" value="advanced"/>
15648 <param name="force" value="false"/>
15649 <param name="test" value="true"/>
15650 </conditional>
15651 <param name="in" value="MascotAdapter_1_input.mzData"/>
15652 <output name="out" file="output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
15653 <param name="mascot_in" value="true"/>
15654 <param name="mascot_out" value="false"/>
15655 <param name="instrument" value="ESI-TRAP"/>
15656 <param name="precursor_mass_tolerance" value="1.3"/>
15657 <param name="peak_mass_tolerance" value="0.3"/>
15658 <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
15659 <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
15660 <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
15661 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
15662 <param name="db" value="MSDB"/>
15663 <param name="hits" value="AUTO"/>
15664 <param name="cleavage" value="Trypsin"/>
15665 <param name="missed_cleavages" value="1"/>
15666 <param name="sig_threshold" value="0.05"/>
15667 <param name="pep_homol" value="1.0"/>
15668 <param name="pep_ident" value="1.0"/>
15669 <param name="pep_rank" value="1"/>
15670 <param name="prot_score" value="1.0"/>
15671 <param name="pep_score" value="1.0"/>
15672 <param name="pep_exp_z" value="1"/>
15673 <param name="show_unassigned" value="1"/>
15674 <param name="first_dim_rt" value="0.0"/>
15675 <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
15676 <param name="mass_type" value="Monoisotopic"/>
15677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15678 <output name="ctd_out" ftype="xml">
15679 <assert_contents>
15680 <is_valid_xml/>
15681 </assert_contents>
15682 </output>
15683 </test>
15684 <test expect_num_outputs="2">
15685 <conditional name="adv_opts_cond">
15686 <param name="adv_opts_selector" value="advanced"/>
15687 <param name="force" value="false"/>
15688 <param name="test" value="true"/>
15689 </conditional>
15690 <param name="in" value="MascotAdapter_2_input.mascotXML"/>
15691 <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
15692 <param name="mascot_in" value="false"/>
15693 <param name="mascot_out" value="true"/>
15694 <param name="instrument" value="Default"/>
15695 <param name="precursor_mass_tolerance" value="2.0"/>
15696 <param name="peak_mass_tolerance" value="1.0"/>
15697 <param name="taxonomy" value="All entries"/>
15698 <param name="modifications" value=""/>
15699 <param name="variable_modifications" value=""/>
15700 <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
15701 <param name="db" value="MSDB"/>
15702 <param name="hits" value="AUTO"/>
15703 <param name="cleavage" value="Trypsin"/>
15704 <param name="missed_cleavages" value="0"/>
15705 <param name="sig_threshold" value="0.05"/>
15706 <param name="pep_homol" value="1.0"/>
15707 <param name="pep_ident" value="1.0"/>
15708 <param name="pep_rank" value="1"/>
15709 <param name="prot_score" value="1.0"/>
15710 <param name="pep_score" value="1.0"/>
15711 <param name="pep_exp_z" value="1"/>
15712 <param name="show_unassigned" value="1"/>
15713 <param name="first_dim_rt" value="0.0"/>
15714 <param name="boundary" value=""/>
15715 <param name="mass_type" value="Monoisotopic"/>
15716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15717 <output name="ctd_out" ftype="xml">
15718 <assert_contents>
15719 <is_valid_xml/>
15720 </assert_contents>
15721 </output>
15722 </test>
15723 </xml>
15724 <xml name="autotest_MassCalculator">
15725 <test expect_num_outputs="2">
15726 <conditional name="adv_opts_cond">
15727 <param name="adv_opts_selector" value="advanced"/>
15728 <param name="force" value="false"/>
15729 <param name="test" value="true"/>
15730 </conditional>
15731 <param name="in" value="MassCalculator_1_input.txt" ftype="txt"/>
15732 <param name="in_seq" value=""/>
15733 <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="txt"/>
15734 <param name="charge" value="0 1"/>
15735 <param name="format" value="table"/>
15736 <param name="average_mass" value="false"/>
15737 <param name="fragment_type" value="full"/>
15738 <param name="separator" value=","/>
15739 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15740 <output name="ctd_out" ftype="xml">
15741 <assert_contents>
15742 <is_valid_xml/>
15743 </assert_contents>
15744 </output>
15745 </test>
15746 <test expect_num_outputs="2">
15747 <conditional name="adv_opts_cond">
15748 <param name="adv_opts_selector" value="advanced"/>
15749 <param name="force" value="false"/>
15750 <param name="test" value="true"/>
15751 </conditional>
15752 <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
15753 <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
15754 <param name="charge" value="1 2 3"/>
15755 <param name="format" value="list"/>
15756 <param name="average_mass" value="false"/>
15757 <param name="fragment_type" value="full"/>
15758 <param name="separator" value=""/>
15759 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
15760 <output name="ctd_out" ftype="xml">
15761 <assert_contents>
15762 <is_valid_xml/>
15763 </assert_contents>
15764 </output>
15765 </test>
15766 </xml>
15767 <xml name="autotest_MassTraceExtractor">
15768 <test expect_num_outputs="2">
15769 <conditional name="adv_opts_cond">
15770 <param name="adv_opts_selector" value="advanced"/>
15771 <param name="force" value="false"/>
15772 <param name="test" value="true"/>
15773 </conditional>
15774 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
15775 <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15776 <param name="out_type" value="featurexml"/>
15777 <section name="algorithm">
15778 <section name="common">
15779 <param name="noise_threshold_int" value="10.0"/>
15780 <param name="chrom_peak_snr" value="3.0"/>
15781 <param name="chrom_fwhm" value="5.0"/>
15782 </section>
15783 <section name="mtd">
15784 <param name="mass_error_ppm" value="20.0"/>
15785 <param name="reestimate_mt_sd" value="true"/>
15786 <param name="quant_method" value="area"/>
15787 <param name="trace_termination_criterion" value="outlier"/>
15788 <param name="trace_termination_outliers" value="5"/>
15789 <param name="min_sample_rate" value="0.5"/>
15790 <param name="min_trace_length" value="5.0"/>
15791 <param name="max_trace_length" value="-1.0"/>
15792 </section>
15793 <section name="epd">
15794 <param name="width_filtering" value="off"/>
15795 <param name="min_fwhm" value="3.0"/>
15796 <param name="max_fwhm" value="60.0"/>
15797 <param name="masstrace_snr_filtering" value="false"/>
15798 <param name="enabled" value="true"/>
15799 </section>
15800 </section>
15801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15802 <output name="ctd_out" ftype="xml">
15803 <assert_contents>
15804 <is_valid_xml/>
15805 </assert_contents>
15806 </output>
15807 </test>
15808 <test expect_num_outputs="2">
15809 <conditional name="adv_opts_cond">
15810 <param name="adv_opts_selector" value="advanced"/>
15811 <param name="force" value="false"/>
15812 <param name="test" value="true"/>
15813 </conditional>
15814 <param name="in" value="MassTraceExtractor_1_input.mzML"/>
15815 <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15816 <param name="out_type" value="featurexml"/>
15817 <section name="algorithm">
15818 <section name="common">
15819 <param name="noise_threshold_int" value="10.0"/>
15820 <param name="chrom_peak_snr" value="3.0"/>
15821 <param name="chrom_fwhm" value="5.0"/>
15822 </section>
15823 <section name="mtd">
15824 <param name="mass_error_ppm" value="20.0"/>
15825 <param name="reestimate_mt_sd" value="true"/>
15826 <param name="quant_method" value="area"/>
15827 <param name="trace_termination_criterion" value="outlier"/>
15828 <param name="trace_termination_outliers" value="5"/>
15829 <param name="min_sample_rate" value="0.5"/>
15830 <param name="min_trace_length" value="6.0"/>
15831 <param name="max_trace_length" value="12.0"/>
15832 </section>
15833 <section name="epd">
15834 <param name="width_filtering" value="off"/>
15835 <param name="min_fwhm" value="3.0"/>
15836 <param name="max_fwhm" value="60.0"/>
15837 <param name="masstrace_snr_filtering" value="false"/>
15838 <param name="enabled" value="true"/>
15839 </section>
15840 </section>
15841 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15842 <output name="ctd_out" ftype="xml">
15843 <assert_contents>
15844 <is_valid_xml/>
15845 </assert_contents>
15846 </output>
15847 </test>
15848 </xml>
15849 <xml name="autotest_MetaboliteAdductDecharger">
15850 </xml>
15851 <xml name="autotest_MetaboliteSpectralMatcher">
15852 </xml>
15853 <xml name="autotest_MetaProSIP">
15854 <test expect_num_outputs="3">
15855 <conditional name="adv_opts_cond">
15856 <param name="adv_opts_selector" value="advanced"/>
15857 <param name="min_correlation_distance_to_averagine" value="-1.0"/>
15858 <param name="pattern_15N_TIC_threshold" value="0.95"/>
15859 <param name="pattern_13C_TIC_threshold" value="0.95"/>
15860 <param name="pattern_2H_TIC_threshold" value="0.95"/>
15861 <param name="pattern_18O_TIC_threshold" value="0.95"/>
15862 <param name="heatmap_bins" value="20"/>
15863 <param name="observed_peak_fraction" value="0.5"/>
15864 <param name="min_consecutive_isotopes" value="2"/>
15865 <param name="score_plot_yaxis_min" value="0.0"/>
15866 <param name="collect_method" value="correlation_maximum"/>
15867 <param name="lowRIA_correlation_threshold" value="-1.0"/>
15868 <param name="force" value="false"/>
15869 <param name="test" value="true"/>
15870 </conditional>
15871 <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
15872 <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
15873 <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/>
15874 <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/>
15875 <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
15876 <param name="mz_tolerance_ppm" value="10.0"/>
15877 <param name="rt_tolerance_s" value="30.0"/>
15878 <param name="intensity_threshold" value="10.0"/>
15879 <param name="correlation_threshold" value="0.7"/>
15880 <param name="xic_threshold" value="0.7"/>
15881 <param name="decomposition_threshold" value="0.7"/>
15882 <param name="weight_merge_window" value="5.0"/>
15883 <param name="plot_extension" value="png"/>
15884 <param name="qc_output_directory" value=""/>
15885 <param name="labeling_element" value="C"/>
15886 <param name="use_unassigned_ids" value="false"/>
15887 <param name="use_averagine_ids" value="false"/>
15888 <param name="report_natural_peptides" value="false"/>
15889 <param name="filter_monoisotopic" value="false"/>
15890 <param name="cluster" value="false"/>
15891 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15892 <output name="ctd_out" ftype="xml">
15893 <assert_contents>
15894 <is_valid_xml/>
15895 </assert_contents>
15896 </output>
15897 </test>
15898 </xml>
15899 <xml name="autotest_MRMMapper">
15900 <test expect_num_outputs="2">
15901 <conditional name="adv_opts_cond">
15902 <param name="adv_opts_selector" value="advanced"/>
15903 <param name="force" value="false"/>
15904 <param name="test" value="true"/>
15905 </conditional>
15906 <param name="in" value="MRMMapping_input.chrom.mzML"/>
15907 <param name="tr" value="MRMMapping_input.TraML"/>
15908 <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
15909 <section name="algorithm">
15910 <param name="precursor_tolerance" value="0.3"/>
15911 <param name="product_tolerance" value="0.3"/>
15912 <param name="map_multiple_assays" value="false"/>
15913 <param name="error_on_unmapped" value="false"/>
15914 </section>
15915 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15916 <output name="ctd_out" ftype="xml">
15917 <assert_contents>
15918 <is_valid_xml/>
15919 </assert_contents>
15920 </output>
15921 </test>
15922 <test expect_num_outputs="2">
15923 <conditional name="adv_opts_cond">
15924 <param name="adv_opts_selector" value="advanced"/>
15925 <param name="force" value="false"/>
15926 <param name="test" value="true"/>
15927 </conditional>
15928 <param name="in" value="MRMMapping_input.chrom.mzML"/>
15929 <param name="tr" value="MRMMapping_input_2.TraML"/>
15930 <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
15931 <section name="algorithm">
15932 <param name="precursor_tolerance" value="0.01"/>
15933 <param name="product_tolerance" value="0.01"/>
15934 <param name="map_multiple_assays" value="false"/>
15935 <param name="error_on_unmapped" value="false"/>
15936 </section>
15937 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15938 <output name="ctd_out" ftype="xml">
15939 <assert_contents>
15940 <is_valid_xml/>
15941 </assert_contents>
15942 </output>
15943 </test>
15944 </xml>
15945 <xml name="autotest_MRMPairFinder">
15946 </xml>
15947 <xml name="autotest_MRMTransitionGroupPicker">
15948 <test expect_num_outputs="2">
15949 <conditional name="adv_opts_cond">
15950 <param name="adv_opts_selector" value="advanced"/>
15951 <param name="force" value="false"/>
15952 <param name="test" value="true"/>
15953 </conditional>
15954 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
15955 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
15956 <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
15957 <section name="algorithm">
15958 <param name="stop_after_feature" value="-1"/>
15959 <param name="stop_after_intensity_ratio" value="0.0001"/>
15960 <param name="min_peak_width" value="-1.0"/>
15961 <param name="peak_integration" value="original"/>
15962 <param name="background_subtraction" value="none"/>
15963 <param name="recalculate_peaks" value="false"/>
15964 <param name="use_precursors" value="false"/>
15965 <param name="use_consensus" value="true"/>
15966 <param name="recalculate_peaks_max_z" value="1.0"/>
15967 <param name="minimal_quality" value="-10000.0"/>
15968 <param name="resample_boundary" value="15.0"/>
15969 <param name="compute_peak_quality" value="false"/>
15970 <param name="compute_peak_shape_metrics" value="false"/>
15971 <param name="compute_total_mi" value="false"/>
15972 <param name="boundary_selection_method" value="largest"/>
15973 <section name="PeakPickerMRM">
15974 <param name="sgolay_frame_length" value="15"/>
15975 <param name="sgolay_polynomial_order" value="3"/>
15976 <param name="gauss_width" value="50.0"/>
15977 <param name="use_gauss" value="true"/>
15978 <param name="peak_width" value="40.0"/>
15979 <param name="signal_to_noise" value="1.0"/>
15980 <param name="sn_win_len" value="1000.0"/>
15981 <param name="sn_bin_count" value="30"/>
15982 <param name="write_sn_log_messages" value="false"/>
15983 <param name="remove_overlapping_peaks" value="true"/>
15984 <param name="method" value="legacy"/>
15985 </section>
15986 <section name="PeakIntegrator">
15987 <param name="integration_type" value="intensity_sum"/>
15988 <param name="baseline_type" value="base_to_base"/>
15989 <param name="fit_EMG" value="false"/>
15990 </section>
15991 </section>
15992 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
15993 <output name="ctd_out" ftype="xml">
15994 <assert_contents>
15995 <is_valid_xml/>
15996 </assert_contents>
15997 </output>
15998 </test>
15999 <test expect_num_outputs="2">
16000 <conditional name="adv_opts_cond">
16001 <param name="adv_opts_selector" value="advanced"/>
16002 <param name="force" value="false"/>
16003 <param name="test" value="true"/>
16004 </conditional>
16005 <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
16006 <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
16007 <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16008 <section name="algorithm">
16009 <param name="stop_after_feature" value="-1"/>
16010 <param name="stop_after_intensity_ratio" value="0.0001"/>
16011 <param name="min_peak_width" value="-1.0"/>
16012 <param name="peak_integration" value="original"/>
16013 <param name="background_subtraction" value="none"/>
16014 <param name="recalculate_peaks" value="false"/>
16015 <param name="use_precursors" value="false"/>
16016 <param name="use_consensus" value="true"/>
16017 <param name="recalculate_peaks_max_z" value="1.0"/>
16018 <param name="minimal_quality" value="-10000.0"/>
16019 <param name="resample_boundary" value="15.0"/>
16020 <param name="compute_peak_quality" value="false"/>
16021 <param name="compute_peak_shape_metrics" value="false"/>
16022 <param name="compute_total_mi" value="true"/>
16023 <param name="boundary_selection_method" value="largest"/>
16024 <section name="PeakPickerMRM">
16025 <param name="sgolay_frame_length" value="15"/>
16026 <param name="sgolay_polynomial_order" value="3"/>
16027 <param name="gauss_width" value="50.0"/>
16028 <param name="use_gauss" value="true"/>
16029 <param name="peak_width" value="40.0"/>
16030 <param name="signal_to_noise" value="1.0"/>
16031 <param name="sn_win_len" value="1000.0"/>
16032 <param name="sn_bin_count" value="30"/>
16033 <param name="write_sn_log_messages" value="false"/>
16034 <param name="remove_overlapping_peaks" value="true"/>
16035 <param name="method" value="legacy"/>
16036 </section>
16037 <section name="PeakIntegrator">
16038 <param name="integration_type" value="intensity_sum"/>
16039 <param name="baseline_type" value="base_to_base"/>
16040 <param name="fit_EMG" value="false"/>
16041 </section>
16042 </section>
16043 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16044 <output name="ctd_out" ftype="xml">
16045 <assert_contents>
16046 <is_valid_xml/>
16047 </assert_contents>
16048 </output>
16049 </test>
16050 </xml>
16051 <xml name="autotest_MSFraggerAdapter"/>
16052 <xml name="autotest_MSGFPlusAdapter">
16053 <test expect_num_outputs="3">
16054 <conditional name="adv_opts_cond">
16055 <param name="adv_opts_selector" value="advanced"/>
16056 <param name="legacy_conversion" value="false"/>
16057 <param name="force" value="false"/>
16058 <param name="test" value="true"/>
16059 </conditional>
16060 <param name="in" value="spectra.mzML"/>
16061 <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16062 <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
16063 <param name="database" value="proteins.fasta"/>
16064 <param name="add_decoys" value="false"/>
16065 <param name="precursor_mass_tolerance" value="10.0"/>
16066 <param name="precursor_error_units" value="ppm"/>
16067 <param name="isotope_error_range" value="0,1"/>
16068 <param name="fragment_method" value="from_spectrum"/>
16069 <param name="instrument" value="high_res"/>
16070 <param name="enzyme" value="Trypsin/P"/>
16071 <param name="protocol" value="none"/>
16072 <param name="tryptic" value="fully"/>
16073 <param name="min_precursor_charge" value="1"/>
16074 <param name="max_precursor_charge" value="3"/>
16075 <param name="min_peptide_length" value="6"/>
16076 <param name="max_peptide_length" value="40"/>
16077 <param name="matches_per_spec" value="1"/>
16078 <param name="add_features" value="false"/>
16079 <param name="max_mods" value="2"/>
16080 <param name="fixed_modifications" value=""/>
16081 <param name="variable_modifications" value="Oxidation (M)"/>
16082 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
16083 <output name="ctd_out" ftype="xml">
16084 <assert_contents>
16085 <is_valid_xml/>
16086 </assert_contents>
16087 </output>
16088 </test>
16089 </xml>
16090 <xml name="autotest_MSSimulator">
16091 </xml>
16092 <xml name="autotest_MSstatsConverter">
16093 <test expect_num_outputs="2">
16094 <conditional name="adv_opts_cond">
16095 <param name="adv_opts_selector" value="advanced"/>
16096 <param name="retention_time_summarization_method" value="max"/>
16097 <param name="force" value="false"/>
16098 <param name="test" value="true"/>
16099 </conditional>
16100 <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
16101 <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
16102 <param name="method" value="LFQ"/>
16103 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16104 <param name="msstats_condition" value="MSstats_Condition"/>
16105 <param name="msstats_mixture" value="MSstats_Mixture"/>
16106 <param name="labeled_reference_peptides" value="false"/>
16107 <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16108 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16109 <output name="ctd_out" ftype="xml">
16110 <assert_contents>
16111 <is_valid_xml/>
16112 </assert_contents>
16113 </output>
16114 </test>
16115 <test expect_num_outputs="2">
16116 <conditional name="adv_opts_cond">
16117 <param name="adv_opts_selector" value="advanced"/>
16118 <param name="retention_time_summarization_method" value="manual"/>
16119 <param name="force" value="false"/>
16120 <param name="test" value="true"/>
16121 </conditional>
16122 <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
16123 <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
16124 <param name="method" value="ISO"/>
16125 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16126 <param name="msstats_condition" value="MSstats_Condition"/>
16127 <param name="msstats_mixture" value="MSstats_Mixture"/>
16128 <param name="labeled_reference_peptides" value="false"/>
16129 <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16131 <output name="ctd_out" ftype="xml">
16132 <assert_contents>
16133 <is_valid_xml/>
16134 </assert_contents>
16135 </output>
16136 </test>
16137 <test expect_num_outputs="2">
16138 <conditional name="adv_opts_cond">
16139 <param name="adv_opts_selector" value="advanced"/>
16140 <param name="retention_time_summarization_method" value="manual"/>
16141 <param name="force" value="false"/>
16142 <param name="test" value="true"/>
16143 </conditional>
16144 <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
16145 <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
16146 <param name="method" value="ISO"/>
16147 <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
16148 <param name="msstats_condition" value="MSstats_Condition"/>
16149 <param name="msstats_mixture" value="MSstats_Mixture"/>
16150 <param name="labeled_reference_peptides" value="false"/>
16151 <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
16152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16153 <output name="ctd_out" ftype="xml">
16154 <assert_contents>
16155 <is_valid_xml/>
16156 </assert_contents>
16157 </output>
16158 </test>
16159 </xml>
16160 <xml name="autotest_MultiplexResolver">
16161 <test expect_num_outputs="3">
16162 <conditional name="adv_opts_cond">
16163 <param name="adv_opts_selector" value="advanced"/>
16164 <param name="force" value="false"/>
16165 <param name="test" value="true"/>
16166 </conditional>
16167 <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
16168 <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16169 <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16170 <section name="algorithm">
16171 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
16172 <param name="missed_cleavages" value="1"/>
16173 <param name="mass_tolerance" value="0.1"/>
16174 <param name="mz_tolerance" value="10"/>
16175 <param name="rt_tolerance" value="5"/>
16176 </section>
16177 <section name="labels">
16178 <param name="Arg6" value="6.0201290268"/>
16179 <param name="Arg10" value="10.0082686"/>
16180 <param name="Lys4" value="4.0251069836"/>
16181 <param name="Lys6" value="6.0201290268"/>
16182 <param name="Lys8" value="8.0141988132"/>
16183 <param name="Leu3" value="3.01883"/>
16184 <param name="Dimethyl0" value="28.0313"/>
16185 <param name="Dimethyl4" value="32.056407"/>
16186 <param name="Dimethyl6" value="34.063117"/>
16187 <param name="Dimethyl8" value="36.07567"/>
16188 <param name="ICPL0" value="105.021464"/>
16189 <param name="ICPL4" value="109.046571"/>
16190 <param name="ICPL6" value="111.041593"/>
16191 <param name="ICPL10" value="115.0667"/>
16192 </section>
16193 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16194 <output name="ctd_out" ftype="xml">
16195 <assert_contents>
16196 <is_valid_xml/>
16197 </assert_contents>
16198 </output>
16199 </test>
16200 <test expect_num_outputs="3">
16201 <conditional name="adv_opts_cond">
16202 <param name="adv_opts_selector" value="advanced"/>
16203 <param name="force" value="false"/>
16204 <param name="test" value="true"/>
16205 </conditional>
16206 <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
16207 <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16208 <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16209 <section name="algorithm">
16210 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
16211 <param name="missed_cleavages" value="4"/>
16212 <param name="mass_tolerance" value="0.1"/>
16213 <param name="mz_tolerance" value="10"/>
16214 <param name="rt_tolerance" value="5"/>
16215 </section>
16216 <section name="labels">
16217 <param name="Arg6" value="6.0201290268"/>
16218 <param name="Arg10" value="10.0082686"/>
16219 <param name="Lys4" value="4.0251069836"/>
16220 <param name="Lys6" value="6.0201290268"/>
16221 <param name="Lys8" value="8.0141988132"/>
16222 <param name="Leu3" value="3.01883"/>
16223 <param name="Dimethyl0" value="28.0313"/>
16224 <param name="Dimethyl4" value="32.056407"/>
16225 <param name="Dimethyl6" value="34.063117"/>
16226 <param name="Dimethyl8" value="36.07567"/>
16227 <param name="ICPL0" value="105.021464"/>
16228 <param name="ICPL4" value="109.046571"/>
16229 <param name="ICPL6" value="111.041593"/>
16230 <param name="ICPL10" value="115.0667"/>
16231 </section>
16232 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16233 <output name="ctd_out" ftype="xml">
16234 <assert_contents>
16235 <is_valid_xml/>
16236 </assert_contents>
16237 </output>
16238 </test>
16239 <test expect_num_outputs="3">
16240 <conditional name="adv_opts_cond">
16241 <param name="adv_opts_selector" value="advanced"/>
16242 <param name="force" value="false"/>
16243 <param name="test" value="true"/>
16244 </conditional>
16245 <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
16246 <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16247 <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16248 <section name="algorithm">
16249 <param name="labels" value="[][Leu3]"/>
16250 <param name="missed_cleavages" value="2"/>
16251 <param name="mass_tolerance" value="0.1"/>
16252 <param name="mz_tolerance" value="10"/>
16253 <param name="rt_tolerance" value="5"/>
16254 </section>
16255 <section name="labels">
16256 <param name="Arg6" value="6.0201290268"/>
16257 <param name="Arg10" value="10.0082686"/>
16258 <param name="Lys4" value="4.0251069836"/>
16259 <param name="Lys6" value="6.0201290268"/>
16260 <param name="Lys8" value="8.0141988132"/>
16261 <param name="Leu3" value="3.01883"/>
16262 <param name="Dimethyl0" value="28.0313"/>
16263 <param name="Dimethyl4" value="32.056407"/>
16264 <param name="Dimethyl6" value="34.063117"/>
16265 <param name="Dimethyl8" value="36.07567"/>
16266 <param name="ICPL0" value="105.021464"/>
16267 <param name="ICPL4" value="109.046571"/>
16268 <param name="ICPL6" value="111.041593"/>
16269 <param name="ICPL10" value="115.0667"/>
16270 </section>
16271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16272 <output name="ctd_out" ftype="xml">
16273 <assert_contents>
16274 <is_valid_xml/>
16275 </assert_contents>
16276 </output>
16277 </test>
16278 <test expect_num_outputs="3">
16279 <conditional name="adv_opts_cond">
16280 <param name="adv_opts_selector" value="advanced"/>
16281 <param name="force" value="false"/>
16282 <param name="test" value="true"/>
16283 </conditional>
16284 <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
16285 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
16286 <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16287 <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
16288 <section name="algorithm">
16289 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
16290 <param name="missed_cleavages" value="3"/>
16291 <param name="mass_tolerance" value="0.1"/>
16292 <param name="mz_tolerance" value="10"/>
16293 <param name="rt_tolerance" value="10"/>
16294 </section>
16295 <section name="labels">
16296 <param name="Arg6" value="6.0201290268"/>
16297 <param name="Arg10" value="10.0082686"/>
16298 <param name="Lys4" value="4.0251069836"/>
16299 <param name="Lys6" value="6.0201290268"/>
16300 <param name="Lys8" value="8.0141988132"/>
16301 <param name="Leu3" value="3.01883"/>
16302 <param name="Dimethyl0" value="28.0313"/>
16303 <param name="Dimethyl4" value="32.056407"/>
16304 <param name="Dimethyl6" value="34.063117"/>
16305 <param name="Dimethyl8" value="36.07567"/>
16306 <param name="ICPL0" value="105.021464"/>
16307 <param name="ICPL4" value="109.046571"/>
16308 <param name="ICPL6" value="111.041593"/>
16309 <param name="ICPL10" value="115.0667"/>
16310 </section>
16311 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
16312 <output name="ctd_out" ftype="xml">
16313 <assert_contents>
16314 <is_valid_xml/>
16315 </assert_contents>
16316 </output>
16317 </test>
16318 </xml>
16319 <xml name="autotest_MyriMatchAdapter">
16320 <test expect_num_outputs="2">
16321 <conditional name="adv_opts_cond">
16322 <param name="adv_opts_selector" value="advanced"/>
16323 <param name="MinPeptideMass" value="0.0"/>
16324 <param name="MaxPeptideMass" value="10000.0"/>
16325 <param name="MinPeptideLength" value="5"/>
16326 <param name="MaxPeptideLength" value="75"/>
16327 <param name="UseSmartPlusThreeModel" value="false"/>
16328 <param name="NumIntensityClasses" value="3"/>
16329 <param name="ClassSizeMultiplier" value="2.0"/>
16330 <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/>
16331 <param name="SpectrumListFilters" value=""/>
16332 <param name="ignoreConfigErrors" value="false"/>
16333 <param name="force" value="false"/>
16334 <param name="test" value="true"/>
16335 </conditional>
16336 <param name="in" value="spectra.mzML"/>
16337 <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16338 <param name="precursor_mass_tolerance" value="5.0"/>
16339 <param name="precursor_mass_tolerance_unit" value="ppm"/>
16340 <param name="precursor_mass_tolerance_avg" value="false"/>
16341 <param name="fragment_mass_tolerance" value="0.3"/>
16342 <param name="fragment_mass_tolerance_unit" value="Da"/>
16343 <param name="database" value="proteins.fasta"/>
16344 <param name="fixed_modifications" value=""/>
16345 <param name="variable_modifications" value="Oxidation (M)"/>
16346 <param name="NumChargeStates" value="3"/>
16347 <param name="TicCutoffPercentage" value="0.98"/>
16348 <param name="MaxDynamicMods" value="2"/>
16349 <param name="MaxResultRank" value="5"/>
16350 <param name="CleavageRules" value=""/>
16351 <param name="MinTerminiCleavages" value="2"/>
16352 <param name="MaxMissedCleavages" value="-1"/>
16353 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16354 <output name="ctd_out" ftype="xml">
16355 <assert_contents>
16356 <is_valid_xml/>
16357 </assert_contents>
16358 </output>
16359 </test>
16360 </xml>
16361 <xml name="autotest_MzMLSplitter"/>
16362 <xml name="autotest_MzTabExporter">
16363 <test expect_num_outputs="2">
16364 <conditional name="adv_opts_cond">
16365 <param name="adv_opts_selector" value="advanced"/>
16366 <param name="first_run_inference_only" value="false"/>
16367 <param name="force" value="false"/>
16368 <param name="test" value="true"/>
16369 </conditional>
16370 <param name="in" value="MzTabExporter_1_input.consensusXML"/>
16371 <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
16372 <param name="opt_columns" value="subfeatures"/>
16373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16374 <output name="ctd_out" ftype="xml">
16375 <assert_contents>
16376 <is_valid_xml/>
16377 </assert_contents>
16378 </output>
16379 </test>
16380 <test expect_num_outputs="2">
16381 <conditional name="adv_opts_cond">
16382 <param name="adv_opts_selector" value="advanced"/>
16383 <param name="first_run_inference_only" value="false"/>
16384 <param name="force" value="false"/>
16385 <param name="test" value="true"/>
16386 </conditional>
16387 <param name="in" value="MzTabExporter_2_input.idXML"/>
16388 <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
16389 <param name="opt_columns" value="subfeatures"/>
16390 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16391 <output name="ctd_out" ftype="xml">
16392 <assert_contents>
16393 <is_valid_xml/>
16394 </assert_contents>
16395 </output>
16396 </test>
16397 <test expect_num_outputs="2">
16398 <conditional name="adv_opts_cond">
16399 <param name="adv_opts_selector" value="advanced"/>
16400 <param name="first_run_inference_only" value="false"/>
16401 <param name="force" value="false"/>
16402 <param name="test" value="true"/>
16403 </conditional>
16404 <param name="in" value="MzTabExporter_3_input.featureXML"/>
16405 <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
16406 <param name="opt_columns" value="subfeatures"/>
16407 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16408 <output name="ctd_out" ftype="xml">
16409 <assert_contents>
16410 <is_valid_xml/>
16411 </assert_contents>
16412 </output>
16413 </test>
16414 </xml>
16415 <xml name="autotest_NoiseFilterGaussian">
16416 <test expect_num_outputs="2">
16417 <conditional name="adv_opts_cond">
16418 <param name="adv_opts_selector" value="advanced"/>
16419 <param name="processOption" value="inmemory"/>
16420 <param name="force" value="false"/>
16421 <param name="test" value="true"/>
16422 </conditional>
16423 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
16424 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16425 <section name="algorithm">
16426 <param name="gaussian_width" value="1.0"/>
16427 <param name="ppm_tolerance" value="10.0"/>
16428 <param name="use_ppm_tolerance" value="false"/>
16429 </section>
16430 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16431 <output name="ctd_out" ftype="xml">
16432 <assert_contents>
16433 <is_valid_xml/>
16434 </assert_contents>
16435 </output>
16436 </test>
16437 <test expect_num_outputs="2">
16438 <conditional name="adv_opts_cond">
16439 <param name="adv_opts_selector" value="advanced"/>
16440 <param name="processOption" value="inmemory"/>
16441 <param name="force" value="false"/>
16442 <param name="test" value="true"/>
16443 </conditional>
16444 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
16445 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16446 <section name="algorithm">
16447 <param name="gaussian_width" value="50.0"/>
16448 <param name="ppm_tolerance" value="10.0"/>
16449 <param name="use_ppm_tolerance" value="false"/>
16450 </section>
16451 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16452 <output name="ctd_out" ftype="xml">
16453 <assert_contents>
16454 <is_valid_xml/>
16455 </assert_contents>
16456 </output>
16457 </test>
16458 <test expect_num_outputs="2">
16459 <conditional name="adv_opts_cond">
16460 <param name="adv_opts_selector" value="advanced"/>
16461 <param name="processOption" value="lowmemory"/>
16462 <param name="force" value="false"/>
16463 <param name="test" value="true"/>
16464 </conditional>
16465 <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
16466 <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16467 <section name="algorithm">
16468 <param name="gaussian_width" value="1.0"/>
16469 <param name="ppm_tolerance" value="10.0"/>
16470 <param name="use_ppm_tolerance" value="false"/>
16471 </section>
16472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16473 <output name="ctd_out" ftype="xml">
16474 <assert_contents>
16475 <is_valid_xml/>
16476 </assert_contents>
16477 </output>
16478 </test>
16479 <test expect_num_outputs="2">
16480 <conditional name="adv_opts_cond">
16481 <param name="adv_opts_selector" value="advanced"/>
16482 <param name="processOption" value="lowmemory"/>
16483 <param name="force" value="false"/>
16484 <param name="test" value="true"/>
16485 </conditional>
16486 <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
16487 <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16488 <section name="algorithm">
16489 <param name="gaussian_width" value="50.0"/>
16490 <param name="ppm_tolerance" value="10.0"/>
16491 <param name="use_ppm_tolerance" value="false"/>
16492 </section>
16493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16494 <output name="ctd_out" ftype="xml">
16495 <assert_contents>
16496 <is_valid_xml/>
16497 </assert_contents>
16498 </output>
16499 </test>
16500 </xml>
16501 <xml name="autotest_NoiseFilterSGolay">
16502 <test expect_num_outputs="2">
16503 <conditional name="adv_opts_cond">
16504 <param name="adv_opts_selector" value="advanced"/>
16505 <param name="processOption" value="inmemory"/>
16506 <param name="force" value="false"/>
16507 <param name="test" value="true"/>
16508 </conditional>
16509 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
16510 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16511 <section name="algorithm">
16512 <param name="frame_length" value="9"/>
16513 <param name="polynomial_order" value="4"/>
16514 </section>
16515 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16516 <output name="ctd_out" ftype="xml">
16517 <assert_contents>
16518 <is_valid_xml/>
16519 </assert_contents>
16520 </output>
16521 </test>
16522 <test expect_num_outputs="2">
16523 <conditional name="adv_opts_cond">
16524 <param name="adv_opts_selector" value="advanced"/>
16525 <param name="processOption" value="inmemory"/>
16526 <param name="force" value="false"/>
16527 <param name="test" value="true"/>
16528 </conditional>
16529 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
16530 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16531 <section name="algorithm">
16532 <param name="frame_length" value="11"/>
16533 <param name="polynomial_order" value="4"/>
16534 </section>
16535 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16536 <output name="ctd_out" ftype="xml">
16537 <assert_contents>
16538 <is_valid_xml/>
16539 </assert_contents>
16540 </output>
16541 </test>
16542 <test expect_num_outputs="2">
16543 <conditional name="adv_opts_cond">
16544 <param name="adv_opts_selector" value="advanced"/>
16545 <param name="processOption" value="lowmemory"/>
16546 <param name="force" value="false"/>
16547 <param name="test" value="true"/>
16548 </conditional>
16549 <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
16550 <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16551 <section name="algorithm">
16552 <param name="frame_length" value="9"/>
16553 <param name="polynomial_order" value="4"/>
16554 </section>
16555 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16556 <output name="ctd_out" ftype="xml">
16557 <assert_contents>
16558 <is_valid_xml/>
16559 </assert_contents>
16560 </output>
16561 </test>
16562 <test expect_num_outputs="2">
16563 <conditional name="adv_opts_cond">
16564 <param name="adv_opts_selector" value="advanced"/>
16565 <param name="processOption" value="lowmemory"/>
16566 <param name="force" value="false"/>
16567 <param name="test" value="true"/>
16568 </conditional>
16569 <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
16570 <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
16571 <section name="algorithm">
16572 <param name="frame_length" value="11"/>
16573 <param name="polynomial_order" value="4"/>
16574 </section>
16575 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16576 <output name="ctd_out" ftype="xml">
16577 <assert_contents>
16578 <is_valid_xml/>
16579 </assert_contents>
16580 </output>
16581 </test>
16582 </xml>
16583 <xml name="autotest_NovorAdapter"/>
16584 <xml name="autotest_NucleicAcidSearchEngine">
16585 <test expect_num_outputs="3">
16586 <conditional name="adv_opts_cond">
16587 <param name="adv_opts_selector" value="advanced"/>
16588 <param name="decharge_ms2" value="false"/>
16589 <param name="force" value="false"/>
16590 <param name="test" value="true"/>
16591 </conditional>
16592 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
16593 <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
16594 <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
16595 <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16596 <section name="precursor">
16597 <param name="mass_tolerance" value="5.0"/>
16598 <param name="mass_tolerance_unit" value="ppm"/>
16599 <param name="min_charge" value="-2"/>
16600 <param name="max_charge" value="-14"/>
16601 <param name="include_unknown_charge" value="true"/>
16602 <param name="use_avg_mass" value="false"/>
16603 <param name="use_adducts" value="false"/>
16604 <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
16605 <param name="isotopes" value="0 1 2"/>
16606 </section>
16607 <section name="fragment">
16608 <param name="mass_tolerance" value="5.0"/>
16609 <param name="mass_tolerance_unit" value="ppm"/>
16610 <param name="ions" value="a-B,c,w,y"/>
16611 </section>
16612 <section name="modifications">
16613 <param name="variable" value=""/>
16614 <param name="variable_max_per_oligo" value="2"/>
16615 <param name="resolve_ambiguities" value="false"/>
16616 </section>
16617 <section name="oligo">
16618 <param name="min_size" value="5"/>
16619 <param name="max_size" value="0"/>
16620 <param name="missed_cleavages" value="22"/>
16621 <param name="enzyme" value="no cleavage"/>
16622 </section>
16623 <section name="report">
16624 <param name="top_hits" value="1"/>
16625 </section>
16626 <section name="fdr">
16627 <param name="decoy_pattern" value="DECOY_"/>
16628 <param name="cutoff" value="0.05"/>
16629 <param name="remove_decoys" value="true"/>
16630 </section>
16631 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/>
16632 <output name="ctd_out" ftype="xml">
16633 <assert_contents>
16634 <is_valid_xml/>
16635 </assert_contents>
16636 </output>
16637 </test>
16638 </xml>
16639 <xml name="autotest_OMSSAAdapter">
16640 <test expect_num_outputs="2">
16641 <conditional name="adv_opts_cond">
16642 <param name="adv_opts_selector" value="advanced"/>
16643 <param name="pc" value="1"/>
16644 <param name="hs" value="4"/>
16645 <param name="tez" value="1"/>
16646 <param name="tom" value="0"/>
16647 <param name="tem" value="0"/>
16648 <param name="tex" value="1446.94"/>
16649 <param name="zt" value="3"/>
16650 <param name="z1" value="0.95"/>
16651 <param name="zc" value="1"/>
16652 <param name="zcc" value="2"/>
16653 <param name="zoh" value="2"/>
16654 <param name="no" value="4"/>
16655 <param name="nox" value="40"/>
16656 <param name="i" value="1,4"/>
16657 <param name="sp" value="100"/>
16658 <param name="sb1" value="1"/>
16659 <param name="sct" value="0"/>
16660 <param name="x" value="0"/>
16661 <param name="hm" value="2"/>
16662 <param name="ht" value="6"/>
16663 <param name="mm" value="128"/>
16664 <param name="mnm" value="false"/>
16665 <param name="is" value="0.0"/>
16666 <param name="ir" value="0.0"/>
16667 <param name="ii" value="0.0"/>
16668 <param name="chunk_size" value="0"/>
16669 <param name="force" value="false"/>
16670 <param name="test" value="true"/>
16671 </conditional>
16672 <param name="in" value="spectra.mzML"/>
16673 <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16674 <param name="precursor_mass_tolerance" value="5.0"/>
16675 <param name="precursor_error_units" value="ppm"/>
16676 <param name="fragment_mass_tolerance" value="0.3"/>
16677 <param name="database" value="proteins.fasta"/>
16678 <param name="min_precursor_charge" value="1"/>
16679 <param name="max_precursor_charge" value="3"/>
16680 <param name="fixed_modifications" value=""/>
16681 <param name="variable_modifications" value="Oxidation (M)"/>
16682 <param name="v" value="1"/>
16683 <param name="enzyme" value="Trypsin"/>
16684 <param name="hl" value="30"/>
16685 <param name="he" value="1.0"/>
16686 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16687 <output name="ctd_out" ftype="xml">
16688 <assert_contents>
16689 <is_valid_xml/>
16690 </assert_contents>
16691 </output>
16692 </test>
16693 </xml>
16694 <xml name="autotest_OpenPepXLLF">
16695 <test expect_num_outputs="5">
16696 <conditional name="adv_opts_cond">
16697 <param name="adv_opts_selector" value="advanced"/>
16698 <param name="force" value="false"/>
16699 <param name="test" value="true"/>
16700 </conditional>
16701 <param name="in" value="OpenPepXLLF_input.mzML"/>
16702 <param name="database" value="OpenPepXLLF_input.fasta"/>
16703 <param name="decoy_string" value="decoy"/>
16704 <param name="decoy_prefix" value="true"/>
16705 <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16706 <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
16707 <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
16708 <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
16709 <section name="precursor">
16710 <param name="mass_tolerance" value="10.0"/>
16711 <param name="mass_tolerance_unit" value="ppm"/>
16712 <param name="min_charge" value="3"/>
16713 <param name="max_charge" value="7"/>
16714 <param name="corrections" value="2 1 0"/>
16715 </section>
16716 <section name="fragment">
16717 <param name="mass_tolerance" value="20.0"/>
16718 <param name="mass_tolerance_xlinks" value="20.0"/>
16719 <param name="mass_tolerance_unit" value="ppm"/>
16720 </section>
16721 <section name="modifications">
16722 <param name="fixed" value=""/>
16723 <param name="variable" value=""/>
16724 <param name="variable_max_per_peptide" value="2"/>
16725 </section>
16726 <section name="peptide">
16727 <param name="min_size" value="5"/>
16728 <param name="missed_cleavages" value="2"/>
16729 <param name="enzyme" value="Trypsin"/>
16730 </section>
16731 <section name="cross_linker">
16732 <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
16733 <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
16734 <param name="mass" value="138.0680796"/>
16735 <param name="mass_mono_link" value="156.07864431 155.094628715"/>
16736 <param name="name" value="DSS"/>
16737 </section>
16738 <section name="algorithm">
16739 <param name="number_top_hits" value="5"/>
16740 <param name="deisotope" value="auto"/>
16741 <param name="use_sequence_tags" value="false"/>
16742 <param name="sequence_tag_min_length" value="2"/>
16743 </section>
16744 <section name="ions">
16745 <param name="b_ions" value="true"/>
16746 <param name="y_ions" value="true"/>
16747 <param name="a_ions" value="false"/>
16748 <param name="x_ions" value="false"/>
16749 <param name="c_ions" value="false"/>
16750 <param name="z_ions" value="false"/>
16751 <param name="neutral_losses" value="true"/>
16752 </section>
16753 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
16754 <output name="ctd_out" ftype="xml">
16755 <assert_contents>
16756 <is_valid_xml/>
16757 </assert_contents>
16758 </output>
16759 </test>
16760 <test expect_num_outputs="2">
16761 <conditional name="adv_opts_cond">
16762 <param name="adv_opts_selector" value="advanced"/>
16763 <param name="force" value="false"/>
16764 <param name="test" value="true"/>
16765 </conditional>
16766 <param name="in" value="OpenPepXLLF_input2.mzML"/>
16767 <param name="database" value="OpenPepXLLF_input2.fasta"/>
16768 <param name="decoy_string" value="decoy_"/>
16769 <param name="decoy_prefix" value="true"/>
16770 <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16771 <section name="precursor">
16772 <param name="mass_tolerance" value="10.0"/>
16773 <param name="mass_tolerance_unit" value="ppm"/>
16774 <param name="min_charge" value="3"/>
16775 <param name="max_charge" value="7"/>
16776 <param name="corrections" value="1 0"/>
16777 </section>
16778 <section name="fragment">
16779 <param name="mass_tolerance" value="0.2"/>
16780 <param name="mass_tolerance_xlinks" value="0.3"/>
16781 <param name="mass_tolerance_unit" value="Da"/>
16782 </section>
16783 <section name="modifications">
16784 <param name="fixed" value="Carbamidomethyl (C)"/>
16785 <param name="variable" value="Oxidation (M)"/>
16786 <param name="variable_max_per_peptide" value="1"/>
16787 </section>
16788 <section name="peptide">
16789 <param name="min_size" value="5"/>
16790 <param name="missed_cleavages" value="1"/>
16791 <param name="enzyme" value="Trypsin"/>
16792 </section>
16793 <section name="cross_linker">
16794 <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
16795 <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
16796 <param name="mass" value="-18.010595"/>
16797 <param name="mass_mono_link" value=""/>
16798 <param name="name" value="DMTMM"/>
16799 </section>
16800 <section name="algorithm">
16801 <param name="number_top_hits" value="1"/>
16802 <param name="deisotope" value="auto"/>
16803 <param name="use_sequence_tags" value="false"/>
16804 <param name="sequence_tag_min_length" value="2"/>
16805 </section>
16806 <section name="ions">
16807 <param name="b_ions" value="true"/>
16808 <param name="y_ions" value="true"/>
16809 <param name="a_ions" value="false"/>
16810 <param name="x_ions" value="false"/>
16811 <param name="c_ions" value="false"/>
16812 <param name="z_ions" value="false"/>
16813 <param name="neutral_losses" value="true"/>
16814 </section>
16815 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
16816 <output name="ctd_out" ftype="xml">
16817 <assert_contents>
16818 <is_valid_xml/>
16819 </assert_contents>
16820 </output>
16821 </test>
16822 </xml>
16823 <xml name="autotest_OpenPepXL">
16824 <test expect_num_outputs="5">
16825 <conditional name="adv_opts_cond">
16826 <param name="adv_opts_selector" value="advanced"/>
16827 <param name="force" value="false"/>
16828 <param name="test" value="true"/>
16829 </conditional>
16830 <param name="in" value="OpenPepXL_input.mzML"/>
16831 <param name="consensus" value="OpenPepXL_input.consensusXML"/>
16832 <param name="database" value="OpenPepXL_input.fasta"/>
16833 <param name="decoy_string" value="decoy"/>
16834 <param name="decoy_prefix" value="true"/>
16835 <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
16836 <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
16837 <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
16838 <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
16839 <section name="precursor">
16840 <param name="mass_tolerance" value="10.0"/>
16841 <param name="mass_tolerance_unit" value="ppm"/>
16842 <param name="min_charge" value="3"/>
16843 <param name="max_charge" value="7"/>
16844 <param name="corrections" value="2 1 0"/>
16845 </section>
16846 <section name="fragment">
16847 <param name="mass_tolerance" value="0.2"/>
16848 <param name="mass_tolerance_xlinks" value="0.3"/>
16849 <param name="mass_tolerance_unit" value="Da"/>
16850 </section>
16851 <section name="modifications">
16852 <param name="fixed" value=""/>
16853 <param name="variable" value=""/>
16854 <param name="variable_max_per_peptide" value="2"/>
16855 </section>
16856 <section name="peptide">
16857 <param name="min_size" value="5"/>
16858 <param name="missed_cleavages" value="2"/>
16859 <param name="enzyme" value="Trypsin"/>
16860 </section>
16861 <section name="cross_linker">
16862 <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
16863 <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
16864 <param name="mass_light" value="138.0680796"/>
16865 <param name="mass_iso_shift" value="12.075321"/>
16866 <param name="mass_mono_link" value="156.07864431 155.094628715"/>
16867 <param name="name" value="DSS"/>
16868 </section>
16869 <section name="algorithm">
16870 <param name="number_top_hits" value="5"/>
16871 <param name="deisotope" value="auto"/>
16872 </section>
16873 <section name="ions">
16874 <param name="b_ions" value="true"/>
16875 <param name="y_ions" value="true"/>
16876 <param name="a_ions" value="false"/>
16877 <param name="x_ions" value="false"/>
16878 <param name="c_ions" value="false"/>
16879 <param name="z_ions" value="false"/>
16880 <param name="neutral_losses" value="true"/>
16881 </section>
16882 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
16883 <output name="ctd_out" ftype="xml">
16884 <assert_contents>
16885 <is_valid_xml/>
16886 </assert_contents>
16887 </output>
16888 </test>
16889 </xml>
16890 <xml name="autotest_OpenSwathAnalyzer">
16891 <test expect_num_outputs="2">
16892 <conditional name="adv_opts_cond">
16893 <param name="adv_opts_selector" value="advanced"/>
16894 <param name="force" value="false"/>
16895 <param name="test" value="true"/>
16896 </conditional>
16897 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
16898 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
16899 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
16900 <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
16901 <param name="no_strict" value="false"/>
16902 <param name="min_upper_edge_dist" value="0.0"/>
16903 <section name="model">
16904 <param name="type" value="linear"/>
16905 <param name="symmetric_regression" value="false"/>
16906 </section>
16907 <section name="algorithm">
16908 <param name="stop_report_after_feature" value="-1"/>
16909 <param name="rt_extraction_window" value="-1.0"/>
16910 <param name="rt_normalization_factor" value="1.0"/>
16911 <param name="quantification_cutoff" value="0.0"/>
16912 <param name="write_convex_hull" value="false"/>
16913 <param name="spectrum_addition_method" value="simple"/>
16914 <param name="add_up_spectra" value="1"/>
16915 <param name="spacing_for_spectra_resampling" value="0.005"/>
16916 <param name="uis_threshold_sn" value="-1"/>
16917 <param name="uis_threshold_peak_area" value="0"/>
16918 <param name="scoring_model" value="default"/>
16919 <param name="im_extra_drift" value="0.0"/>
16920 <section name="TransitionGroupPicker">
16921 <param name="stop_after_feature" value="-1"/>
16922 <param name="stop_after_intensity_ratio" value="0.0001"/>
16923 <param name="min_peak_width" value="-1.0"/>
16924 <param name="peak_integration" value="original"/>
16925 <param name="background_subtraction" value="none"/>
16926 <param name="recalculate_peaks" value="false"/>
16927 <param name="use_precursors" value="false"/>
16928 <param name="use_consensus" value="true"/>
16929 <param name="recalculate_peaks_max_z" value="1.0"/>
16930 <param name="minimal_quality" value="-10000.0"/>
16931 <param name="resample_boundary" value="15.0"/>
16932 <param name="compute_peak_quality" value="false"/>
16933 <param name="compute_peak_shape_metrics" value="false"/>
16934 <param name="compute_total_mi" value="false"/>
16935 <param name="boundary_selection_method" value="largest"/>
16936 <section name="PeakPickerMRM">
16937 <param name="sgolay_frame_length" value="15"/>
16938 <param name="sgolay_polynomial_order" value="3"/>
16939 <param name="gauss_width" value="50.0"/>
16940 <param name="use_gauss" value="true"/>
16941 <param name="peak_width" value="40.0"/>
16942 <param name="signal_to_noise" value="1.0"/>
16943 <param name="sn_win_len" value="1000.0"/>
16944 <param name="sn_bin_count" value="30"/>
16945 <param name="write_sn_log_messages" value="false"/>
16946 <param name="remove_overlapping_peaks" value="false"/>
16947 <param name="method" value="legacy"/>
16948 </section>
16949 <section name="PeakIntegrator">
16950 <param name="integration_type" value="intensity_sum"/>
16951 <param name="baseline_type" value="base_to_base"/>
16952 <param name="fit_EMG" value="false"/>
16953 </section>
16954 </section>
16955 <section name="DIAScoring">
16956 <param name="dia_extraction_window" value="0.05"/>
16957 <param name="dia_extraction_unit" value="Th"/>
16958 <param name="dia_centroided" value="false"/>
16959 <param name="dia_byseries_intensity_min" value="300.0"/>
16960 <param name="dia_byseries_ppm_diff" value="10.0"/>
16961 <param name="dia_nr_isotopes" value="4"/>
16962 <param name="dia_nr_charges" value="4"/>
16963 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
16964 </section>
16965 <section name="EMGScoring">
16966 <param name="interpolation_step" value="0.2"/>
16967 <param name="tolerance_stdev_bounding_box" value="3.0"/>
16968 <param name="max_iteration" value="500"/>
16969 <section name="statistics">
16970 <param name="mean" value="1.0"/>
16971 <param name="variance" value="1.0"/>
16972 </section>
16973 </section>
16974 <section name="Scores">
16975 <param name="use_shape_score" value="true"/>
16976 <param name="use_coelution_score" value="true"/>
16977 <param name="use_rt_score" value="true"/>
16978 <param name="use_library_score" value="true"/>
16979 <param name="use_elution_model_score" value="true"/>
16980 <param name="use_intensity_score" value="true"/>
16981 <param name="use_nr_peaks_score" value="true"/>
16982 <param name="use_total_xic_score" value="true"/>
16983 <param name="use_total_mi_score" value="false"/>
16984 <param name="use_sn_score" value="true"/>
16985 <param name="use_mi_score" value="false"/>
16986 <param name="use_dia_scores" value="true"/>
16987 <param name="use_ms1_correlation" value="false"/>
16988 <param name="use_sonar_scores" value="false"/>
16989 <param name="use_ion_mobility_scores" value="false"/>
16990 <param name="use_ms1_fullscan" value="false"/>
16991 <param name="use_ms1_mi" value="false"/>
16992 <param name="use_uis_scores" value="false"/>
16993 </section>
16994 </section>
16995 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
16996 <output name="ctd_out" ftype="xml">
16997 <assert_contents>
16998 <is_valid_xml/>
16999 </assert_contents>
17000 </output>
17001 </test>
17002 <test expect_num_outputs="2">
17003 <conditional name="adv_opts_cond">
17004 <param name="adv_opts_selector" value="advanced"/>
17005 <param name="force" value="false"/>
17006 <param name="test" value="true"/>
17007 </conditional>
17008 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17009 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17010 <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17011 <param name="no_strict" value="false"/>
17012 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
17013 <param name="min_upper_edge_dist" value="0.0"/>
17014 <section name="model">
17015 <param name="type" value="linear"/>
17016 <param name="symmetric_regression" value="false"/>
17017 </section>
17018 <section name="algorithm">
17019 <param name="stop_report_after_feature" value="-1"/>
17020 <param name="rt_extraction_window" value="-1.0"/>
17021 <param name="rt_normalization_factor" value="1.0"/>
17022 <param name="quantification_cutoff" value="0.0"/>
17023 <param name="write_convex_hull" value="false"/>
17024 <param name="spectrum_addition_method" value="simple"/>
17025 <param name="add_up_spectra" value="1"/>
17026 <param name="spacing_for_spectra_resampling" value="0.005"/>
17027 <param name="uis_threshold_sn" value="-1"/>
17028 <param name="uis_threshold_peak_area" value="0"/>
17029 <param name="scoring_model" value="default"/>
17030 <param name="im_extra_drift" value="0.0"/>
17031 <section name="TransitionGroupPicker">
17032 <param name="stop_after_feature" value="-1"/>
17033 <param name="stop_after_intensity_ratio" value="0.0001"/>
17034 <param name="min_peak_width" value="-1.0"/>
17035 <param name="peak_integration" value="original"/>
17036 <param name="background_subtraction" value="none"/>
17037 <param name="recalculate_peaks" value="false"/>
17038 <param name="use_precursors" value="false"/>
17039 <param name="use_consensus" value="true"/>
17040 <param name="recalculate_peaks_max_z" value="1.0"/>
17041 <param name="minimal_quality" value="-10000.0"/>
17042 <param name="resample_boundary" value="15.0"/>
17043 <param name="compute_peak_quality" value="false"/>
17044 <param name="compute_peak_shape_metrics" value="false"/>
17045 <param name="compute_total_mi" value="false"/>
17046 <param name="boundary_selection_method" value="largest"/>
17047 <section name="PeakPickerMRM">
17048 <param name="sgolay_frame_length" value="15"/>
17049 <param name="sgolay_polynomial_order" value="3"/>
17050 <param name="gauss_width" value="50.0"/>
17051 <param name="use_gauss" value="true"/>
17052 <param name="peak_width" value="40.0"/>
17053 <param name="signal_to_noise" value="1.0"/>
17054 <param name="sn_win_len" value="1000.0"/>
17055 <param name="sn_bin_count" value="30"/>
17056 <param name="write_sn_log_messages" value="false"/>
17057 <param name="remove_overlapping_peaks" value="false"/>
17058 <param name="method" value="legacy"/>
17059 </section>
17060 <section name="PeakIntegrator">
17061 <param name="integration_type" value="intensity_sum"/>
17062 <param name="baseline_type" value="base_to_base"/>
17063 <param name="fit_EMG" value="false"/>
17064 </section>
17065 </section>
17066 <section name="DIAScoring">
17067 <param name="dia_extraction_window" value="0.05"/>
17068 <param name="dia_extraction_unit" value="Th"/>
17069 <param name="dia_centroided" value="false"/>
17070 <param name="dia_byseries_intensity_min" value="300.0"/>
17071 <param name="dia_byseries_ppm_diff" value="10.0"/>
17072 <param name="dia_nr_isotopes" value="4"/>
17073 <param name="dia_nr_charges" value="4"/>
17074 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17075 </section>
17076 <section name="EMGScoring">
17077 <param name="interpolation_step" value="0.2"/>
17078 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17079 <param name="max_iteration" value="500"/>
17080 <section name="statistics">
17081 <param name="mean" value="1.0"/>
17082 <param name="variance" value="1.0"/>
17083 </section>
17084 </section>
17085 <section name="Scores">
17086 <param name="use_shape_score" value="true"/>
17087 <param name="use_coelution_score" value="true"/>
17088 <param name="use_rt_score" value="true"/>
17089 <param name="use_library_score" value="true"/>
17090 <param name="use_elution_model_score" value="true"/>
17091 <param name="use_intensity_score" value="true"/>
17092 <param name="use_nr_peaks_score" value="true"/>
17093 <param name="use_total_xic_score" value="true"/>
17094 <param name="use_total_mi_score" value="false"/>
17095 <param name="use_sn_score" value="true"/>
17096 <param name="use_mi_score" value="false"/>
17097 <param name="use_dia_scores" value="true"/>
17098 <param name="use_ms1_correlation" value="false"/>
17099 <param name="use_sonar_scores" value="false"/>
17100 <param name="use_ion_mobility_scores" value="false"/>
17101 <param name="use_ms1_fullscan" value="false"/>
17102 <param name="use_ms1_mi" value="false"/>
17103 <param name="use_uis_scores" value="false"/>
17104 </section>
17105 </section>
17106 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17107 <output name="ctd_out" ftype="xml">
17108 <assert_contents>
17109 <is_valid_xml/>
17110 </assert_contents>
17111 </output>
17112 </test>
17113 <test expect_num_outputs="2">
17114 <conditional name="adv_opts_cond">
17115 <param name="adv_opts_selector" value="advanced"/>
17116 <param name="force" value="false"/>
17117 <param name="test" value="true"/>
17118 </conditional>
17119 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17120 <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
17121 <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17122 <param name="no_strict" value="false"/>
17123 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
17124 <param name="min_upper_edge_dist" value="0.0"/>
17125 <section name="model">
17126 <param name="type" value="linear"/>
17127 <param name="symmetric_regression" value="false"/>
17128 </section>
17129 <section name="algorithm">
17130 <param name="stop_report_after_feature" value="-1"/>
17131 <param name="rt_extraction_window" value="-1.0"/>
17132 <param name="rt_normalization_factor" value="1.0"/>
17133 <param name="quantification_cutoff" value="0.0"/>
17134 <param name="write_convex_hull" value="false"/>
17135 <param name="spectrum_addition_method" value="simple"/>
17136 <param name="add_up_spectra" value="1"/>
17137 <param name="spacing_for_spectra_resampling" value="0.005"/>
17138 <param name="uis_threshold_sn" value="-1"/>
17139 <param name="uis_threshold_peak_area" value="0"/>
17140 <param name="scoring_model" value="default"/>
17141 <param name="im_extra_drift" value="0.0"/>
17142 <section name="TransitionGroupPicker">
17143 <param name="stop_after_feature" value="-1"/>
17144 <param name="stop_after_intensity_ratio" value="0.0001"/>
17145 <param name="min_peak_width" value="-1.0"/>
17146 <param name="peak_integration" value="original"/>
17147 <param name="background_subtraction" value="none"/>
17148 <param name="recalculate_peaks" value="false"/>
17149 <param name="use_precursors" value="false"/>
17150 <param name="use_consensus" value="true"/>
17151 <param name="recalculate_peaks_max_z" value="1.0"/>
17152 <param name="minimal_quality" value="-10000.0"/>
17153 <param name="resample_boundary" value="15.0"/>
17154 <param name="compute_peak_quality" value="false"/>
17155 <param name="compute_peak_shape_metrics" value="false"/>
17156 <param name="compute_total_mi" value="false"/>
17157 <param name="boundary_selection_method" value="largest"/>
17158 <section name="PeakPickerMRM">
17159 <param name="sgolay_frame_length" value="15"/>
17160 <param name="sgolay_polynomial_order" value="3"/>
17161 <param name="gauss_width" value="50.0"/>
17162 <param name="use_gauss" value="true"/>
17163 <param name="peak_width" value="40.0"/>
17164 <param name="signal_to_noise" value="1.0"/>
17165 <param name="sn_win_len" value="1000.0"/>
17166 <param name="sn_bin_count" value="30"/>
17167 <param name="write_sn_log_messages" value="true"/>
17168 <param name="remove_overlapping_peaks" value="false"/>
17169 <param name="method" value="legacy"/>
17170 </section>
17171 <section name="PeakIntegrator">
17172 <param name="integration_type" value="intensity_sum"/>
17173 <param name="baseline_type" value="base_to_base"/>
17174 <param name="fit_EMG" value="false"/>
17175 </section>
17176 </section>
17177 <section name="DIAScoring">
17178 <param name="dia_extraction_window" value="0.05"/>
17179 <param name="dia_extraction_unit" value="Th"/>
17180 <param name="dia_centroided" value="false"/>
17181 <param name="dia_byseries_intensity_min" value="8.0"/>
17182 <param name="dia_byseries_ppm_diff" value="15.0"/>
17183 <param name="dia_nr_isotopes" value="4"/>
17184 <param name="dia_nr_charges" value="4"/>
17185 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17186 </section>
17187 <section name="EMGScoring">
17188 <param name="interpolation_step" value="0.2"/>
17189 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17190 <param name="max_iteration" value="500"/>
17191 <section name="statistics">
17192 <param name="mean" value="1.0"/>
17193 <param name="variance" value="1.0"/>
17194 </section>
17195 </section>
17196 <section name="Scores">
17197 <param name="use_shape_score" value="true"/>
17198 <param name="use_coelution_score" value="true"/>
17199 <param name="use_rt_score" value="true"/>
17200 <param name="use_library_score" value="true"/>
17201 <param name="use_elution_model_score" value="true"/>
17202 <param name="use_intensity_score" value="true"/>
17203 <param name="use_nr_peaks_score" value="true"/>
17204 <param name="use_total_xic_score" value="true"/>
17205 <param name="use_total_mi_score" value="false"/>
17206 <param name="use_sn_score" value="true"/>
17207 <param name="use_mi_score" value="false"/>
17208 <param name="use_dia_scores" value="true"/>
17209 <param name="use_ms1_correlation" value="false"/>
17210 <param name="use_sonar_scores" value="false"/>
17211 <param name="use_ion_mobility_scores" value="false"/>
17212 <param name="use_ms1_fullscan" value="false"/>
17213 <param name="use_ms1_mi" value="false"/>
17214 <param name="use_uis_scores" value="false"/>
17215 </section>
17216 </section>
17217 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17218 <output name="ctd_out" ftype="xml">
17219 <assert_contents>
17220 <is_valid_xml/>
17221 </assert_contents>
17222 </output>
17223 </test>
17224 <test expect_num_outputs="2">
17225 <conditional name="adv_opts_cond">
17226 <param name="adv_opts_selector" value="advanced"/>
17227 <param name="force" value="false"/>
17228 <param name="test" value="true"/>
17229 </conditional>
17230 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17231 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17232 <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17233 <param name="no_strict" value="false"/>
17234 <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
17235 <param name="min_upper_edge_dist" value="0.0"/>
17236 <section name="model">
17237 <param name="type" value="linear"/>
17238 <param name="symmetric_regression" value="false"/>
17239 </section>
17240 <section name="algorithm">
17241 <param name="stop_report_after_feature" value="-1"/>
17242 <param name="rt_extraction_window" value="-1.0"/>
17243 <param name="rt_normalization_factor" value="1.0"/>
17244 <param name="quantification_cutoff" value="0.0"/>
17245 <param name="write_convex_hull" value="false"/>
17246 <param name="spectrum_addition_method" value="simple"/>
17247 <param name="add_up_spectra" value="1"/>
17248 <param name="spacing_for_spectra_resampling" value="0.005"/>
17249 <param name="uis_threshold_sn" value="-1"/>
17250 <param name="uis_threshold_peak_area" value="0"/>
17251 <param name="scoring_model" value="default"/>
17252 <param name="im_extra_drift" value="0.0"/>
17253 <section name="TransitionGroupPicker">
17254 <param name="stop_after_feature" value="-1"/>
17255 <param name="stop_after_intensity_ratio" value="0.0001"/>
17256 <param name="min_peak_width" value="-1.0"/>
17257 <param name="peak_integration" value="original"/>
17258 <param name="background_subtraction" value="none"/>
17259 <param name="recalculate_peaks" value="false"/>
17260 <param name="use_precursors" value="false"/>
17261 <param name="use_consensus" value="true"/>
17262 <param name="recalculate_peaks_max_z" value="1.0"/>
17263 <param name="minimal_quality" value="-10000.0"/>
17264 <param name="resample_boundary" value="15.0"/>
17265 <param name="compute_peak_quality" value="false"/>
17266 <param name="compute_peak_shape_metrics" value="false"/>
17267 <param name="compute_total_mi" value="false"/>
17268 <param name="boundary_selection_method" value="largest"/>
17269 <section name="PeakPickerMRM">
17270 <param name="sgolay_frame_length" value="15"/>
17271 <param name="sgolay_polynomial_order" value="3"/>
17272 <param name="gauss_width" value="50.0"/>
17273 <param name="use_gauss" value="true"/>
17274 <param name="peak_width" value="40.0"/>
17275 <param name="signal_to_noise" value="1.0"/>
17276 <param name="sn_win_len" value="1000.0"/>
17277 <param name="sn_bin_count" value="30"/>
17278 <param name="write_sn_log_messages" value="true"/>
17279 <param name="remove_overlapping_peaks" value="false"/>
17280 <param name="method" value="legacy"/>
17281 </section>
17282 <section name="PeakIntegrator">
17283 <param name="integration_type" value="intensity_sum"/>
17284 <param name="baseline_type" value="base_to_base"/>
17285 <param name="fit_EMG" value="false"/>
17286 </section>
17287 </section>
17288 <section name="DIAScoring">
17289 <param name="dia_extraction_window" value="0.05"/>
17290 <param name="dia_extraction_unit" value="Th"/>
17291 <param name="dia_centroided" value="false"/>
17292 <param name="dia_byseries_intensity_min" value="8.0"/>
17293 <param name="dia_byseries_ppm_diff" value="15.0"/>
17294 <param name="dia_nr_isotopes" value="4"/>
17295 <param name="dia_nr_charges" value="4"/>
17296 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17297 </section>
17298 <section name="EMGScoring">
17299 <param name="interpolation_step" value="0.2"/>
17300 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17301 <param name="max_iteration" value="500"/>
17302 <section name="statistics">
17303 <param name="mean" value="1.0"/>
17304 <param name="variance" value="1.0"/>
17305 </section>
17306 </section>
17307 <section name="Scores">
17308 <param name="use_shape_score" value="true"/>
17309 <param name="use_coelution_score" value="true"/>
17310 <param name="use_rt_score" value="true"/>
17311 <param name="use_library_score" value="true"/>
17312 <param name="use_elution_model_score" value="true"/>
17313 <param name="use_intensity_score" value="true"/>
17314 <param name="use_nr_peaks_score" value="true"/>
17315 <param name="use_total_xic_score" value="true"/>
17316 <param name="use_total_mi_score" value="false"/>
17317 <param name="use_sn_score" value="true"/>
17318 <param name="use_mi_score" value="false"/>
17319 <param name="use_dia_scores" value="true"/>
17320 <param name="use_ms1_correlation" value="false"/>
17321 <param name="use_sonar_scores" value="false"/>
17322 <param name="use_ion_mobility_scores" value="false"/>
17323 <param name="use_ms1_fullscan" value="false"/>
17324 <param name="use_ms1_mi" value="false"/>
17325 <param name="use_uis_scores" value="false"/>
17326 </section>
17327 </section>
17328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17329 <output name="ctd_out" ftype="xml">
17330 <assert_contents>
17331 <is_valid_xml/>
17332 </assert_contents>
17333 </output>
17334 </test>
17335 <test expect_num_outputs="2">
17336 <conditional name="adv_opts_cond">
17337 <param name="adv_opts_selector" value="advanced"/>
17338 <param name="force" value="false"/>
17339 <param name="test" value="true"/>
17340 </conditional>
17341 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17342 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17343 <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17344 <param name="no_strict" value="false"/>
17345 <param name="min_upper_edge_dist" value="0.0"/>
17346 <section name="model">
17347 <param name="type" value="linear"/>
17348 <param name="symmetric_regression" value="false"/>
17349 </section>
17350 <section name="algorithm">
17351 <param name="stop_report_after_feature" value="-1"/>
17352 <param name="rt_extraction_window" value="-1.0"/>
17353 <param name="rt_normalization_factor" value="1.0"/>
17354 <param name="quantification_cutoff" value="0.0"/>
17355 <param name="write_convex_hull" value="false"/>
17356 <param name="spectrum_addition_method" value="simple"/>
17357 <param name="add_up_spectra" value="1"/>
17358 <param name="spacing_for_spectra_resampling" value="0.005"/>
17359 <param name="uis_threshold_sn" value="-1"/>
17360 <param name="uis_threshold_peak_area" value="0"/>
17361 <param name="scoring_model" value="default"/>
17362 <param name="im_extra_drift" value="0.0"/>
17363 <section name="TransitionGroupPicker">
17364 <param name="stop_after_feature" value="-1"/>
17365 <param name="stop_after_intensity_ratio" value="0.0001"/>
17366 <param name="min_peak_width" value="-1.0"/>
17367 <param name="peak_integration" value="original"/>
17368 <param name="background_subtraction" value="original"/>
17369 <param name="recalculate_peaks" value="false"/>
17370 <param name="use_precursors" value="false"/>
17371 <param name="use_consensus" value="true"/>
17372 <param name="recalculate_peaks_max_z" value="1.0"/>
17373 <param name="minimal_quality" value="-10000.0"/>
17374 <param name="resample_boundary" value="15.0"/>
17375 <param name="compute_peak_quality" value="false"/>
17376 <param name="compute_peak_shape_metrics" value="false"/>
17377 <param name="compute_total_mi" value="false"/>
17378 <param name="boundary_selection_method" value="largest"/>
17379 <section name="PeakPickerMRM">
17380 <param name="sgolay_frame_length" value="15"/>
17381 <param name="sgolay_polynomial_order" value="3"/>
17382 <param name="gauss_width" value="50.0"/>
17383 <param name="use_gauss" value="true"/>
17384 <param name="peak_width" value="40.0"/>
17385 <param name="signal_to_noise" value="1.0"/>
17386 <param name="sn_win_len" value="1000.0"/>
17387 <param name="sn_bin_count" value="30"/>
17388 <param name="write_sn_log_messages" value="true"/>
17389 <param name="remove_overlapping_peaks" value="false"/>
17390 <param name="method" value="legacy"/>
17391 </section>
17392 <section name="PeakIntegrator">
17393 <param name="integration_type" value="intensity_sum"/>
17394 <param name="baseline_type" value="base_to_base"/>
17395 <param name="fit_EMG" value="false"/>
17396 </section>
17397 </section>
17398 <section name="DIAScoring">
17399 <param name="dia_extraction_window" value="0.05"/>
17400 <param name="dia_extraction_unit" value="Th"/>
17401 <param name="dia_centroided" value="false"/>
17402 <param name="dia_byseries_intensity_min" value="300.0"/>
17403 <param name="dia_byseries_ppm_diff" value="10.0"/>
17404 <param name="dia_nr_isotopes" value="4"/>
17405 <param name="dia_nr_charges" value="4"/>
17406 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17407 </section>
17408 <section name="EMGScoring">
17409 <param name="interpolation_step" value="0.2"/>
17410 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17411 <param name="max_iteration" value="500"/>
17412 <section name="statistics">
17413 <param name="mean" value="1.0"/>
17414 <param name="variance" value="1.0"/>
17415 </section>
17416 </section>
17417 <section name="Scores">
17418 <param name="use_shape_score" value="true"/>
17419 <param name="use_coelution_score" value="true"/>
17420 <param name="use_rt_score" value="true"/>
17421 <param name="use_library_score" value="true"/>
17422 <param name="use_elution_model_score" value="true"/>
17423 <param name="use_intensity_score" value="true"/>
17424 <param name="use_nr_peaks_score" value="true"/>
17425 <param name="use_total_xic_score" value="true"/>
17426 <param name="use_total_mi_score" value="false"/>
17427 <param name="use_sn_score" value="true"/>
17428 <param name="use_mi_score" value="false"/>
17429 <param name="use_dia_scores" value="true"/>
17430 <param name="use_ms1_correlation" value="false"/>
17431 <param name="use_sonar_scores" value="false"/>
17432 <param name="use_ion_mobility_scores" value="false"/>
17433 <param name="use_ms1_fullscan" value="false"/>
17434 <param name="use_ms1_mi" value="false"/>
17435 <param name="use_uis_scores" value="false"/>
17436 </section>
17437 </section>
17438 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17439 <output name="ctd_out" ftype="xml">
17440 <assert_contents>
17441 <is_valid_xml/>
17442 </assert_contents>
17443 </output>
17444 </test>
17445 <test expect_num_outputs="2">
17446 <conditional name="adv_opts_cond">
17447 <param name="adv_opts_selector" value="advanced"/>
17448 <param name="force" value="false"/>
17449 <param name="test" value="true"/>
17450 </conditional>
17451 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17452 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17453 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
17454 <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17455 <param name="no_strict" value="false"/>
17456 <param name="min_upper_edge_dist" value="0.0"/>
17457 <section name="model">
17458 <param name="type" value="linear"/>
17459 <param name="symmetric_regression" value="false"/>
17460 </section>
17461 <section name="algorithm">
17462 <param name="stop_report_after_feature" value="-1"/>
17463 <param name="rt_extraction_window" value="-1.0"/>
17464 <param name="rt_normalization_factor" value="1.0"/>
17465 <param name="quantification_cutoff" value="0.0"/>
17466 <param name="write_convex_hull" value="false"/>
17467 <param name="spectrum_addition_method" value="simple"/>
17468 <param name="add_up_spectra" value="1"/>
17469 <param name="spacing_for_spectra_resampling" value="0.005"/>
17470 <param name="uis_threshold_sn" value="-1"/>
17471 <param name="uis_threshold_peak_area" value="0"/>
17472 <param name="scoring_model" value="default"/>
17473 <param name="im_extra_drift" value="0.0"/>
17474 <section name="TransitionGroupPicker">
17475 <param name="stop_after_feature" value="-1"/>
17476 <param name="stop_after_intensity_ratio" value="0.0001"/>
17477 <param name="min_peak_width" value="-1.0"/>
17478 <param name="peak_integration" value="original"/>
17479 <param name="background_subtraction" value="none"/>
17480 <param name="recalculate_peaks" value="false"/>
17481 <param name="use_precursors" value="false"/>
17482 <param name="use_consensus" value="true"/>
17483 <param name="recalculate_peaks_max_z" value="1.0"/>
17484 <param name="minimal_quality" value="-10000.0"/>
17485 <param name="resample_boundary" value="15.0"/>
17486 <param name="compute_peak_quality" value="false"/>
17487 <param name="compute_peak_shape_metrics" value="false"/>
17488 <param name="compute_total_mi" value="false"/>
17489 <param name="boundary_selection_method" value="largest"/>
17490 <section name="PeakPickerMRM">
17491 <param name="sgolay_frame_length" value="15"/>
17492 <param name="sgolay_polynomial_order" value="3"/>
17493 <param name="gauss_width" value="50.0"/>
17494 <param name="use_gauss" value="true"/>
17495 <param name="peak_width" value="40.0"/>
17496 <param name="signal_to_noise" value="1.0"/>
17497 <param name="sn_win_len" value="1000.0"/>
17498 <param name="sn_bin_count" value="30"/>
17499 <param name="write_sn_log_messages" value="false"/>
17500 <param name="remove_overlapping_peaks" value="false"/>
17501 <param name="method" value="legacy"/>
17502 </section>
17503 <section name="PeakIntegrator">
17504 <param name="integration_type" value="intensity_sum"/>
17505 <param name="baseline_type" value="base_to_base"/>
17506 <param name="fit_EMG" value="false"/>
17507 </section>
17508 </section>
17509 <section name="DIAScoring">
17510 <param name="dia_extraction_window" value="0.05"/>
17511 <param name="dia_extraction_unit" value="Th"/>
17512 <param name="dia_centroided" value="false"/>
17513 <param name="dia_byseries_intensity_min" value="300.0"/>
17514 <param name="dia_byseries_ppm_diff" value="10.0"/>
17515 <param name="dia_nr_isotopes" value="4"/>
17516 <param name="dia_nr_charges" value="4"/>
17517 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17518 </section>
17519 <section name="EMGScoring">
17520 <param name="interpolation_step" value="0.2"/>
17521 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17522 <param name="max_iteration" value="500"/>
17523 <section name="statistics">
17524 <param name="mean" value="1.0"/>
17525 <param name="variance" value="1.0"/>
17526 </section>
17527 </section>
17528 <section name="Scores">
17529 <param name="use_shape_score" value="true"/>
17530 <param name="use_coelution_score" value="true"/>
17531 <param name="use_rt_score" value="true"/>
17532 <param name="use_library_score" value="true"/>
17533 <param name="use_elution_model_score" value="true"/>
17534 <param name="use_intensity_score" value="true"/>
17535 <param name="use_nr_peaks_score" value="true"/>
17536 <param name="use_total_xic_score" value="true"/>
17537 <param name="use_total_mi_score" value="true"/>
17538 <param name="use_sn_score" value="true"/>
17539 <param name="use_mi_score" value="true"/>
17540 <param name="use_dia_scores" value="true"/>
17541 <param name="use_ms1_correlation" value="false"/>
17542 <param name="use_sonar_scores" value="false"/>
17543 <param name="use_ion_mobility_scores" value="false"/>
17544 <param name="use_ms1_fullscan" value="false"/>
17545 <param name="use_ms1_mi" value="true"/>
17546 <param name="use_uis_scores" value="false"/>
17547 </section>
17548 </section>
17549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17550 <output name="ctd_out" ftype="xml">
17551 <assert_contents>
17552 <is_valid_xml/>
17553 </assert_contents>
17554 </output>
17555 </test>
17556 <test expect_num_outputs="2">
17557 <conditional name="adv_opts_cond">
17558 <param name="adv_opts_selector" value="advanced"/>
17559 <param name="force" value="false"/>
17560 <param name="test" value="true"/>
17561 </conditional>
17562 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17563 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17564 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
17565 <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17566 <param name="no_strict" value="false"/>
17567 <param name="min_upper_edge_dist" value="0.0"/>
17568 <section name="model">
17569 <param name="type" value="linear"/>
17570 <param name="symmetric_regression" value="false"/>
17571 </section>
17572 <section name="algorithm">
17573 <param name="stop_report_after_feature" value="-1"/>
17574 <param name="rt_extraction_window" value="-1.0"/>
17575 <param name="rt_normalization_factor" value="1.0"/>
17576 <param name="quantification_cutoff" value="0.0"/>
17577 <param name="write_convex_hull" value="false"/>
17578 <param name="spectrum_addition_method" value="simple"/>
17579 <param name="add_up_spectra" value="1"/>
17580 <param name="spacing_for_spectra_resampling" value="0.005"/>
17581 <param name="uis_threshold_sn" value="-1"/>
17582 <param name="uis_threshold_peak_area" value="0"/>
17583 <param name="scoring_model" value="default"/>
17584 <param name="im_extra_drift" value="0.0"/>
17585 <section name="TransitionGroupPicker">
17586 <param name="stop_after_feature" value="-1"/>
17587 <param name="stop_after_intensity_ratio" value="0.0001"/>
17588 <param name="min_peak_width" value="-1.0"/>
17589 <param name="peak_integration" value="original"/>
17590 <param name="background_subtraction" value="none"/>
17591 <param name="recalculate_peaks" value="false"/>
17592 <param name="use_precursors" value="false"/>
17593 <param name="use_consensus" value="true"/>
17594 <param name="recalculate_peaks_max_z" value="1.0"/>
17595 <param name="minimal_quality" value="-10000.0"/>
17596 <param name="resample_boundary" value="15.0"/>
17597 <param name="compute_peak_quality" value="false"/>
17598 <param name="compute_peak_shape_metrics" value="false"/>
17599 <param name="compute_total_mi" value="false"/>
17600 <param name="boundary_selection_method" value="largest"/>
17601 <section name="PeakPickerMRM">
17602 <param name="sgolay_frame_length" value="15"/>
17603 <param name="sgolay_polynomial_order" value="3"/>
17604 <param name="gauss_width" value="50.0"/>
17605 <param name="use_gauss" value="true"/>
17606 <param name="peak_width" value="40.0"/>
17607 <param name="signal_to_noise" value="1.0"/>
17608 <param name="sn_win_len" value="1000.0"/>
17609 <param name="sn_bin_count" value="30"/>
17610 <param name="write_sn_log_messages" value="false"/>
17611 <param name="remove_overlapping_peaks" value="false"/>
17612 <param name="method" value="legacy"/>
17613 </section>
17614 <section name="PeakIntegrator">
17615 <param name="integration_type" value="intensity_sum"/>
17616 <param name="baseline_type" value="base_to_base"/>
17617 <param name="fit_EMG" value="false"/>
17618 </section>
17619 </section>
17620 <section name="DIAScoring">
17621 <param name="dia_extraction_window" value="0.05"/>
17622 <param name="dia_extraction_unit" value="Th"/>
17623 <param name="dia_centroided" value="false"/>
17624 <param name="dia_byseries_intensity_min" value="300.0"/>
17625 <param name="dia_byseries_ppm_diff" value="10.0"/>
17626 <param name="dia_nr_isotopes" value="4"/>
17627 <param name="dia_nr_charges" value="4"/>
17628 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17629 </section>
17630 <section name="EMGScoring">
17631 <param name="interpolation_step" value="0.2"/>
17632 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17633 <param name="max_iteration" value="500"/>
17634 <section name="statistics">
17635 <param name="mean" value="1.0"/>
17636 <param name="variance" value="1.0"/>
17637 </section>
17638 </section>
17639 <section name="Scores">
17640 <param name="use_shape_score" value="true"/>
17641 <param name="use_coelution_score" value="true"/>
17642 <param name="use_rt_score" value="true"/>
17643 <param name="use_library_score" value="true"/>
17644 <param name="use_elution_model_score" value="true"/>
17645 <param name="use_intensity_score" value="true"/>
17646 <param name="use_nr_peaks_score" value="true"/>
17647 <param name="use_total_xic_score" value="true"/>
17648 <param name="use_total_mi_score" value="false"/>
17649 <param name="use_sn_score" value="true"/>
17650 <param name="use_mi_score" value="true"/>
17651 <param name="use_dia_scores" value="true"/>
17652 <param name="use_ms1_correlation" value="false"/>
17653 <param name="use_sonar_scores" value="false"/>
17654 <param name="use_ion_mobility_scores" value="false"/>
17655 <param name="use_ms1_fullscan" value="false"/>
17656 <param name="use_ms1_mi" value="false"/>
17657 <param name="use_uis_scores" value="false"/>
17658 </section>
17659 </section>
17660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17661 <output name="ctd_out" ftype="xml">
17662 <assert_contents>
17663 <is_valid_xml/>
17664 </assert_contents>
17665 </output>
17666 </test>
17667 <test expect_num_outputs="2">
17668 <conditional name="adv_opts_cond">
17669 <param name="adv_opts_selector" value="advanced"/>
17670 <param name="force" value="false"/>
17671 <param name="test" value="true"/>
17672 </conditional>
17673 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17674 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17675 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
17676 <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17677 <param name="no_strict" value="false"/>
17678 <param name="min_upper_edge_dist" value="0.0"/>
17679 <section name="model">
17680 <param name="type" value="linear"/>
17681 <param name="symmetric_regression" value="false"/>
17682 </section>
17683 <section name="algorithm">
17684 <param name="stop_report_after_feature" value="-1"/>
17685 <param name="rt_extraction_window" value="-1.0"/>
17686 <param name="rt_normalization_factor" value="1.0"/>
17687 <param name="quantification_cutoff" value="0.0"/>
17688 <param name="write_convex_hull" value="false"/>
17689 <param name="spectrum_addition_method" value="simple"/>
17690 <param name="add_up_spectra" value="1"/>
17691 <param name="spacing_for_spectra_resampling" value="0.005"/>
17692 <param name="uis_threshold_sn" value="-1"/>
17693 <param name="uis_threshold_peak_area" value="0"/>
17694 <param name="scoring_model" value="default"/>
17695 <param name="im_extra_drift" value="0.0"/>
17696 <section name="TransitionGroupPicker">
17697 <param name="stop_after_feature" value="-1"/>
17698 <param name="stop_after_intensity_ratio" value="0.0001"/>
17699 <param name="min_peak_width" value="-1.0"/>
17700 <param name="peak_integration" value="original"/>
17701 <param name="background_subtraction" value="none"/>
17702 <param name="recalculate_peaks" value="false"/>
17703 <param name="use_precursors" value="false"/>
17704 <param name="use_consensus" value="true"/>
17705 <param name="recalculate_peaks_max_z" value="1.0"/>
17706 <param name="minimal_quality" value="-10000.0"/>
17707 <param name="resample_boundary" value="15.0"/>
17708 <param name="compute_peak_quality" value="false"/>
17709 <param name="compute_peak_shape_metrics" value="false"/>
17710 <param name="compute_total_mi" value="false"/>
17711 <param name="boundary_selection_method" value="largest"/>
17712 <section name="PeakPickerMRM">
17713 <param name="sgolay_frame_length" value="15"/>
17714 <param name="sgolay_polynomial_order" value="3"/>
17715 <param name="gauss_width" value="50.0"/>
17716 <param name="use_gauss" value="true"/>
17717 <param name="peak_width" value="40.0"/>
17718 <param name="signal_to_noise" value="1.0"/>
17719 <param name="sn_win_len" value="1000.0"/>
17720 <param name="sn_bin_count" value="30"/>
17721 <param name="write_sn_log_messages" value="false"/>
17722 <param name="remove_overlapping_peaks" value="false"/>
17723 <param name="method" value="legacy"/>
17724 </section>
17725 <section name="PeakIntegrator">
17726 <param name="integration_type" value="intensity_sum"/>
17727 <param name="baseline_type" value="base_to_base"/>
17728 <param name="fit_EMG" value="false"/>
17729 </section>
17730 </section>
17731 <section name="DIAScoring">
17732 <param name="dia_extraction_window" value="0.05"/>
17733 <param name="dia_extraction_unit" value="Th"/>
17734 <param name="dia_centroided" value="false"/>
17735 <param name="dia_byseries_intensity_min" value="300.0"/>
17736 <param name="dia_byseries_ppm_diff" value="10.0"/>
17737 <param name="dia_nr_isotopes" value="4"/>
17738 <param name="dia_nr_charges" value="4"/>
17739 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17740 </section>
17741 <section name="EMGScoring">
17742 <param name="interpolation_step" value="0.2"/>
17743 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17744 <param name="max_iteration" value="500"/>
17745 <section name="statistics">
17746 <param name="mean" value="1.0"/>
17747 <param name="variance" value="1.0"/>
17748 </section>
17749 </section>
17750 <section name="Scores">
17751 <param name="use_shape_score" value="true"/>
17752 <param name="use_coelution_score" value="true"/>
17753 <param name="use_rt_score" value="true"/>
17754 <param name="use_library_score" value="true"/>
17755 <param name="use_elution_model_score" value="true"/>
17756 <param name="use_intensity_score" value="true"/>
17757 <param name="use_nr_peaks_score" value="true"/>
17758 <param name="use_total_xic_score" value="true"/>
17759 <param name="use_total_mi_score" value="true"/>
17760 <param name="use_sn_score" value="true"/>
17761 <param name="use_mi_score" value="true"/>
17762 <param name="use_dia_scores" value="true"/>
17763 <param name="use_ms1_correlation" value="false"/>
17764 <param name="use_sonar_scores" value="false"/>
17765 <param name="use_ion_mobility_scores" value="false"/>
17766 <param name="use_ms1_fullscan" value="false"/>
17767 <param name="use_ms1_mi" value="false"/>
17768 <param name="use_uis_scores" value="false"/>
17769 </section>
17770 </section>
17771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17772 <output name="ctd_out" ftype="xml">
17773 <assert_contents>
17774 <is_valid_xml/>
17775 </assert_contents>
17776 </output>
17777 </test>
17778 <test expect_num_outputs="2">
17779 <conditional name="adv_opts_cond">
17780 <param name="adv_opts_selector" value="advanced"/>
17781 <param name="force" value="false"/>
17782 <param name="test" value="true"/>
17783 </conditional>
17784 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
17785 <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
17786 <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
17787 <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
17788 <param name="no_strict" value="false"/>
17789 <param name="min_upper_edge_dist" value="0.0"/>
17790 <section name="model">
17791 <param name="type" value="linear"/>
17792 <param name="symmetric_regression" value="false"/>
17793 </section>
17794 <section name="algorithm">
17795 <param name="stop_report_after_feature" value="-1"/>
17796 <param name="rt_extraction_window" value="-1.0"/>
17797 <param name="rt_normalization_factor" value="1.0"/>
17798 <param name="quantification_cutoff" value="0.0"/>
17799 <param name="write_convex_hull" value="false"/>
17800 <param name="spectrum_addition_method" value="simple"/>
17801 <param name="add_up_spectra" value="1"/>
17802 <param name="spacing_for_spectra_resampling" value="0.005"/>
17803 <param name="uis_threshold_sn" value="-1"/>
17804 <param name="uis_threshold_peak_area" value="0"/>
17805 <param name="scoring_model" value="default"/>
17806 <param name="im_extra_drift" value="0.0"/>
17807 <section name="TransitionGroupPicker">
17808 <param name="stop_after_feature" value="-1"/>
17809 <param name="stop_after_intensity_ratio" value="0.0001"/>
17810 <param name="min_peak_width" value="-1.0"/>
17811 <param name="peak_integration" value="original"/>
17812 <param name="background_subtraction" value="none"/>
17813 <param name="recalculate_peaks" value="false"/>
17814 <param name="use_precursors" value="false"/>
17815 <param name="use_consensus" value="true"/>
17816 <param name="recalculate_peaks_max_z" value="1.0"/>
17817 <param name="minimal_quality" value="-10000.0"/>
17818 <param name="resample_boundary" value="15.0"/>
17819 <param name="compute_peak_quality" value="false"/>
17820 <param name="compute_peak_shape_metrics" value="false"/>
17821 <param name="compute_total_mi" value="false"/>
17822 <param name="boundary_selection_method" value="largest"/>
17823 <section name="PeakPickerMRM">
17824 <param name="sgolay_frame_length" value="15"/>
17825 <param name="sgolay_polynomial_order" value="3"/>
17826 <param name="gauss_width" value="50.0"/>
17827 <param name="use_gauss" value="true"/>
17828 <param name="peak_width" value="40.0"/>
17829 <param name="signal_to_noise" value="1.0"/>
17830 <param name="sn_win_len" value="1000.0"/>
17831 <param name="sn_bin_count" value="30"/>
17832 <param name="write_sn_log_messages" value="false"/>
17833 <param name="remove_overlapping_peaks" value="false"/>
17834 <param name="method" value="legacy"/>
17835 </section>
17836 <section name="PeakIntegrator">
17837 <param name="integration_type" value="intensity_sum"/>
17838 <param name="baseline_type" value="base_to_base"/>
17839 <param name="fit_EMG" value="false"/>
17840 </section>
17841 </section>
17842 <section name="DIAScoring">
17843 <param name="dia_extraction_window" value="0.05"/>
17844 <param name="dia_extraction_unit" value="Th"/>
17845 <param name="dia_centroided" value="false"/>
17846 <param name="dia_byseries_intensity_min" value="300.0"/>
17847 <param name="dia_byseries_ppm_diff" value="10.0"/>
17848 <param name="dia_nr_isotopes" value="4"/>
17849 <param name="dia_nr_charges" value="4"/>
17850 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
17851 </section>
17852 <section name="EMGScoring">
17853 <param name="interpolation_step" value="0.2"/>
17854 <param name="tolerance_stdev_bounding_box" value="3.0"/>
17855 <param name="max_iteration" value="500"/>
17856 <section name="statistics">
17857 <param name="mean" value="1.0"/>
17858 <param name="variance" value="1.0"/>
17859 </section>
17860 </section>
17861 <section name="Scores">
17862 <param name="use_shape_score" value="true"/>
17863 <param name="use_coelution_score" value="true"/>
17864 <param name="use_rt_score" value="true"/>
17865 <param name="use_library_score" value="true"/>
17866 <param name="use_elution_model_score" value="true"/>
17867 <param name="use_intensity_score" value="true"/>
17868 <param name="use_nr_peaks_score" value="true"/>
17869 <param name="use_total_xic_score" value="true"/>
17870 <param name="use_total_mi_score" value="true"/>
17871 <param name="use_sn_score" value="true"/>
17872 <param name="use_mi_score" value="false"/>
17873 <param name="use_dia_scores" value="true"/>
17874 <param name="use_ms1_correlation" value="false"/>
17875 <param name="use_sonar_scores" value="false"/>
17876 <param name="use_ion_mobility_scores" value="false"/>
17877 <param name="use_ms1_fullscan" value="false"/>
17878 <param name="use_ms1_mi" value="false"/>
17879 <param name="use_uis_scores" value="false"/>
17880 </section>
17881 </section>
17882 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17883 <output name="ctd_out" ftype="xml">
17884 <assert_contents>
17885 <is_valid_xml/>
17886 </assert_contents>
17887 </output>
17888 </test>
17889 </xml>
17890 <xml name="autotest_OpenSwathAssayGenerator">
17891 <test expect_num_outputs="2">
17892 <conditional name="adv_opts_cond">
17893 <param name="adv_opts_selector" value="advanced"/>
17894 <param name="max_num_alternative_localizations" value="10000"/>
17895 <param name="disable_identification_ms2_precursors" value="false"/>
17896 <param name="disable_identification_specific_losses" value="false"/>
17897 <param name="enable_identification_unspecific_losses" value="false"/>
17898 <param name="enable_swath_specifity" value="false"/>
17899 <param name="force" value="false"/>
17900 <param name="test" value="true"/>
17901 </conditional>
17902 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
17903 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
17904 <param name="out_type" value="TraML"/>
17905 <param name="min_transitions" value="6"/>
17906 <param name="max_transitions" value="6"/>
17907 <param name="allowed_fragment_types" value="b,y"/>
17908 <param name="allowed_fragment_charges" value="2,3"/>
17909 <param name="enable_detection_specific_losses" value="true"/>
17910 <param name="enable_detection_unspecific_losses" value="false"/>
17911 <param name="precursor_mz_threshold" value="0.025"/>
17912 <param name="precursor_lower_mz_limit" value="400.0"/>
17913 <param name="precursor_upper_mz_limit" value="1200.0"/>
17914 <param name="product_mz_threshold" value="0.025"/>
17915 <param name="product_lower_mz_limit" value="350.0"/>
17916 <param name="product_upper_mz_limit" value="2000.0"/>
17917 <param name="enable_ipf" value="false"/>
17918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17919 <output name="ctd_out" ftype="xml">
17920 <assert_contents>
17921 <is_valid_xml/>
17922 </assert_contents>
17923 </output>
17924 </test>
17925 <test expect_num_outputs="2">
17926 <conditional name="adv_opts_cond">
17927 <param name="adv_opts_selector" value="advanced"/>
17928 <param name="max_num_alternative_localizations" value="10000"/>
17929 <param name="disable_identification_ms2_precursors" value="false"/>
17930 <param name="disable_identification_specific_losses" value="false"/>
17931 <param name="enable_identification_unspecific_losses" value="false"/>
17932 <param name="enable_swath_specifity" value="false"/>
17933 <param name="force" value="false"/>
17934 <param name="test" value="true"/>
17935 </conditional>
17936 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
17937 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
17938 <param name="out_type" value="TraML"/>
17939 <param name="min_transitions" value="6"/>
17940 <param name="max_transitions" value="6"/>
17941 <param name="allowed_fragment_types" value="b,y"/>
17942 <param name="allowed_fragment_charges" value="1,2,3,4"/>
17943 <param name="enable_detection_specific_losses" value="false"/>
17944 <param name="enable_detection_unspecific_losses" value="false"/>
17945 <param name="precursor_mz_threshold" value="0.025"/>
17946 <param name="precursor_lower_mz_limit" value="400.0"/>
17947 <param name="precursor_upper_mz_limit" value="1200.0"/>
17948 <param name="product_mz_threshold" value="0.025"/>
17949 <param name="product_lower_mz_limit" value="350.0"/>
17950 <param name="product_upper_mz_limit" value="2000.0"/>
17951 <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
17952 <param name="enable_ipf" value="true"/>
17953 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17954 <output name="ctd_out" ftype="xml">
17955 <assert_contents>
17956 <is_valid_xml/>
17957 </assert_contents>
17958 </output>
17959 </test>
17960 <test expect_num_outputs="2">
17961 <conditional name="adv_opts_cond">
17962 <param name="adv_opts_selector" value="advanced"/>
17963 <param name="max_num_alternative_localizations" value="10000"/>
17964 <param name="disable_identification_ms2_precursors" value="false"/>
17965 <param name="disable_identification_specific_losses" value="false"/>
17966 <param name="enable_identification_unspecific_losses" value="false"/>
17967 <param name="enable_swath_specifity" value="false"/>
17968 <param name="force" value="false"/>
17969 <param name="test" value="true"/>
17970 </conditional>
17971 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
17972 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
17973 <param name="out_type" value="TraML"/>
17974 <param name="min_transitions" value="6"/>
17975 <param name="max_transitions" value="6"/>
17976 <param name="allowed_fragment_types" value="b,y"/>
17977 <param name="allowed_fragment_charges" value="1,2,3,4"/>
17978 <param name="enable_detection_specific_losses" value="false"/>
17979 <param name="enable_detection_unspecific_losses" value="false"/>
17980 <param name="precursor_mz_threshold" value="0.025"/>
17981 <param name="precursor_lower_mz_limit" value="400.0"/>
17982 <param name="precursor_upper_mz_limit" value="1200.0"/>
17983 <param name="product_mz_threshold" value="0.025"/>
17984 <param name="product_lower_mz_limit" value="350.0"/>
17985 <param name="product_upper_mz_limit" value="2000.0"/>
17986 <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
17987 <param name="enable_ipf" value="true"/>
17988 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
17989 <output name="ctd_out" ftype="xml">
17990 <assert_contents>
17991 <is_valid_xml/>
17992 </assert_contents>
17993 </output>
17994 </test>
17995 </xml>
17996 <xml name="autotest_OpenSwathChromatogramExtractor">
17997 <test expect_num_outputs="2">
17998 <conditional name="adv_opts_cond">
17999 <param name="adv_opts_selector" value="advanced"/>
18000 <param name="extraction_function" value="tophat"/>
18001 <param name="force" value="false"/>
18002 <param name="test" value="true"/>
18003 </conditional>
18004 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18005 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18006 <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18007 <param name="min_upper_edge_dist" value="0.0"/>
18008 <param name="rt_window" value="-1.0"/>
18009 <param name="ion_mobility_window" value="-1.0"/>
18010 <param name="mz_window" value="0.05"/>
18011 <param name="ppm" value="false"/>
18012 <param name="is_swath" value="false"/>
18013 <param name="extract_MS1" value="false"/>
18014 <section name="model">
18015 <param name="type" value="linear"/>
18016 <param name="symmetric_regression" value="false"/>
18017 </section>
18018 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18019 <output name="ctd_out" ftype="xml">
18020 <assert_contents>
18021 <is_valid_xml/>
18022 </assert_contents>
18023 </output>
18024 </test>
18025 <test expect_num_outputs="2">
18026 <conditional name="adv_opts_cond">
18027 <param name="adv_opts_selector" value="advanced"/>
18028 <param name="extraction_function" value="tophat"/>
18029 <param name="force" value="false"/>
18030 <param name="test" value="true"/>
18031 </conditional>
18032 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18033 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18034 <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
18035 <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18036 <param name="min_upper_edge_dist" value="0.0"/>
18037 <param name="rt_window" value="50.0"/>
18038 <param name="ion_mobility_window" value="-1.0"/>
18039 <param name="mz_window" value="0.05"/>
18040 <param name="ppm" value="false"/>
18041 <param name="is_swath" value="false"/>
18042 <param name="extract_MS1" value="false"/>
18043 <section name="model">
18044 <param name="type" value="linear"/>
18045 <param name="symmetric_regression" value="false"/>
18046 </section>
18047 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18048 <output name="ctd_out" ftype="xml">
18049 <assert_contents>
18050 <is_valid_xml/>
18051 </assert_contents>
18052 </output>
18053 </test>
18054 <test expect_num_outputs="2">
18055 <conditional name="adv_opts_cond">
18056 <param name="adv_opts_selector" value="advanced"/>
18057 <param name="extraction_function" value="tophat"/>
18058 <param name="force" value="false"/>
18059 <param name="test" value="true"/>
18060 </conditional>
18061 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18062 <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
18063 <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18064 <param name="min_upper_edge_dist" value="0.0"/>
18065 <param name="rt_window" value="-1.0"/>
18066 <param name="ion_mobility_window" value="-1.0"/>
18067 <param name="mz_window" value="0.05"/>
18068 <param name="ppm" value="false"/>
18069 <param name="is_swath" value="false"/>
18070 <param name="extract_MS1" value="true"/>
18071 <section name="model">
18072 <param name="type" value="linear"/>
18073 <param name="symmetric_regression" value="false"/>
18074 </section>
18075 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18076 <output name="ctd_out" ftype="xml">
18077 <assert_contents>
18078 <is_valid_xml/>
18079 </assert_contents>
18080 </output>
18081 </test>
18082 <test expect_num_outputs="2">
18083 <conditional name="adv_opts_cond">
18084 <param name="adv_opts_selector" value="advanced"/>
18085 <param name="extraction_function" value="tophat"/>
18086 <param name="force" value="false"/>
18087 <param name="test" value="true"/>
18088 </conditional>
18089 <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
18090 <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
18091 <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18092 <param name="min_upper_edge_dist" value="0.0"/>
18093 <param name="rt_window" value="-1.0"/>
18094 <param name="ion_mobility_window" value="0.05"/>
18095 <param name="mz_window" value="0.05"/>
18096 <param name="ppm" value="false"/>
18097 <param name="is_swath" value="true"/>
18098 <param name="extract_MS1" value="false"/>
18099 <section name="model">
18100 <param name="type" value="linear"/>
18101 <param name="symmetric_regression" value="false"/>
18102 </section>
18103 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18104 <output name="ctd_out" ftype="xml">
18105 <assert_contents>
18106 <is_valid_xml/>
18107 </assert_contents>
18108 </output>
18109 </test>
18110 <test expect_num_outputs="2">
18111 <conditional name="adv_opts_cond">
18112 <param name="adv_opts_selector" value="advanced"/>
18113 <param name="extraction_function" value="tophat"/>
18114 <param name="force" value="false"/>
18115 <param name="test" value="true"/>
18116 </conditional>
18117 <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
18118 <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
18119 <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18120 <param name="min_upper_edge_dist" value="0.0"/>
18121 <param name="rt_window" value="-1.0"/>
18122 <param name="ion_mobility_window" value="-1.0"/>
18123 <param name="mz_window" value="0.05"/>
18124 <param name="ppm" value="false"/>
18125 <param name="is_swath" value="false"/>
18126 <param name="extract_MS1" value="true"/>
18127 <section name="model">
18128 <param name="type" value="linear"/>
18129 <param name="symmetric_regression" value="false"/>
18130 </section>
18131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18132 <output name="ctd_out" ftype="xml">
18133 <assert_contents>
18134 <is_valid_xml/>
18135 </assert_contents>
18136 </output>
18137 </test>
18138 </xml>
18139 <xml name="autotest_OpenSwathConfidenceScoring">
18140 <test expect_num_outputs="2">
18141 <conditional name="adv_opts_cond">
18142 <param name="adv_opts_selector" value="advanced"/>
18143 <param name="force" value="false"/>
18144 <param name="test" value="true"/>
18145 </conditional>
18146 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
18147 <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
18148 <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18149 <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
18150 <param name="decoys" value="1"/>
18151 <param name="transitions" value="2"/>
18152 <section name="GLM">
18153 <param name="intercept" value="3.87333466"/>
18154 <param name="delta_rt" value="-0.02898629"/>
18155 <param name="dist_int" value="-7.75880768"/>
18156 </section>
18157 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18158 <output name="ctd_out" ftype="xml">
18159 <assert_contents>
18160 <is_valid_xml/>
18161 </assert_contents>
18162 </output>
18163 </test>
18164 </xml>
18165 <xml name="autotest_OpenSwathDecoyGenerator">
18166 <test expect_num_outputs="2">
18167 <conditional name="adv_opts_cond">
18168 <param name="adv_opts_selector" value="advanced"/>
18169 <param name="min_decoy_fraction" value="0.8"/>
18170 <param name="aim_decoy_fraction" value="1.0"/>
18171 <param name="shuffle_max_attempts" value="30"/>
18172 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
18173 <param name="shift_precursor_mz_shift" value="0.0"/>
18174 <param name="shift_product_mz_shift" value="20.0"/>
18175 <param name="product_mz_threshold" value="0.025"/>
18176 <param name="allowed_fragment_types" value="b,y"/>
18177 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18178 <param name="enable_detection_specific_losses" value="false"/>
18179 <param name="enable_detection_unspecific_losses" value="false"/>
18180 <param name="separate" value="true"/>
18181 <param name="force" value="false"/>
18182 <param name="test" value="true"/>
18183 </conditional>
18184 <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
18185 <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18186 <param name="out_type" value="TraML"/>
18187 <param name="method" value="pseudo-reverse"/>
18188 <param name="decoy_tag" value="DECOY_"/>
18189 <param name="switchKR" value="false"/>
18190 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18191 <output name="ctd_out" ftype="xml">
18192 <assert_contents>
18193 <is_valid_xml/>
18194 </assert_contents>
18195 </output>
18196 </test>
18197 <test expect_num_outputs="2">
18198 <conditional name="adv_opts_cond">
18199 <param name="adv_opts_selector" value="advanced"/>
18200 <param name="min_decoy_fraction" value="0.8"/>
18201 <param name="aim_decoy_fraction" value="1.0"/>
18202 <param name="shuffle_max_attempts" value="30"/>
18203 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
18204 <param name="shift_precursor_mz_shift" value="0.0"/>
18205 <param name="shift_product_mz_shift" value="20.0"/>
18206 <param name="product_mz_threshold" value="0.8"/>
18207 <param name="allowed_fragment_types" value="b,y"/>
18208 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18209 <param name="enable_detection_specific_losses" value="false"/>
18210 <param name="enable_detection_unspecific_losses" value="false"/>
18211 <param name="separate" value="false"/>
18212 <param name="force" value="false"/>
18213 <param name="test" value="true"/>
18214 </conditional>
18215 <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
18216 <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18217 <param name="out_type" value="TraML"/>
18218 <param name="method" value="pseudo-reverse"/>
18219 <param name="decoy_tag" value="DECOY_"/>
18220 <param name="switchKR" value="false"/>
18221 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18222 <output name="ctd_out" ftype="xml">
18223 <assert_contents>
18224 <is_valid_xml/>
18225 </assert_contents>
18226 </output>
18227 </test>
18228 <test expect_num_outputs="2">
18229 <conditional name="adv_opts_cond">
18230 <param name="adv_opts_selector" value="advanced"/>
18231 <param name="min_decoy_fraction" value="0.8"/>
18232 <param name="aim_decoy_fraction" value="1.0"/>
18233 <param name="shuffle_max_attempts" value="30"/>
18234 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
18235 <param name="shift_precursor_mz_shift" value="0.0"/>
18236 <param name="shift_product_mz_shift" value="20.0"/>
18237 <param name="product_mz_threshold" value="0.025"/>
18238 <param name="allowed_fragment_types" value="b,y"/>
18239 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18240 <param name="enable_detection_specific_losses" value="false"/>
18241 <param name="enable_detection_unspecific_losses" value="false"/>
18242 <param name="separate" value="true"/>
18243 <param name="force" value="false"/>
18244 <param name="test" value="true"/>
18245 </conditional>
18246 <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
18247 <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18248 <param name="out_type" value="TraML"/>
18249 <param name="method" value="pseudo-reverse"/>
18250 <param name="decoy_tag" value="DECOY_"/>
18251 <param name="switchKR" value="false"/>
18252 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18253 <output name="ctd_out" ftype="xml">
18254 <assert_contents>
18255 <is_valid_xml/>
18256 </assert_contents>
18257 </output>
18258 </test>
18259 <test expect_num_outputs="2">
18260 <conditional name="adv_opts_cond">
18261 <param name="adv_opts_selector" value="advanced"/>
18262 <param name="min_decoy_fraction" value="0.4"/>
18263 <param name="aim_decoy_fraction" value="1.0"/>
18264 <param name="shuffle_max_attempts" value="30"/>
18265 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
18266 <param name="shift_precursor_mz_shift" value="0.0"/>
18267 <param name="shift_product_mz_shift" value="20.0"/>
18268 <param name="product_mz_threshold" value="0.025"/>
18269 <param name="allowed_fragment_types" value="b,y"/>
18270 <param name="allowed_fragment_charges" value="1,2,3,4"/>
18271 <param name="enable_detection_specific_losses" value="true"/>
18272 <param name="enable_detection_unspecific_losses" value="true"/>
18273 <param name="separate" value="true"/>
18274 <param name="force" value="false"/>
18275 <param name="test" value="true"/>
18276 </conditional>
18277 <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
18278 <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/>
18279 <param name="out_type" value="TraML"/>
18280 <param name="method" value="pseudo-reverse"/>
18281 <param name="decoy_tag" value="DECOY_"/>
18282 <param name="switchKR" value="true"/>
18283 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18284 <output name="ctd_out" ftype="xml">
18285 <assert_contents>
18286 <is_valid_xml/>
18287 </assert_contents>
18288 </output>
18289 </test>
18290 </xml>
18291 <xml name="autotest_OpenSwathFeatureXMLToTSV">
18292 <test expect_num_outputs="2">
18293 <conditional name="adv_opts_cond">
18294 <param name="adv_opts_selector" value="advanced"/>
18295 <param name="force" value="false"/>
18296 <param name="test" value="true"/>
18297 </conditional>
18298 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
18299 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
18300 <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
18301 <param name="short_format" value="true"/>
18302 <param name="best_scoring_peptide" value=""/>
18303 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18304 <output name="ctd_out" ftype="xml">
18305 <assert_contents>
18306 <is_valid_xml/>
18307 </assert_contents>
18308 </output>
18309 </test>
18310 <test expect_num_outputs="2">
18311 <conditional name="adv_opts_cond">
18312 <param name="adv_opts_selector" value="advanced"/>
18313 <param name="force" value="false"/>
18314 <param name="test" value="true"/>
18315 </conditional>
18316 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
18317 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
18318 <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/>
18319 <param name="short_format" value="false"/>
18320 <param name="best_scoring_peptide" value=""/>
18321 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18322 <output name="ctd_out" ftype="xml">
18323 <assert_contents>
18324 <is_valid_xml/>
18325 </assert_contents>
18326 </output>
18327 </test>
18328 <test expect_num_outputs="2">
18329 <conditional name="adv_opts_cond">
18330 <param name="adv_opts_selector" value="advanced"/>
18331 <param name="force" value="false"/>
18332 <param name="test" value="true"/>
18333 </conditional>
18334 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
18335 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
18336 <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
18337 <param name="short_format" value="true"/>
18338 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
18339 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18340 <output name="ctd_out" ftype="xml">
18341 <assert_contents>
18342 <is_valid_xml/>
18343 </assert_contents>
18344 </output>
18345 </test>
18346 </xml>
18347 <xml name="autotest_OpenSwathFileSplitter"/>
18348 <xml name="autotest_OpenSwathMzMLFileCacher">
18349 <test expect_num_outputs="2">
18350 <conditional name="adv_opts_cond">
18351 <param name="adv_opts_selector" value="advanced"/>
18352 <param name="lossy_mass_accuracy" value="-1.0"/>
18353 <param name="process_lowmemory" value="false"/>
18354 <param name="lowmem_batchsize" value="500"/>
18355 <param name="force" value="false"/>
18356 <param name="test" value="true"/>
18357 </conditional>
18358 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
18359 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18360 <param name="out_type" value="mzml"/>
18361 <param name="lossy_compression" value="true"/>
18362 <param name="full_meta" value="true"/>
18363 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18364 <output name="ctd_out" ftype="xml">
18365 <assert_contents>
18366 <is_valid_xml/>
18367 </assert_contents>
18368 </output>
18369 </test>
18370 <test expect_num_outputs="2">
18371 <conditional name="adv_opts_cond">
18372 <param name="adv_opts_selector" value="advanced"/>
18373 <param name="lossy_mass_accuracy" value="-1.0"/>
18374 <param name="process_lowmemory" value="false"/>
18375 <param name="lowmem_batchsize" value="500"/>
18376 <param name="force" value="false"/>
18377 <param name="test" value="true"/>
18378 </conditional>
18379 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
18380 <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18381 <param name="out_type" value="mzml"/>
18382 <param name="lossy_compression" value="true"/>
18383 <param name="full_meta" value="true"/>
18384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18385 <output name="ctd_out" ftype="xml">
18386 <assert_contents>
18387 <is_valid_xml/>
18388 </assert_contents>
18389 </output>
18390 </test>
18391 <test expect_num_outputs="2">
18392 <conditional name="adv_opts_cond">
18393 <param name="adv_opts_selector" value="advanced"/>
18394 <param name="lossy_mass_accuracy" value="0.0001"/>
18395 <param name="process_lowmemory" value="false"/>
18396 <param name="lowmem_batchsize" value="500"/>
18397 <param name="force" value="false"/>
18398 <param name="test" value="true"/>
18399 </conditional>
18400 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
18401 <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
18402 <param name="out_type" value="sqmass"/>
18403 <param name="lossy_compression" value="true"/>
18404 <param name="full_meta" value="true"/>
18405 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18406 <output name="ctd_out" ftype="xml">
18407 <assert_contents>
18408 <is_valid_xml/>
18409 </assert_contents>
18410 </output>
18411 </test>
18412 <test expect_num_outputs="2">
18413 <conditional name="adv_opts_cond">
18414 <param name="adv_opts_selector" value="advanced"/>
18415 <param name="lossy_mass_accuracy" value="-1.0"/>
18416 <param name="process_lowmemory" value="false"/>
18417 <param name="lowmem_batchsize" value="500"/>
18418 <param name="force" value="false"/>
18419 <param name="test" value="true"/>
18420 </conditional>
18421 <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
18422 <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18423 <param name="out_type" value="mzml"/>
18424 <param name="lossy_compression" value="true"/>
18425 <param name="full_meta" value="true"/>
18426 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18427 <output name="ctd_out" ftype="xml">
18428 <assert_contents>
18429 <is_valid_xml/>
18430 </assert_contents>
18431 </output>
18432 </test>
18433 <test expect_num_outputs="2">
18434 <conditional name="adv_opts_cond">
18435 <param name="adv_opts_selector" value="advanced"/>
18436 <param name="lossy_mass_accuracy" value="-1.0"/>
18437 <param name="process_lowmemory" value="false"/>
18438 <param name="lowmem_batchsize" value="500"/>
18439 <param name="force" value="false"/>
18440 <param name="test" value="true"/>
18441 </conditional>
18442 <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
18443 <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
18444 <param name="out_type" value="sqmass"/>
18445 <param name="lossy_compression" value="true"/>
18446 <param name="full_meta" value="true"/>
18447 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18448 <output name="ctd_out" ftype="xml">
18449 <assert_contents>
18450 <is_valid_xml/>
18451 </assert_contents>
18452 </output>
18453 </test>
18454 <test expect_num_outputs="2">
18455 <conditional name="adv_opts_cond">
18456 <param name="adv_opts_selector" value="advanced"/>
18457 <param name="lossy_mass_accuracy" value="-1.0"/>
18458 <param name="process_lowmemory" value="false"/>
18459 <param name="lowmem_batchsize" value="500"/>
18460 <param name="force" value="false"/>
18461 <param name="test" value="true"/>
18462 </conditional>
18463 <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
18464 <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18465 <param name="out_type" value="mzml"/>
18466 <param name="lossy_compression" value="true"/>
18467 <param name="full_meta" value="true"/>
18468 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18469 <output name="ctd_out" ftype="xml">
18470 <assert_contents>
18471 <is_valid_xml/>
18472 </assert_contents>
18473 </output>
18474 </test>
18475 <test expect_num_outputs="2">
18476 <conditional name="adv_opts_cond">
18477 <param name="adv_opts_selector" value="advanced"/>
18478 <param name="lossy_mass_accuracy" value="-1.0"/>
18479 <param name="process_lowmemory" value="true"/>
18480 <param name="lowmem_batchsize" value="500"/>
18481 <param name="force" value="false"/>
18482 <param name="test" value="true"/>
18483 </conditional>
18484 <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
18485 <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18486 <param name="out_type" value="mzml"/>
18487 <param name="lossy_compression" value="true"/>
18488 <param name="full_meta" value="true"/>
18489 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18490 <output name="ctd_out" ftype="xml">
18491 <assert_contents>
18492 <is_valid_xml/>
18493 </assert_contents>
18494 </output>
18495 </test>
18496 <test expect_num_outputs="2">
18497 <conditional name="adv_opts_cond">
18498 <param name="adv_opts_selector" value="advanced"/>
18499 <param name="lossy_mass_accuracy" value="-1.0"/>
18500 <param name="process_lowmemory" value="false"/>
18501 <param name="lowmem_batchsize" value="500"/>
18502 <param name="force" value="false"/>
18503 <param name="test" value="true"/>
18504 </conditional>
18505 <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
18506 <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/>
18507 <param name="out_type" value="mzML"/>
18508 <param name="lossy_compression" value="true"/>
18509 <param name="full_meta" value="true"/>
18510 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18511 <output name="ctd_out" ftype="xml">
18512 <assert_contents>
18513 <is_valid_xml/>
18514 </assert_contents>
18515 </output>
18516 </test>
18517 <test expect_num_outputs="2">
18518 <conditional name="adv_opts_cond">
18519 <param name="adv_opts_selector" value="advanced"/>
18520 <param name="lossy_mass_accuracy" value="-1.0"/>
18521 <param name="process_lowmemory" value="false"/>
18522 <param name="lowmem_batchsize" value="500"/>
18523 <param name="force" value="false"/>
18524 <param name="test" value="true"/>
18525 </conditional>
18526 <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
18527 <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/>
18528 <param name="out_type" value="mzML"/>
18529 <param name="lossy_compression" value="true"/>
18530 <param name="full_meta" value="true"/>
18531 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18532 <output name="ctd_out" ftype="xml">
18533 <assert_contents>
18534 <is_valid_xml/>
18535 </assert_contents>
18536 </output>
18537 </test>
18538 <test expect_num_outputs="2">
18539 <conditional name="adv_opts_cond">
18540 <param name="adv_opts_selector" value="advanced"/>
18541 <param name="lossy_mass_accuracy" value="0.0001"/>
18542 <param name="process_lowmemory" value="false"/>
18543 <param name="lowmem_batchsize" value="500"/>
18544 <param name="force" value="false"/>
18545 <param name="test" value="true"/>
18546 </conditional>
18547 <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
18548 <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18549 <param name="out_type" value="mzml"/>
18550 <param name="lossy_compression" value="false"/>
18551 <param name="full_meta" value="false"/>
18552 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18553 <output name="ctd_out" ftype="xml">
18554 <assert_contents>
18555 <is_valid_xml/>
18556 </assert_contents>
18557 </output>
18558 </test>
18559 </xml>
18560 <xml name="autotest_OpenSwathRewriteToFeatureXML">
18561 </xml>
18562 <xml name="autotest_OpenSwathRTNormalizer">
18563 <test expect_num_outputs="2">
18564 <conditional name="adv_opts_cond">
18565 <param name="adv_opts_selector" value="advanced"/>
18566 <param name="force" value="false"/>
18567 <param name="test" value="true"/>
18568 </conditional>
18569 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
18570 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
18571 <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
18572 <param name="min_rsq" value="0.95"/>
18573 <param name="min_coverage" value="0.6"/>
18574 <param name="estimateBestPeptides" value="false"/>
18575 <section name="RTNormalization">
18576 <param name="outlierMethod" value="iter_residual"/>
18577 <param name="useIterativeChauvenet" value="false"/>
18578 <param name="RANSACMaxIterations" value="1000"/>
18579 <param name="RANSACMaxPercentRTThreshold" value="3"/>
18580 <param name="RANSACSamplingSize" value="10"/>
18581 </section>
18582 <section name="algorithm">
18583 <param name="stop_report_after_feature" value="-1"/>
18584 <param name="rt_extraction_window" value="-1.0"/>
18585 <param name="rt_normalization_factor" value="1.0"/>
18586 <param name="quantification_cutoff" value="0.0"/>
18587 <param name="write_convex_hull" value="false"/>
18588 <param name="spectrum_addition_method" value="simple"/>
18589 <param name="add_up_spectra" value="1"/>
18590 <param name="spacing_for_spectra_resampling" value="0.005"/>
18591 <param name="uis_threshold_sn" value="-1"/>
18592 <param name="uis_threshold_peak_area" value="0"/>
18593 <param name="scoring_model" value="default"/>
18594 <param name="im_extra_drift" value="0.0"/>
18595 <section name="TransitionGroupPicker">
18596 <param name="stop_after_feature" value="-1"/>
18597 <param name="stop_after_intensity_ratio" value="0.0001"/>
18598 <param name="min_peak_width" value="-1.0"/>
18599 <param name="peak_integration" value="original"/>
18600 <param name="background_subtraction" value="none"/>
18601 <param name="recalculate_peaks" value="false"/>
18602 <param name="use_precursors" value="false"/>
18603 <param name="use_consensus" value="true"/>
18604 <param name="recalculate_peaks_max_z" value="1.0"/>
18605 <param name="minimal_quality" value="-10000.0"/>
18606 <param name="resample_boundary" value="15.0"/>
18607 <param name="compute_peak_quality" value="false"/>
18608 <param name="compute_peak_shape_metrics" value="false"/>
18609 <param name="compute_total_mi" value="false"/>
18610 <param name="boundary_selection_method" value="largest"/>
18611 <section name="PeakPickerMRM">
18612 <param name="sgolay_frame_length" value="15"/>
18613 <param name="sgolay_polynomial_order" value="3"/>
18614 <param name="gauss_width" value="50.0"/>
18615 <param name="use_gauss" value="true"/>
18616 <param name="peak_width" value="-1.0"/>
18617 <param name="signal_to_noise" value="1.0"/>
18618 <param name="sn_win_len" value="1000.0"/>
18619 <param name="sn_bin_count" value="30"/>
18620 <param name="write_sn_log_messages" value="false"/>
18621 <param name="remove_overlapping_peaks" value="false"/>
18622 <param name="method" value="corrected"/>
18623 </section>
18624 <section name="PeakIntegrator">
18625 <param name="integration_type" value="intensity_sum"/>
18626 <param name="baseline_type" value="base_to_base"/>
18627 <param name="fit_EMG" value="false"/>
18628 </section>
18629 </section>
18630 <section name="DIAScoring">
18631 <param name="dia_extraction_window" value="0.05"/>
18632 <param name="dia_extraction_unit" value="Th"/>
18633 <param name="dia_centroided" value="false"/>
18634 <param name="dia_byseries_intensity_min" value="300.0"/>
18635 <param name="dia_byseries_ppm_diff" value="10.0"/>
18636 <param name="dia_nr_isotopes" value="4"/>
18637 <param name="dia_nr_charges" value="4"/>
18638 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18639 </section>
18640 <section name="EMGScoring">
18641 <param name="interpolation_step" value="0.2"/>
18642 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18643 <param name="max_iteration" value="500"/>
18644 <section name="statistics">
18645 <param name="mean" value="1.0"/>
18646 <param name="variance" value="1.0"/>
18647 </section>
18648 </section>
18649 <section name="Scores">
18650 <param name="use_shape_score" value="true"/>
18651 <param name="use_coelution_score" value="true"/>
18652 <param name="use_rt_score" value="true"/>
18653 <param name="use_library_score" value="true"/>
18654 <param name="use_elution_model_score" value="true"/>
18655 <param name="use_intensity_score" value="true"/>
18656 <param name="use_nr_peaks_score" value="true"/>
18657 <param name="use_total_xic_score" value="true"/>
18658 <param name="use_total_mi_score" value="false"/>
18659 <param name="use_sn_score" value="true"/>
18660 <param name="use_mi_score" value="false"/>
18661 <param name="use_dia_scores" value="true"/>
18662 <param name="use_ms1_correlation" value="false"/>
18663 <param name="use_sonar_scores" value="false"/>
18664 <param name="use_ion_mobility_scores" value="false"/>
18665 <param name="use_ms1_fullscan" value="false"/>
18666 <param name="use_ms1_mi" value="false"/>
18667 <param name="use_uis_scores" value="false"/>
18668 </section>
18669 </section>
18670 <section name="peptideEstimation">
18671 <param name="InitialQualityCutoff" value="0.5"/>
18672 <param name="OverallQualityCutoff" value="5.5"/>
18673 <param name="NrRTBins" value="10"/>
18674 <param name="MinPeptidesPerBin" value="1"/>
18675 <param name="MinBinsFilled" value="8"/>
18676 </section>
18677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18678 <output name="ctd_out" ftype="xml">
18679 <assert_contents>
18680 <is_valid_xml/>
18681 </assert_contents>
18682 </output>
18683 </test>
18684 <test expect_num_outputs="2">
18685 <conditional name="adv_opts_cond">
18686 <param name="adv_opts_selector" value="advanced"/>
18687 <param name="force" value="false"/>
18688 <param name="test" value="true"/>
18689 </conditional>
18690 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
18691 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
18692 <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
18693 <param name="min_rsq" value="0.95"/>
18694 <param name="min_coverage" value="0.6"/>
18695 <param name="estimateBestPeptides" value="true"/>
18696 <section name="RTNormalization">
18697 <param name="outlierMethod" value="iter_residual"/>
18698 <param name="useIterativeChauvenet" value="false"/>
18699 <param name="RANSACMaxIterations" value="1000"/>
18700 <param name="RANSACMaxPercentRTThreshold" value="3"/>
18701 <param name="RANSACSamplingSize" value="10"/>
18702 </section>
18703 <section name="algorithm">
18704 <param name="stop_report_after_feature" value="-1"/>
18705 <param name="rt_extraction_window" value="-1.0"/>
18706 <param name="rt_normalization_factor" value="1.0"/>
18707 <param name="quantification_cutoff" value="0.0"/>
18708 <param name="write_convex_hull" value="false"/>
18709 <param name="spectrum_addition_method" value="simple"/>
18710 <param name="add_up_spectra" value="1"/>
18711 <param name="spacing_for_spectra_resampling" value="0.005"/>
18712 <param name="uis_threshold_sn" value="-1"/>
18713 <param name="uis_threshold_peak_area" value="0"/>
18714 <param name="scoring_model" value="default"/>
18715 <param name="im_extra_drift" value="0.0"/>
18716 <section name="TransitionGroupPicker">
18717 <param name="stop_after_feature" value="-1"/>
18718 <param name="stop_after_intensity_ratio" value="0.0001"/>
18719 <param name="min_peak_width" value="-1.0"/>
18720 <param name="peak_integration" value="original"/>
18721 <param name="background_subtraction" value="none"/>
18722 <param name="recalculate_peaks" value="false"/>
18723 <param name="use_precursors" value="false"/>
18724 <param name="use_consensus" value="true"/>
18725 <param name="recalculate_peaks_max_z" value="1.0"/>
18726 <param name="minimal_quality" value="-10000.0"/>
18727 <param name="resample_boundary" value="15.0"/>
18728 <param name="compute_peak_quality" value="false"/>
18729 <param name="compute_peak_shape_metrics" value="false"/>
18730 <param name="compute_total_mi" value="false"/>
18731 <param name="boundary_selection_method" value="largest"/>
18732 <section name="PeakPickerMRM">
18733 <param name="sgolay_frame_length" value="15"/>
18734 <param name="sgolay_polynomial_order" value="3"/>
18735 <param name="gauss_width" value="50.0"/>
18736 <param name="use_gauss" value="true"/>
18737 <param name="peak_width" value="-1.0"/>
18738 <param name="signal_to_noise" value="1.0"/>
18739 <param name="sn_win_len" value="1000.0"/>
18740 <param name="sn_bin_count" value="30"/>
18741 <param name="write_sn_log_messages" value="false"/>
18742 <param name="remove_overlapping_peaks" value="false"/>
18743 <param name="method" value="corrected"/>
18744 </section>
18745 <section name="PeakIntegrator">
18746 <param name="integration_type" value="intensity_sum"/>
18747 <param name="baseline_type" value="base_to_base"/>
18748 <param name="fit_EMG" value="false"/>
18749 </section>
18750 </section>
18751 <section name="DIAScoring">
18752 <param name="dia_extraction_window" value="0.05"/>
18753 <param name="dia_extraction_unit" value="Th"/>
18754 <param name="dia_centroided" value="false"/>
18755 <param name="dia_byseries_intensity_min" value="300.0"/>
18756 <param name="dia_byseries_ppm_diff" value="10.0"/>
18757 <param name="dia_nr_isotopes" value="4"/>
18758 <param name="dia_nr_charges" value="4"/>
18759 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18760 </section>
18761 <section name="EMGScoring">
18762 <param name="interpolation_step" value="0.2"/>
18763 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18764 <param name="max_iteration" value="500"/>
18765 <section name="statistics">
18766 <param name="mean" value="1.0"/>
18767 <param name="variance" value="1.0"/>
18768 </section>
18769 </section>
18770 <section name="Scores">
18771 <param name="use_shape_score" value="true"/>
18772 <param name="use_coelution_score" value="true"/>
18773 <param name="use_rt_score" value="true"/>
18774 <param name="use_library_score" value="true"/>
18775 <param name="use_elution_model_score" value="true"/>
18776 <param name="use_intensity_score" value="true"/>
18777 <param name="use_nr_peaks_score" value="true"/>
18778 <param name="use_total_xic_score" value="true"/>
18779 <param name="use_total_mi_score" value="false"/>
18780 <param name="use_sn_score" value="true"/>
18781 <param name="use_mi_score" value="false"/>
18782 <param name="use_dia_scores" value="true"/>
18783 <param name="use_ms1_correlation" value="false"/>
18784 <param name="use_sonar_scores" value="false"/>
18785 <param name="use_ion_mobility_scores" value="false"/>
18786 <param name="use_ms1_fullscan" value="false"/>
18787 <param name="use_ms1_mi" value="false"/>
18788 <param name="use_uis_scores" value="false"/>
18789 </section>
18790 </section>
18791 <section name="peptideEstimation">
18792 <param name="InitialQualityCutoff" value="0.5"/>
18793 <param name="OverallQualityCutoff" value="5.5"/>
18794 <param name="NrRTBins" value="3"/>
18795 <param name="MinPeptidesPerBin" value="1"/>
18796 <param name="MinBinsFilled" value="3"/>
18797 </section>
18798 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18799 <output name="ctd_out" ftype="xml">
18800 <assert_contents>
18801 <is_valid_xml/>
18802 </assert_contents>
18803 </output>
18804 </test>
18805 <test expect_num_outputs="2">
18806 <conditional name="adv_opts_cond">
18807 <param name="adv_opts_selector" value="advanced"/>
18808 <param name="force" value="false"/>
18809 <param name="test" value="true"/>
18810 </conditional>
18811 <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
18812 <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
18813 <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
18814 <param name="min_rsq" value="0.95"/>
18815 <param name="min_coverage" value="0.6"/>
18816 <param name="estimateBestPeptides" value="false"/>
18817 <section name="RTNormalization">
18818 <param name="outlierMethod" value="iter_residual"/>
18819 <param name="useIterativeChauvenet" value="false"/>
18820 <param name="RANSACMaxIterations" value="1000"/>
18821 <param name="RANSACMaxPercentRTThreshold" value="3"/>
18822 <param name="RANSACSamplingSize" value="10"/>
18823 </section>
18824 <section name="algorithm">
18825 <param name="stop_report_after_feature" value="-1"/>
18826 <param name="rt_extraction_window" value="-1.0"/>
18827 <param name="rt_normalization_factor" value="1.0"/>
18828 <param name="quantification_cutoff" value="0.0"/>
18829 <param name="write_convex_hull" value="false"/>
18830 <param name="spectrum_addition_method" value="simple"/>
18831 <param name="add_up_spectra" value="1"/>
18832 <param name="spacing_for_spectra_resampling" value="0.005"/>
18833 <param name="uis_threshold_sn" value="-1"/>
18834 <param name="uis_threshold_peak_area" value="0"/>
18835 <param name="scoring_model" value="default"/>
18836 <param name="im_extra_drift" value="0.0"/>
18837 <section name="TransitionGroupPicker">
18838 <param name="stop_after_feature" value="-1"/>
18839 <param name="stop_after_intensity_ratio" value="0.0001"/>
18840 <param name="min_peak_width" value="-1.0"/>
18841 <param name="peak_integration" value="original"/>
18842 <param name="background_subtraction" value="none"/>
18843 <param name="recalculate_peaks" value="false"/>
18844 <param name="use_precursors" value="false"/>
18845 <param name="use_consensus" value="true"/>
18846 <param name="recalculate_peaks_max_z" value="1.0"/>
18847 <param name="minimal_quality" value="-10000.0"/>
18848 <param name="resample_boundary" value="15.0"/>
18849 <param name="compute_peak_quality" value="false"/>
18850 <param name="compute_peak_shape_metrics" value="false"/>
18851 <param name="compute_total_mi" value="false"/>
18852 <param name="boundary_selection_method" value="largest"/>
18853 <section name="PeakPickerMRM">
18854 <param name="sgolay_frame_length" value="15"/>
18855 <param name="sgolay_polynomial_order" value="3"/>
18856 <param name="gauss_width" value="50.0"/>
18857 <param name="use_gauss" value="true"/>
18858 <param name="peak_width" value="-1.0"/>
18859 <param name="signal_to_noise" value="1.0"/>
18860 <param name="sn_win_len" value="1000.0"/>
18861 <param name="sn_bin_count" value="30"/>
18862 <param name="write_sn_log_messages" value="false"/>
18863 <param name="remove_overlapping_peaks" value="false"/>
18864 <param name="method" value="corrected"/>
18865 </section>
18866 <section name="PeakIntegrator">
18867 <param name="integration_type" value="intensity_sum"/>
18868 <param name="baseline_type" value="base_to_base"/>
18869 <param name="fit_EMG" value="false"/>
18870 </section>
18871 </section>
18872 <section name="DIAScoring">
18873 <param name="dia_extraction_window" value="0.05"/>
18874 <param name="dia_extraction_unit" value="Th"/>
18875 <param name="dia_centroided" value="false"/>
18876 <param name="dia_byseries_intensity_min" value="300.0"/>
18877 <param name="dia_byseries_ppm_diff" value="10.0"/>
18878 <param name="dia_nr_isotopes" value="4"/>
18879 <param name="dia_nr_charges" value="4"/>
18880 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
18881 </section>
18882 <section name="EMGScoring">
18883 <param name="interpolation_step" value="0.2"/>
18884 <param name="tolerance_stdev_bounding_box" value="3.0"/>
18885 <param name="max_iteration" value="500"/>
18886 <section name="statistics">
18887 <param name="mean" value="1.0"/>
18888 <param name="variance" value="1.0"/>
18889 </section>
18890 </section>
18891 <section name="Scores">
18892 <param name="use_shape_score" value="true"/>
18893 <param name="use_coelution_score" value="true"/>
18894 <param name="use_rt_score" value="true"/>
18895 <param name="use_library_score" value="true"/>
18896 <param name="use_elution_model_score" value="true"/>
18897 <param name="use_intensity_score" value="true"/>
18898 <param name="use_nr_peaks_score" value="true"/>
18899 <param name="use_total_xic_score" value="true"/>
18900 <param name="use_total_mi_score" value="false"/>
18901 <param name="use_sn_score" value="true"/>
18902 <param name="use_mi_score" value="false"/>
18903 <param name="use_dia_scores" value="true"/>
18904 <param name="use_ms1_correlation" value="false"/>
18905 <param name="use_sonar_scores" value="false"/>
18906 <param name="use_ion_mobility_scores" value="false"/>
18907 <param name="use_ms1_fullscan" value="false"/>
18908 <param name="use_ms1_mi" value="false"/>
18909 <param name="use_uis_scores" value="false"/>
18910 </section>
18911 </section>
18912 <section name="peptideEstimation">
18913 <param name="InitialQualityCutoff" value="0.5"/>
18914 <param name="OverallQualityCutoff" value="5.5"/>
18915 <param name="NrRTBins" value="10"/>
18916 <param name="MinPeptidesPerBin" value="1"/>
18917 <param name="MinBinsFilled" value="8"/>
18918 </section>
18919 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
18920 <output name="ctd_out" ftype="xml">
18921 <assert_contents>
18922 <is_valid_xml/>
18923 </assert_contents>
18924 </output>
18925 </test>
18926 </xml>
18927 <xml name="autotest_OpenSwathWorkflow">
18928 <test expect_num_outputs="4">
18929 <conditional name="adv_opts_cond">
18930 <param name="adv_opts_selector" value="advanced"/>
18931 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
18932 <param name="sort_swath_maps" value="false"/>
18933 <param name="use_ms1_traces" value="false"/>
18934 <param name="enable_uis_scoring" value="false"/>
18935 <param name="out_chrom_type" value="mzML"/>
18936 <param name="min_upper_edge_dist" value="0.0"/>
18937 <param name="extra_rt_extraction_window" value="0.0"/>
18938 <param name="mz_extraction_window_unit" value="Th"/>
18939 <param name="mz_extraction_window_ms1_unit" value="Th"/>
18940 <param name="use_ms1_ion_mobility" value="true"/>
18941 <param name="matching_window_only" value="false"/>
18942 <param name="irt_mz_extraction_window" value="0.05"/>
18943 <param name="irt_mz_extraction_window_unit" value="Th"/>
18944 <param name="irt_im_extraction_window" value="-1.0"/>
18945 <param name="min_rsq" value="0.95"/>
18946 <param name="min_coverage" value="0.6"/>
18947 <param name="split_file_input" value="false"/>
18948 <param name="use_elution_model_score" value="false"/>
18949 <param name="readOptions" value="normal"/>
18950 <param name="mz_correction_function" value="none"/>
18951 <param name="extraction_function" value="tophat"/>
18952 <param name="batchSize" value="250"/>
18953 <param name="ms1_isotopes" value="0"/>
18954 <param name="force" value="false"/>
18955 <param name="test" value="true"/>
18956 </conditional>
18957 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
18958 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
18959 <param name="tr_type" value=""/>
18960 <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
18961 <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
18962 <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
18963 <param name="sonar" value="false"/>
18964 <param name="rt_extraction_window" value="600.0"/>
18965 <param name="ion_mobility_window" value="-1.0"/>
18966 <param name="mz_extraction_window" value="0.05"/>
18967 <param name="mz_extraction_window_ms1" value="0.05"/>
18968 <param name="im_extraction_window_ms1" value="-1.0"/>
18969 <section name="Debugging"/>
18970 <section name="Calibration">
18971 <param name="ms1_im_calibration" value="false"/>
18972 <param name="im_correction_function" value="linear"/>
18973 <param name="debug_im_file" value=""/>
18974 <param name="debug_mz_file" value=""/>
18975 </section>
18976 <section name="Library">
18977 <param name="retentionTimeInterpretation" value="iRT"/>
18978 <param name="override_group_label_check" value="false"/>
18979 <param name="force_invalid_mods" value="false"/>
18980 </section>
18981 <section name="RTNormalization">
18982 <param name="alignmentMethod" value="linear"/>
18983 <param name="outlierMethod" value="iter_residual"/>
18984 <param name="useIterativeChauvenet" value="false"/>
18985 <param name="RANSACMaxIterations" value="1000"/>
18986 <param name="RANSACMaxPercentRTThreshold" value="3"/>
18987 <param name="RANSACSamplingSize" value="10"/>
18988 <param name="estimateBestPeptides" value="false"/>
18989 <param name="InitialQualityCutoff" value="0.5"/>
18990 <param name="OverallQualityCutoff" value="5.5"/>
18991 <param name="NrRTBins" value="10"/>
18992 <param name="MinPeptidesPerBin" value="1"/>
18993 <param name="MinBinsFilled" value="8"/>
18994 <section name="lowess">
18995 <param name="span" value="0.666666666666667"/>
18996 </section>
18997 <section name="b_spline">
18998 <param name="num_nodes" value="5"/>
18999 </section>
19000 </section>
19001 <section name="Scoring">
19002 <param name="stop_report_after_feature" value="5"/>
19003 <param name="rt_normalization_factor" value="100.0"/>
19004 <param name="quantification_cutoff" value="0.0"/>
19005 <param name="write_convex_hull" value="false"/>
19006 <param name="spectrum_addition_method" value="simple"/>
19007 <param name="add_up_spectra" value="1"/>
19008 <param name="spacing_for_spectra_resampling" value="0.005"/>
19009 <param name="uis_threshold_sn" value="0"/>
19010 <param name="uis_threshold_peak_area" value="0"/>
19011 <param name="scoring_model" value="default"/>
19012 <param name="im_extra_drift" value="0.0"/>
19013 <section name="TransitionGroupPicker">
19014 <param name="stop_after_feature" value="-1"/>
19015 <param name="min_peak_width" value="-1.0"/>
19016 <param name="peak_integration" value="original"/>
19017 <param name="background_subtraction" value="none"/>
19018 <param name="recalculate_peaks" value="true"/>
19019 <param name="use_precursors" value="false"/>
19020 <param name="use_consensus" value="true"/>
19021 <param name="recalculate_peaks_max_z" value="0.75"/>
19022 <param name="minimal_quality" value="-1.5"/>
19023 <param name="resample_boundary" value="15.0"/>
19024 <param name="compute_peak_quality" value="true"/>
19025 <param name="compute_peak_shape_metrics" value="false"/>
19026 <param name="compute_total_mi" value="false"/>
19027 <param name="boundary_selection_method" value="largest"/>
19028 <section name="PeakPickerMRM">
19029 <param name="sgolay_frame_length" value="11"/>
19030 <param name="sgolay_polynomial_order" value="3"/>
19031 <param name="gauss_width" value="30.0"/>
19032 <param name="use_gauss" value="false"/>
19033 <param name="peak_width" value="-1.0"/>
19034 <param name="signal_to_noise" value="0.1"/>
19035 <param name="write_sn_log_messages" value="false"/>
19036 <param name="remove_overlapping_peaks" value="true"/>
19037 <param name="method" value="corrected"/>
19038 </section>
19039 <section name="PeakIntegrator">
19040 <param name="integration_type" value="intensity_sum"/>
19041 <param name="baseline_type" value="base_to_base"/>
19042 <param name="fit_EMG" value="false"/>
19043 </section>
19044 </section>
19045 <section name="DIAScoring">
19046 <param name="dia_extraction_window" value="0.05"/>
19047 <param name="dia_extraction_unit" value="Th"/>
19048 <param name="dia_centroided" value="false"/>
19049 <param name="dia_byseries_intensity_min" value="300.0"/>
19050 <param name="dia_byseries_ppm_diff" value="10.0"/>
19051 <param name="dia_nr_isotopes" value="4"/>
19052 <param name="dia_nr_charges" value="4"/>
19053 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19054 </section>
19055 <section name="EMGScoring">
19056 <param name="max_iteration" value="10"/>
19057 </section>
19058 <section name="Scores">
19059 <param name="use_shape_score" value="true"/>
19060 <param name="use_coelution_score" value="true"/>
19061 <param name="use_rt_score" value="true"/>
19062 <param name="use_library_score" value="true"/>
19063 <param name="use_intensity_score" value="true"/>
19064 <param name="use_nr_peaks_score" value="true"/>
19065 <param name="use_total_xic_score" value="true"/>
19066 <param name="use_total_mi_score" value="false"/>
19067 <param name="use_sn_score" value="true"/>
19068 <param name="use_mi_score" value="false"/>
19069 <param name="use_dia_scores" value="true"/>
19070 <param name="use_ms1_correlation" value="false"/>
19071 <param name="use_sonar_scores" value="false"/>
19072 <param name="use_ion_mobility_scores" value="false"/>
19073 <param name="use_ms1_fullscan" value="false"/>
19074 <param name="use_ms1_mi" value="false"/>
19075 <param name="use_uis_scores" value="false"/>
19076 </section>
19077 </section>
19078 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
19079 <output name="ctd_out" ftype="xml">
19080 <assert_contents>
19081 <is_valid_xml/>
19082 </assert_contents>
19083 </output>
19084 </test>
19085 <test expect_num_outputs="3">
19086 <conditional name="adv_opts_cond">
19087 <param name="adv_opts_selector" value="advanced"/>
19088 <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
19089 <param name="sort_swath_maps" value="false"/>
19090 <param name="use_ms1_traces" value="false"/>
19091 <param name="enable_uis_scoring" value="false"/>
19092 <param name="out_chrom_type" value="mzML"/>
19093 <param name="min_upper_edge_dist" value="0.0"/>
19094 <param name="extra_rt_extraction_window" value="0.0"/>
19095 <param name="mz_extraction_window_unit" value="Th"/>
19096 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19097 <param name="use_ms1_ion_mobility" value="true"/>
19098 <param name="matching_window_only" value="false"/>
19099 <param name="irt_mz_extraction_window" value="0.05"/>
19100 <param name="irt_mz_extraction_window_unit" value="Th"/>
19101 <param name="irt_im_extraction_window" value="-1.0"/>
19102 <param name="min_rsq" value="0.95"/>
19103 <param name="min_coverage" value="0.6"/>
19104 <param name="split_file_input" value="false"/>
19105 <param name="use_elution_model_score" value="false"/>
19106 <param name="readOptions" value="normal"/>
19107 <param name="mz_correction_function" value="none"/>
19108 <param name="extraction_function" value="tophat"/>
19109 <param name="batchSize" value="250"/>
19110 <param name="ms1_isotopes" value="0"/>
19111 <param name="force" value="false"/>
19112 <param name="test" value="true"/>
19113 </conditional>
19114 <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
19115 <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
19116 <param name="tr_type" value=""/>
19117 <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19118 <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19119 <param name="sonar" value="false"/>
19120 <param name="rt_extraction_window" value="600.0"/>
19121 <param name="ion_mobility_window" value="-1.0"/>
19122 <param name="mz_extraction_window" value="0.05"/>
19123 <param name="mz_extraction_window_ms1" value="0.05"/>
19124 <param name="im_extraction_window_ms1" value="-1.0"/>
19125 <section name="Debugging"/>
19126 <section name="Calibration">
19127 <param name="ms1_im_calibration" value="false"/>
19128 <param name="im_correction_function" value="linear"/>
19129 <param name="debug_im_file" value=""/>
19130 <param name="debug_mz_file" value=""/>
19131 </section>
19132 <section name="Library">
19133 <param name="retentionTimeInterpretation" value="iRT"/>
19134 <param name="override_group_label_check" value="false"/>
19135 <param name="force_invalid_mods" value="false"/>
19136 </section>
19137 <section name="RTNormalization">
19138 <param name="alignmentMethod" value="linear"/>
19139 <param name="outlierMethod" value="iter_residual"/>
19140 <param name="useIterativeChauvenet" value="false"/>
19141 <param name="RANSACMaxIterations" value="1000"/>
19142 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19143 <param name="RANSACSamplingSize" value="10"/>
19144 <param name="estimateBestPeptides" value="false"/>
19145 <param name="InitialQualityCutoff" value="0.5"/>
19146 <param name="OverallQualityCutoff" value="5.5"/>
19147 <param name="NrRTBins" value="10"/>
19148 <param name="MinPeptidesPerBin" value="1"/>
19149 <param name="MinBinsFilled" value="8"/>
19150 <section name="lowess">
19151 <param name="span" value="0.666666666666667"/>
19152 </section>
19153 <section name="b_spline">
19154 <param name="num_nodes" value="5"/>
19155 </section>
19156 </section>
19157 <section name="Scoring">
19158 <param name="stop_report_after_feature" value="5"/>
19159 <param name="rt_normalization_factor" value="100.0"/>
19160 <param name="quantification_cutoff" value="0.0"/>
19161 <param name="write_convex_hull" value="false"/>
19162 <param name="spectrum_addition_method" value="simple"/>
19163 <param name="add_up_spectra" value="1"/>
19164 <param name="spacing_for_spectra_resampling" value="0.005"/>
19165 <param name="uis_threshold_sn" value="0"/>
19166 <param name="uis_threshold_peak_area" value="0"/>
19167 <param name="scoring_model" value="default"/>
19168 <param name="im_extra_drift" value="0.0"/>
19169 <section name="TransitionGroupPicker">
19170 <param name="stop_after_feature" value="-1"/>
19171 <param name="min_peak_width" value="-1.0"/>
19172 <param name="peak_integration" value="original"/>
19173 <param name="background_subtraction" value="none"/>
19174 <param name="recalculate_peaks" value="true"/>
19175 <param name="use_precursors" value="false"/>
19176 <param name="use_consensus" value="true"/>
19177 <param name="recalculate_peaks_max_z" value="0.75"/>
19178 <param name="minimal_quality" value="-1.5"/>
19179 <param name="resample_boundary" value="15.0"/>
19180 <param name="compute_peak_quality" value="true"/>
19181 <param name="compute_peak_shape_metrics" value="false"/>
19182 <param name="compute_total_mi" value="false"/>
19183 <param name="boundary_selection_method" value="largest"/>
19184 <section name="PeakPickerMRM">
19185 <param name="sgolay_frame_length" value="11"/>
19186 <param name="sgolay_polynomial_order" value="3"/>
19187 <param name="gauss_width" value="30.0"/>
19188 <param name="use_gauss" value="false"/>
19189 <param name="peak_width" value="-1.0"/>
19190 <param name="signal_to_noise" value="0.1"/>
19191 <param name="write_sn_log_messages" value="false"/>
19192 <param name="remove_overlapping_peaks" value="true"/>
19193 <param name="method" value="corrected"/>
19194 </section>
19195 <section name="PeakIntegrator">
19196 <param name="integration_type" value="intensity_sum"/>
19197 <param name="baseline_type" value="base_to_base"/>
19198 <param name="fit_EMG" value="false"/>
19199 </section>
19200 </section>
19201 <section name="DIAScoring">
19202 <param name="dia_extraction_window" value="0.05"/>
19203 <param name="dia_extraction_unit" value="Th"/>
19204 <param name="dia_centroided" value="false"/>
19205 <param name="dia_byseries_intensity_min" value="300.0"/>
19206 <param name="dia_byseries_ppm_diff" value="10.0"/>
19207 <param name="dia_nr_isotopes" value="4"/>
19208 <param name="dia_nr_charges" value="4"/>
19209 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19210 </section>
19211 <section name="EMGScoring">
19212 <param name="max_iteration" value="10"/>
19213 </section>
19214 <section name="Scores">
19215 <param name="use_shape_score" value="true"/>
19216 <param name="use_coelution_score" value="true"/>
19217 <param name="use_rt_score" value="true"/>
19218 <param name="use_library_score" value="true"/>
19219 <param name="use_intensity_score" value="true"/>
19220 <param name="use_nr_peaks_score" value="true"/>
19221 <param name="use_total_xic_score" value="true"/>
19222 <param name="use_total_mi_score" value="false"/>
19223 <param name="use_sn_score" value="true"/>
19224 <param name="use_mi_score" value="false"/>
19225 <param name="use_dia_scores" value="true"/>
19226 <param name="use_ms1_correlation" value="false"/>
19227 <param name="use_sonar_scores" value="false"/>
19228 <param name="use_ion_mobility_scores" value="false"/>
19229 <param name="use_ms1_fullscan" value="false"/>
19230 <param name="use_ms1_mi" value="false"/>
19231 <param name="use_uis_scores" value="false"/>
19232 </section>
19233 </section>
19234 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19235 <output name="ctd_out" ftype="xml">
19236 <assert_contents>
19237 <is_valid_xml/>
19238 </assert_contents>
19239 </output>
19240 </test>
19241 <test expect_num_outputs="3">
19242 <conditional name="adv_opts_cond">
19243 <param name="adv_opts_selector" value="advanced"/>
19244 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19245 <param name="sort_swath_maps" value="false"/>
19246 <param name="use_ms1_traces" value="true"/>
19247 <param name="enable_uis_scoring" value="false"/>
19248 <param name="out_chrom_type" value="mzML"/>
19249 <param name="min_upper_edge_dist" value="0.0"/>
19250 <param name="extra_rt_extraction_window" value="0.0"/>
19251 <param name="mz_extraction_window_unit" value="Th"/>
19252 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19253 <param name="use_ms1_ion_mobility" value="true"/>
19254 <param name="matching_window_only" value="false"/>
19255 <param name="irt_mz_extraction_window" value="0.05"/>
19256 <param name="irt_mz_extraction_window_unit" value="Th"/>
19257 <param name="irt_im_extraction_window" value="-1.0"/>
19258 <param name="min_rsq" value="0.95"/>
19259 <param name="min_coverage" value="0.6"/>
19260 <param name="split_file_input" value="false"/>
19261 <param name="use_elution_model_score" value="false"/>
19262 <param name="readOptions" value="normal"/>
19263 <param name="mz_correction_function" value="none"/>
19264 <param name="extraction_function" value="tophat"/>
19265 <param name="batchSize" value="250"/>
19266 <param name="ms1_isotopes" value="0"/>
19267 <param name="force" value="false"/>
19268 <param name="test" value="true"/>
19269 </conditional>
19270 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19271 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19272 <param name="tr_type" value=""/>
19273 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19274 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19275 <param name="sonar" value="false"/>
19276 <param name="rt_extraction_window" value="600.0"/>
19277 <param name="ion_mobility_window" value="-1.0"/>
19278 <param name="mz_extraction_window" value="0.05"/>
19279 <param name="mz_extraction_window_ms1" value="0.05"/>
19280 <param name="im_extraction_window_ms1" value="-1.0"/>
19281 <section name="Debugging"/>
19282 <section name="Calibration">
19283 <param name="ms1_im_calibration" value="false"/>
19284 <param name="im_correction_function" value="linear"/>
19285 <param name="debug_im_file" value=""/>
19286 <param name="debug_mz_file" value=""/>
19287 </section>
19288 <section name="Library">
19289 <param name="retentionTimeInterpretation" value="iRT"/>
19290 <param name="override_group_label_check" value="false"/>
19291 <param name="force_invalid_mods" value="false"/>
19292 </section>
19293 <section name="RTNormalization">
19294 <param name="alignmentMethod" value="linear"/>
19295 <param name="outlierMethod" value="iter_residual"/>
19296 <param name="useIterativeChauvenet" value="false"/>
19297 <param name="RANSACMaxIterations" value="1000"/>
19298 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19299 <param name="RANSACSamplingSize" value="10"/>
19300 <param name="estimateBestPeptides" value="false"/>
19301 <param name="InitialQualityCutoff" value="0.5"/>
19302 <param name="OverallQualityCutoff" value="5.5"/>
19303 <param name="NrRTBins" value="10"/>
19304 <param name="MinPeptidesPerBin" value="1"/>
19305 <param name="MinBinsFilled" value="8"/>
19306 <section name="lowess">
19307 <param name="span" value="0.666666666666667"/>
19308 </section>
19309 <section name="b_spline">
19310 <param name="num_nodes" value="5"/>
19311 </section>
19312 </section>
19313 <section name="Scoring">
19314 <param name="stop_report_after_feature" value="5"/>
19315 <param name="rt_normalization_factor" value="100.0"/>
19316 <param name="quantification_cutoff" value="0.0"/>
19317 <param name="write_convex_hull" value="false"/>
19318 <param name="spectrum_addition_method" value="simple"/>
19319 <param name="add_up_spectra" value="1"/>
19320 <param name="spacing_for_spectra_resampling" value="0.005"/>
19321 <param name="uis_threshold_sn" value="0"/>
19322 <param name="uis_threshold_peak_area" value="0"/>
19323 <param name="scoring_model" value="default"/>
19324 <param name="im_extra_drift" value="0.0"/>
19325 <section name="TransitionGroupPicker">
19326 <param name="stop_after_feature" value="-1"/>
19327 <param name="min_peak_width" value="-1.0"/>
19328 <param name="peak_integration" value="original"/>
19329 <param name="background_subtraction" value="none"/>
19330 <param name="recalculate_peaks" value="true"/>
19331 <param name="use_precursors" value="false"/>
19332 <param name="use_consensus" value="true"/>
19333 <param name="recalculate_peaks_max_z" value="0.75"/>
19334 <param name="minimal_quality" value="-1.5"/>
19335 <param name="resample_boundary" value="15.0"/>
19336 <param name="compute_peak_quality" value="true"/>
19337 <param name="compute_peak_shape_metrics" value="false"/>
19338 <param name="compute_total_mi" value="false"/>
19339 <param name="boundary_selection_method" value="largest"/>
19340 <section name="PeakPickerMRM">
19341 <param name="sgolay_frame_length" value="11"/>
19342 <param name="sgolay_polynomial_order" value="3"/>
19343 <param name="gauss_width" value="30.0"/>
19344 <param name="use_gauss" value="false"/>
19345 <param name="peak_width" value="-1.0"/>
19346 <param name="signal_to_noise" value="0.1"/>
19347 <param name="write_sn_log_messages" value="false"/>
19348 <param name="remove_overlapping_peaks" value="true"/>
19349 <param name="method" value="corrected"/>
19350 </section>
19351 <section name="PeakIntegrator">
19352 <param name="integration_type" value="intensity_sum"/>
19353 <param name="baseline_type" value="base_to_base"/>
19354 <param name="fit_EMG" value="false"/>
19355 </section>
19356 </section>
19357 <section name="DIAScoring">
19358 <param name="dia_extraction_window" value="0.05"/>
19359 <param name="dia_extraction_unit" value="Th"/>
19360 <param name="dia_centroided" value="false"/>
19361 <param name="dia_byseries_intensity_min" value="300.0"/>
19362 <param name="dia_byseries_ppm_diff" value="10.0"/>
19363 <param name="dia_nr_isotopes" value="4"/>
19364 <param name="dia_nr_charges" value="4"/>
19365 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19366 </section>
19367 <section name="EMGScoring">
19368 <param name="max_iteration" value="10"/>
19369 </section>
19370 <section name="Scores">
19371 <param name="use_shape_score" value="true"/>
19372 <param name="use_coelution_score" value="true"/>
19373 <param name="use_rt_score" value="true"/>
19374 <param name="use_library_score" value="true"/>
19375 <param name="use_intensity_score" value="true"/>
19376 <param name="use_nr_peaks_score" value="true"/>
19377 <param name="use_total_xic_score" value="true"/>
19378 <param name="use_total_mi_score" value="false"/>
19379 <param name="use_sn_score" value="true"/>
19380 <param name="use_mi_score" value="false"/>
19381 <param name="use_dia_scores" value="true"/>
19382 <param name="use_ms1_correlation" value="false"/>
19383 <param name="use_sonar_scores" value="false"/>
19384 <param name="use_ion_mobility_scores" value="false"/>
19385 <param name="use_ms1_fullscan" value="false"/>
19386 <param name="use_ms1_mi" value="false"/>
19387 <param name="use_uis_scores" value="false"/>
19388 </section>
19389 </section>
19390 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19391 <output name="ctd_out" ftype="xml">
19392 <assert_contents>
19393 <is_valid_xml/>
19394 </assert_contents>
19395 </output>
19396 </test>
19397 <test expect_num_outputs="3">
19398 <conditional name="adv_opts_cond">
19399 <param name="adv_opts_selector" value="advanced"/>
19400 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19401 <param name="sort_swath_maps" value="false"/>
19402 <param name="use_ms1_traces" value="true"/>
19403 <param name="enable_uis_scoring" value="false"/>
19404 <param name="out_chrom_type" value="mzML"/>
19405 <param name="min_upper_edge_dist" value="0.0"/>
19406 <param name="extra_rt_extraction_window" value="0.0"/>
19407 <param name="mz_extraction_window_unit" value="Th"/>
19408 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19409 <param name="use_ms1_ion_mobility" value="true"/>
19410 <param name="matching_window_only" value="false"/>
19411 <param name="irt_mz_extraction_window" value="0.05"/>
19412 <param name="irt_mz_extraction_window_unit" value="Th"/>
19413 <param name="irt_im_extraction_window" value="-1.0"/>
19414 <param name="min_rsq" value="0.95"/>
19415 <param name="min_coverage" value="0.6"/>
19416 <param name="split_file_input" value="false"/>
19417 <param name="use_elution_model_score" value="false"/>
19418 <param name="readOptions" value="normal"/>
19419 <param name="mz_correction_function" value="none"/>
19420 <param name="extraction_function" value="tophat"/>
19421 <param name="batchSize" value="250"/>
19422 <param name="ms1_isotopes" value="0"/>
19423 <param name="force" value="false"/>
19424 <param name="test" value="true"/>
19425 </conditional>
19426 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19427 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19428 <param name="tr_type" value=""/>
19429 <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
19430 <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
19431 <param name="sonar" value="false"/>
19432 <param name="rt_extraction_window" value="600.0"/>
19433 <param name="ion_mobility_window" value="-1.0"/>
19434 <param name="mz_extraction_window" value="0.05"/>
19435 <param name="mz_extraction_window_ms1" value="0.05"/>
19436 <param name="im_extraction_window_ms1" value="-1.0"/>
19437 <section name="Debugging"/>
19438 <section name="Calibration">
19439 <param name="ms1_im_calibration" value="false"/>
19440 <param name="im_correction_function" value="linear"/>
19441 <param name="debug_im_file" value=""/>
19442 <param name="debug_mz_file" value=""/>
19443 </section>
19444 <section name="Library">
19445 <param name="retentionTimeInterpretation" value="iRT"/>
19446 <param name="override_group_label_check" value="false"/>
19447 <param name="force_invalid_mods" value="false"/>
19448 </section>
19449 <section name="RTNormalization">
19450 <param name="alignmentMethod" value="linear"/>
19451 <param name="outlierMethod" value="iter_residual"/>
19452 <param name="useIterativeChauvenet" value="false"/>
19453 <param name="RANSACMaxIterations" value="1000"/>
19454 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19455 <param name="RANSACSamplingSize" value="10"/>
19456 <param name="estimateBestPeptides" value="false"/>
19457 <param name="InitialQualityCutoff" value="0.5"/>
19458 <param name="OverallQualityCutoff" value="5.5"/>
19459 <param name="NrRTBins" value="10"/>
19460 <param name="MinPeptidesPerBin" value="1"/>
19461 <param name="MinBinsFilled" value="8"/>
19462 <section name="lowess">
19463 <param name="span" value="0.666666666666667"/>
19464 </section>
19465 <section name="b_spline">
19466 <param name="num_nodes" value="5"/>
19467 </section>
19468 </section>
19469 <section name="Scoring">
19470 <param name="stop_report_after_feature" value="5"/>
19471 <param name="rt_normalization_factor" value="100.0"/>
19472 <param name="quantification_cutoff" value="0.0"/>
19473 <param name="write_convex_hull" value="false"/>
19474 <param name="spectrum_addition_method" value="simple"/>
19475 <param name="add_up_spectra" value="1"/>
19476 <param name="spacing_for_spectra_resampling" value="0.005"/>
19477 <param name="uis_threshold_sn" value="0"/>
19478 <param name="uis_threshold_peak_area" value="0"/>
19479 <param name="scoring_model" value="default"/>
19480 <param name="im_extra_drift" value="0.0"/>
19481 <section name="TransitionGroupPicker">
19482 <param name="stop_after_feature" value="-1"/>
19483 <param name="min_peak_width" value="-1.0"/>
19484 <param name="peak_integration" value="original"/>
19485 <param name="background_subtraction" value="none"/>
19486 <param name="recalculate_peaks" value="true"/>
19487 <param name="use_precursors" value="false"/>
19488 <param name="use_consensus" value="true"/>
19489 <param name="recalculate_peaks_max_z" value="0.75"/>
19490 <param name="minimal_quality" value="-1.5"/>
19491 <param name="resample_boundary" value="15.0"/>
19492 <param name="compute_peak_quality" value="true"/>
19493 <param name="compute_peak_shape_metrics" value="false"/>
19494 <param name="compute_total_mi" value="false"/>
19495 <param name="boundary_selection_method" value="largest"/>
19496 <section name="PeakPickerMRM">
19497 <param name="sgolay_frame_length" value="11"/>
19498 <param name="sgolay_polynomial_order" value="3"/>
19499 <param name="gauss_width" value="30.0"/>
19500 <param name="use_gauss" value="false"/>
19501 <param name="peak_width" value="-1.0"/>
19502 <param name="signal_to_noise" value="0.1"/>
19503 <param name="write_sn_log_messages" value="false"/>
19504 <param name="remove_overlapping_peaks" value="true"/>
19505 <param name="method" value="corrected"/>
19506 </section>
19507 <section name="PeakIntegrator">
19508 <param name="integration_type" value="intensity_sum"/>
19509 <param name="baseline_type" value="base_to_base"/>
19510 <param name="fit_EMG" value="false"/>
19511 </section>
19512 </section>
19513 <section name="DIAScoring">
19514 <param name="dia_extraction_window" value="0.05"/>
19515 <param name="dia_extraction_unit" value="Th"/>
19516 <param name="dia_centroided" value="false"/>
19517 <param name="dia_byseries_intensity_min" value="300.0"/>
19518 <param name="dia_byseries_ppm_diff" value="10.0"/>
19519 <param name="dia_nr_isotopes" value="4"/>
19520 <param name="dia_nr_charges" value="4"/>
19521 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19522 </section>
19523 <section name="EMGScoring">
19524 <param name="max_iteration" value="10"/>
19525 </section>
19526 <section name="Scores">
19527 <param name="use_shape_score" value="true"/>
19528 <param name="use_coelution_score" value="true"/>
19529 <param name="use_rt_score" value="true"/>
19530 <param name="use_library_score" value="true"/>
19531 <param name="use_intensity_score" value="true"/>
19532 <param name="use_nr_peaks_score" value="true"/>
19533 <param name="use_total_xic_score" value="true"/>
19534 <param name="use_total_mi_score" value="false"/>
19535 <param name="use_sn_score" value="true"/>
19536 <param name="use_mi_score" value="false"/>
19537 <param name="use_dia_scores" value="true"/>
19538 <param name="use_ms1_correlation" value="false"/>
19539 <param name="use_sonar_scores" value="false"/>
19540 <param name="use_ion_mobility_scores" value="false"/>
19541 <param name="use_ms1_fullscan" value="false"/>
19542 <param name="use_ms1_mi" value="false"/>
19543 <param name="use_uis_scores" value="false"/>
19544 </section>
19545 </section>
19546 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
19547 <output name="ctd_out" ftype="xml">
19548 <assert_contents>
19549 <is_valid_xml/>
19550 </assert_contents>
19551 </output>
19552 </test>
19553 <test expect_num_outputs="3">
19554 <conditional name="adv_opts_cond">
19555 <param name="adv_opts_selector" value="advanced"/>
19556 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19557 <param name="sort_swath_maps" value="false"/>
19558 <param name="use_ms1_traces" value="true"/>
19559 <param name="enable_uis_scoring" value="false"/>
19560 <param name="out_chrom_type" value="mzML"/>
19561 <param name="min_upper_edge_dist" value="0.0"/>
19562 <param name="extra_rt_extraction_window" value="0.0"/>
19563 <param name="mz_extraction_window_unit" value="Th"/>
19564 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19565 <param name="use_ms1_ion_mobility" value="true"/>
19566 <param name="matching_window_only" value="false"/>
19567 <param name="irt_mz_extraction_window" value="0.05"/>
19568 <param name="irt_mz_extraction_window_unit" value="Th"/>
19569 <param name="irt_im_extraction_window" value="-1.0"/>
19570 <param name="min_rsq" value="0.95"/>
19571 <param name="min_coverage" value="0.6"/>
19572 <param name="split_file_input" value="false"/>
19573 <param name="use_elution_model_score" value="false"/>
19574 <param name="readOptions" value="cache"/>
19575 <param name="mz_correction_function" value="none"/>
19576 <param name="extraction_function" value="tophat"/>
19577 <param name="batchSize" value="250"/>
19578 <param name="ms1_isotopes" value="0"/>
19579 <param name="force" value="false"/>
19580 <param name="test" value="true"/>
19581 </conditional>
19582 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19583 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19584 <param name="tr_type" value=""/>
19585 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19586 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19587 <param name="sonar" value="false"/>
19588 <param name="rt_extraction_window" value="600.0"/>
19589 <param name="ion_mobility_window" value="-1.0"/>
19590 <param name="mz_extraction_window" value="0.05"/>
19591 <param name="mz_extraction_window_ms1" value="0.05"/>
19592 <param name="im_extraction_window_ms1" value="-1.0"/>
19593 <section name="Debugging"/>
19594 <section name="Calibration">
19595 <param name="ms1_im_calibration" value="false"/>
19596 <param name="im_correction_function" value="linear"/>
19597 <param name="debug_im_file" value=""/>
19598 <param name="debug_mz_file" value=""/>
19599 </section>
19600 <section name="Library">
19601 <param name="retentionTimeInterpretation" value="iRT"/>
19602 <param name="override_group_label_check" value="false"/>
19603 <param name="force_invalid_mods" value="false"/>
19604 </section>
19605 <section name="RTNormalization">
19606 <param name="alignmentMethod" value="linear"/>
19607 <param name="outlierMethod" value="iter_residual"/>
19608 <param name="useIterativeChauvenet" value="false"/>
19609 <param name="RANSACMaxIterations" value="1000"/>
19610 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19611 <param name="RANSACSamplingSize" value="10"/>
19612 <param name="estimateBestPeptides" value="false"/>
19613 <param name="InitialQualityCutoff" value="0.5"/>
19614 <param name="OverallQualityCutoff" value="5.5"/>
19615 <param name="NrRTBins" value="10"/>
19616 <param name="MinPeptidesPerBin" value="1"/>
19617 <param name="MinBinsFilled" value="8"/>
19618 <section name="lowess">
19619 <param name="span" value="0.666666666666667"/>
19620 </section>
19621 <section name="b_spline">
19622 <param name="num_nodes" value="5"/>
19623 </section>
19624 </section>
19625 <section name="Scoring">
19626 <param name="stop_report_after_feature" value="5"/>
19627 <param name="rt_normalization_factor" value="100.0"/>
19628 <param name="quantification_cutoff" value="0.0"/>
19629 <param name="write_convex_hull" value="false"/>
19630 <param name="spectrum_addition_method" value="simple"/>
19631 <param name="add_up_spectra" value="1"/>
19632 <param name="spacing_for_spectra_resampling" value="0.005"/>
19633 <param name="uis_threshold_sn" value="0"/>
19634 <param name="uis_threshold_peak_area" value="0"/>
19635 <param name="scoring_model" value="default"/>
19636 <param name="im_extra_drift" value="0.0"/>
19637 <section name="TransitionGroupPicker">
19638 <param name="stop_after_feature" value="-1"/>
19639 <param name="min_peak_width" value="-1.0"/>
19640 <param name="peak_integration" value="original"/>
19641 <param name="background_subtraction" value="none"/>
19642 <param name="recalculate_peaks" value="true"/>
19643 <param name="use_precursors" value="false"/>
19644 <param name="use_consensus" value="true"/>
19645 <param name="recalculate_peaks_max_z" value="0.75"/>
19646 <param name="minimal_quality" value="-1.5"/>
19647 <param name="resample_boundary" value="15.0"/>
19648 <param name="compute_peak_quality" value="true"/>
19649 <param name="compute_peak_shape_metrics" value="false"/>
19650 <param name="compute_total_mi" value="false"/>
19651 <param name="boundary_selection_method" value="largest"/>
19652 <section name="PeakPickerMRM">
19653 <param name="sgolay_frame_length" value="11"/>
19654 <param name="sgolay_polynomial_order" value="3"/>
19655 <param name="gauss_width" value="30.0"/>
19656 <param name="use_gauss" value="false"/>
19657 <param name="peak_width" value="-1.0"/>
19658 <param name="signal_to_noise" value="0.1"/>
19659 <param name="write_sn_log_messages" value="false"/>
19660 <param name="remove_overlapping_peaks" value="true"/>
19661 <param name="method" value="corrected"/>
19662 </section>
19663 <section name="PeakIntegrator">
19664 <param name="integration_type" value="intensity_sum"/>
19665 <param name="baseline_type" value="base_to_base"/>
19666 <param name="fit_EMG" value="false"/>
19667 </section>
19668 </section>
19669 <section name="DIAScoring">
19670 <param name="dia_extraction_window" value="0.05"/>
19671 <param name="dia_extraction_unit" value="Th"/>
19672 <param name="dia_centroided" value="false"/>
19673 <param name="dia_byseries_intensity_min" value="300.0"/>
19674 <param name="dia_byseries_ppm_diff" value="10.0"/>
19675 <param name="dia_nr_isotopes" value="4"/>
19676 <param name="dia_nr_charges" value="4"/>
19677 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19678 </section>
19679 <section name="EMGScoring">
19680 <param name="max_iteration" value="10"/>
19681 </section>
19682 <section name="Scores">
19683 <param name="use_shape_score" value="true"/>
19684 <param name="use_coelution_score" value="true"/>
19685 <param name="use_rt_score" value="true"/>
19686 <param name="use_library_score" value="true"/>
19687 <param name="use_intensity_score" value="true"/>
19688 <param name="use_nr_peaks_score" value="true"/>
19689 <param name="use_total_xic_score" value="true"/>
19690 <param name="use_total_mi_score" value="false"/>
19691 <param name="use_sn_score" value="true"/>
19692 <param name="use_mi_score" value="false"/>
19693 <param name="use_dia_scores" value="true"/>
19694 <param name="use_ms1_correlation" value="false"/>
19695 <param name="use_sonar_scores" value="false"/>
19696 <param name="use_ion_mobility_scores" value="false"/>
19697 <param name="use_ms1_fullscan" value="false"/>
19698 <param name="use_ms1_mi" value="false"/>
19699 <param name="use_uis_scores" value="false"/>
19700 </section>
19701 </section>
19702 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19703 <output name="ctd_out" ftype="xml">
19704 <assert_contents>
19705 <is_valid_xml/>
19706 </assert_contents>
19707 </output>
19708 </test>
19709 <test expect_num_outputs="3">
19710 <conditional name="adv_opts_cond">
19711 <param name="adv_opts_selector" value="advanced"/>
19712 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19713 <param name="sort_swath_maps" value="false"/>
19714 <param name="use_ms1_traces" value="true"/>
19715 <param name="enable_uis_scoring" value="false"/>
19716 <param name="out_chrom_type" value="mzML"/>
19717 <param name="min_upper_edge_dist" value="0.0"/>
19718 <param name="extra_rt_extraction_window" value="0.0"/>
19719 <param name="mz_extraction_window_unit" value="Th"/>
19720 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19721 <param name="use_ms1_ion_mobility" value="true"/>
19722 <param name="matching_window_only" value="false"/>
19723 <param name="irt_mz_extraction_window" value="0.05"/>
19724 <param name="irt_mz_extraction_window_unit" value="Th"/>
19725 <param name="irt_im_extraction_window" value="-1.0"/>
19726 <param name="min_rsq" value="0.95"/>
19727 <param name="min_coverage" value="0.6"/>
19728 <param name="split_file_input" value="false"/>
19729 <param name="use_elution_model_score" value="false"/>
19730 <param name="readOptions" value="cacheWorkingInMemory"/>
19731 <param name="mz_correction_function" value="none"/>
19732 <param name="extraction_function" value="tophat"/>
19733 <param name="batchSize" value="250"/>
19734 <param name="ms1_isotopes" value="0"/>
19735 <param name="force" value="false"/>
19736 <param name="test" value="true"/>
19737 </conditional>
19738 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19739 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19740 <param name="tr_type" value=""/>
19741 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19742 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19743 <param name="sonar" value="false"/>
19744 <param name="rt_extraction_window" value="600.0"/>
19745 <param name="ion_mobility_window" value="-1.0"/>
19746 <param name="mz_extraction_window" value="0.05"/>
19747 <param name="mz_extraction_window_ms1" value="0.05"/>
19748 <param name="im_extraction_window_ms1" value="-1.0"/>
19749 <section name="Debugging"/>
19750 <section name="Calibration">
19751 <param name="ms1_im_calibration" value="false"/>
19752 <param name="im_correction_function" value="linear"/>
19753 <param name="debug_im_file" value=""/>
19754 <param name="debug_mz_file" value=""/>
19755 </section>
19756 <section name="Library">
19757 <param name="retentionTimeInterpretation" value="iRT"/>
19758 <param name="override_group_label_check" value="false"/>
19759 <param name="force_invalid_mods" value="false"/>
19760 </section>
19761 <section name="RTNormalization">
19762 <param name="alignmentMethod" value="linear"/>
19763 <param name="outlierMethod" value="iter_residual"/>
19764 <param name="useIterativeChauvenet" value="false"/>
19765 <param name="RANSACMaxIterations" value="1000"/>
19766 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19767 <param name="RANSACSamplingSize" value="10"/>
19768 <param name="estimateBestPeptides" value="false"/>
19769 <param name="InitialQualityCutoff" value="0.5"/>
19770 <param name="OverallQualityCutoff" value="5.5"/>
19771 <param name="NrRTBins" value="10"/>
19772 <param name="MinPeptidesPerBin" value="1"/>
19773 <param name="MinBinsFilled" value="8"/>
19774 <section name="lowess">
19775 <param name="span" value="0.666666666666667"/>
19776 </section>
19777 <section name="b_spline">
19778 <param name="num_nodes" value="5"/>
19779 </section>
19780 </section>
19781 <section name="Scoring">
19782 <param name="stop_report_after_feature" value="5"/>
19783 <param name="rt_normalization_factor" value="100.0"/>
19784 <param name="quantification_cutoff" value="0.0"/>
19785 <param name="write_convex_hull" value="false"/>
19786 <param name="spectrum_addition_method" value="simple"/>
19787 <param name="add_up_spectra" value="1"/>
19788 <param name="spacing_for_spectra_resampling" value="0.005"/>
19789 <param name="uis_threshold_sn" value="0"/>
19790 <param name="uis_threshold_peak_area" value="0"/>
19791 <param name="scoring_model" value="default"/>
19792 <param name="im_extra_drift" value="0.0"/>
19793 <section name="TransitionGroupPicker">
19794 <param name="stop_after_feature" value="-1"/>
19795 <param name="min_peak_width" value="-1.0"/>
19796 <param name="peak_integration" value="original"/>
19797 <param name="background_subtraction" value="none"/>
19798 <param name="recalculate_peaks" value="true"/>
19799 <param name="use_precursors" value="false"/>
19800 <param name="use_consensus" value="true"/>
19801 <param name="recalculate_peaks_max_z" value="0.75"/>
19802 <param name="minimal_quality" value="-1.5"/>
19803 <param name="resample_boundary" value="15.0"/>
19804 <param name="compute_peak_quality" value="true"/>
19805 <param name="compute_peak_shape_metrics" value="false"/>
19806 <param name="compute_total_mi" value="false"/>
19807 <param name="boundary_selection_method" value="largest"/>
19808 <section name="PeakPickerMRM">
19809 <param name="sgolay_frame_length" value="11"/>
19810 <param name="sgolay_polynomial_order" value="3"/>
19811 <param name="gauss_width" value="30.0"/>
19812 <param name="use_gauss" value="false"/>
19813 <param name="peak_width" value="-1.0"/>
19814 <param name="signal_to_noise" value="0.1"/>
19815 <param name="write_sn_log_messages" value="false"/>
19816 <param name="remove_overlapping_peaks" value="true"/>
19817 <param name="method" value="corrected"/>
19818 </section>
19819 <section name="PeakIntegrator">
19820 <param name="integration_type" value="intensity_sum"/>
19821 <param name="baseline_type" value="base_to_base"/>
19822 <param name="fit_EMG" value="false"/>
19823 </section>
19824 </section>
19825 <section name="DIAScoring">
19826 <param name="dia_extraction_window" value="0.05"/>
19827 <param name="dia_extraction_unit" value="Th"/>
19828 <param name="dia_centroided" value="false"/>
19829 <param name="dia_byseries_intensity_min" value="300.0"/>
19830 <param name="dia_byseries_ppm_diff" value="10.0"/>
19831 <param name="dia_nr_isotopes" value="4"/>
19832 <param name="dia_nr_charges" value="4"/>
19833 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19834 </section>
19835 <section name="EMGScoring">
19836 <param name="max_iteration" value="10"/>
19837 </section>
19838 <section name="Scores">
19839 <param name="use_shape_score" value="true"/>
19840 <param name="use_coelution_score" value="true"/>
19841 <param name="use_rt_score" value="true"/>
19842 <param name="use_library_score" value="true"/>
19843 <param name="use_intensity_score" value="true"/>
19844 <param name="use_nr_peaks_score" value="true"/>
19845 <param name="use_total_xic_score" value="true"/>
19846 <param name="use_total_mi_score" value="false"/>
19847 <param name="use_sn_score" value="true"/>
19848 <param name="use_mi_score" value="false"/>
19849 <param name="use_dia_scores" value="true"/>
19850 <param name="use_ms1_correlation" value="false"/>
19851 <param name="use_sonar_scores" value="false"/>
19852 <param name="use_ion_mobility_scores" value="false"/>
19853 <param name="use_ms1_fullscan" value="false"/>
19854 <param name="use_ms1_mi" value="false"/>
19855 <param name="use_uis_scores" value="false"/>
19856 </section>
19857 </section>
19858 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
19859 <output name="ctd_out" ftype="xml">
19860 <assert_contents>
19861 <is_valid_xml/>
19862 </assert_contents>
19863 </output>
19864 </test>
19865 <test expect_num_outputs="3">
19866 <conditional name="adv_opts_cond">
19867 <param name="adv_opts_selector" value="advanced"/>
19868 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
19869 <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
19870 <param name="sort_swath_maps" value="false"/>
19871 <param name="use_ms1_traces" value="true"/>
19872 <param name="enable_uis_scoring" value="false"/>
19873 <param name="out_chrom_type" value="mzML"/>
19874 <param name="min_upper_edge_dist" value="0.0"/>
19875 <param name="extra_rt_extraction_window" value="0.0"/>
19876 <param name="mz_extraction_window_unit" value="Th"/>
19877 <param name="mz_extraction_window_ms1_unit" value="Th"/>
19878 <param name="use_ms1_ion_mobility" value="true"/>
19879 <param name="matching_window_only" value="false"/>
19880 <param name="irt_mz_extraction_window" value="0.05"/>
19881 <param name="irt_mz_extraction_window_unit" value="Th"/>
19882 <param name="irt_im_extraction_window" value="-1.0"/>
19883 <param name="min_rsq" value="0.95"/>
19884 <param name="min_coverage" value="0.6"/>
19885 <param name="split_file_input" value="false"/>
19886 <param name="use_elution_model_score" value="false"/>
19887 <param name="readOptions" value="normal"/>
19888 <param name="mz_correction_function" value="none"/>
19889 <param name="extraction_function" value="tophat"/>
19890 <param name="batchSize" value="250"/>
19891 <param name="ms1_isotopes" value="0"/>
19892 <param name="force" value="false"/>
19893 <param name="test" value="true"/>
19894 </conditional>
19895 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
19896 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
19897 <param name="tr_type" value=""/>
19898 <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
19899 <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
19900 <param name="sonar" value="false"/>
19901 <param name="rt_extraction_window" value="600.0"/>
19902 <param name="ion_mobility_window" value="-1.0"/>
19903 <param name="mz_extraction_window" value="0.05"/>
19904 <param name="mz_extraction_window_ms1" value="0.05"/>
19905 <param name="im_extraction_window_ms1" value="-1.0"/>
19906 <section name="Debugging"/>
19907 <section name="Calibration">
19908 <param name="ms1_im_calibration" value="false"/>
19909 <param name="im_correction_function" value="linear"/>
19910 <param name="debug_im_file" value=""/>
19911 <param name="debug_mz_file" value=""/>
19912 </section>
19913 <section name="Library">
19914 <param name="retentionTimeInterpretation" value="iRT"/>
19915 <param name="override_group_label_check" value="false"/>
19916 <param name="force_invalid_mods" value="false"/>
19917 </section>
19918 <section name="RTNormalization">
19919 <param name="alignmentMethod" value="linear"/>
19920 <param name="outlierMethod" value="iter_residual"/>
19921 <param name="useIterativeChauvenet" value="false"/>
19922 <param name="RANSACMaxIterations" value="1000"/>
19923 <param name="RANSACMaxPercentRTThreshold" value="3"/>
19924 <param name="RANSACSamplingSize" value="10"/>
19925 <param name="estimateBestPeptides" value="false"/>
19926 <param name="InitialQualityCutoff" value="0.5"/>
19927 <param name="OverallQualityCutoff" value="5.5"/>
19928 <param name="NrRTBins" value="10"/>
19929 <param name="MinPeptidesPerBin" value="1"/>
19930 <param name="MinBinsFilled" value="8"/>
19931 <section name="lowess">
19932 <param name="span" value="0.666666666666667"/>
19933 </section>
19934 <section name="b_spline">
19935 <param name="num_nodes" value="5"/>
19936 </section>
19937 </section>
19938 <section name="Scoring">
19939 <param name="stop_report_after_feature" value="5"/>
19940 <param name="rt_normalization_factor" value="100.0"/>
19941 <param name="quantification_cutoff" value="0.0"/>
19942 <param name="write_convex_hull" value="false"/>
19943 <param name="spectrum_addition_method" value="simple"/>
19944 <param name="add_up_spectra" value="1"/>
19945 <param name="spacing_for_spectra_resampling" value="0.005"/>
19946 <param name="uis_threshold_sn" value="0"/>
19947 <param name="uis_threshold_peak_area" value="0"/>
19948 <param name="scoring_model" value="default"/>
19949 <param name="im_extra_drift" value="0.0"/>
19950 <section name="TransitionGroupPicker">
19951 <param name="stop_after_feature" value="-1"/>
19952 <param name="min_peak_width" value="-1.0"/>
19953 <param name="peak_integration" value="original"/>
19954 <param name="background_subtraction" value="none"/>
19955 <param name="recalculate_peaks" value="true"/>
19956 <param name="use_precursors" value="false"/>
19957 <param name="use_consensus" value="true"/>
19958 <param name="recalculate_peaks_max_z" value="0.75"/>
19959 <param name="minimal_quality" value="-1.5"/>
19960 <param name="resample_boundary" value="15.0"/>
19961 <param name="compute_peak_quality" value="true"/>
19962 <param name="compute_peak_shape_metrics" value="false"/>
19963 <param name="compute_total_mi" value="false"/>
19964 <param name="boundary_selection_method" value="largest"/>
19965 <section name="PeakPickerMRM">
19966 <param name="sgolay_frame_length" value="11"/>
19967 <param name="sgolay_polynomial_order" value="3"/>
19968 <param name="gauss_width" value="30.0"/>
19969 <param name="use_gauss" value="false"/>
19970 <param name="peak_width" value="-1.0"/>
19971 <param name="signal_to_noise" value="0.1"/>
19972 <param name="write_sn_log_messages" value="false"/>
19973 <param name="remove_overlapping_peaks" value="true"/>
19974 <param name="method" value="corrected"/>
19975 </section>
19976 <section name="PeakIntegrator">
19977 <param name="integration_type" value="intensity_sum"/>
19978 <param name="baseline_type" value="base_to_base"/>
19979 <param name="fit_EMG" value="false"/>
19980 </section>
19981 </section>
19982 <section name="DIAScoring">
19983 <param name="dia_extraction_window" value="0.05"/>
19984 <param name="dia_extraction_unit" value="Th"/>
19985 <param name="dia_centroided" value="false"/>
19986 <param name="dia_byseries_intensity_min" value="300.0"/>
19987 <param name="dia_byseries_ppm_diff" value="10.0"/>
19988 <param name="dia_nr_isotopes" value="4"/>
19989 <param name="dia_nr_charges" value="4"/>
19990 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
19991 </section>
19992 <section name="EMGScoring">
19993 <param name="max_iteration" value="10"/>
19994 </section>
19995 <section name="Scores">
19996 <param name="use_shape_score" value="true"/>
19997 <param name="use_coelution_score" value="true"/>
19998 <param name="use_rt_score" value="true"/>
19999 <param name="use_library_score" value="true"/>
20000 <param name="use_intensity_score" value="true"/>
20001 <param name="use_nr_peaks_score" value="true"/>
20002 <param name="use_total_xic_score" value="true"/>
20003 <param name="use_total_mi_score" value="false"/>
20004 <param name="use_sn_score" value="true"/>
20005 <param name="use_mi_score" value="false"/>
20006 <param name="use_dia_scores" value="true"/>
20007 <param name="use_ms1_correlation" value="false"/>
20008 <param name="use_sonar_scores" value="false"/>
20009 <param name="use_ion_mobility_scores" value="false"/>
20010 <param name="use_ms1_fullscan" value="false"/>
20011 <param name="use_ms1_mi" value="false"/>
20012 <param name="use_uis_scores" value="false"/>
20013 </section>
20014 </section>
20015 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20016 <output name="ctd_out" ftype="xml">
20017 <assert_contents>
20018 <is_valid_xml/>
20019 </assert_contents>
20020 </output>
20021 </test>
20022 <test expect_num_outputs="3">
20023 <conditional name="adv_opts_cond">
20024 <param name="adv_opts_selector" value="advanced"/>
20025 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20026 <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
20027 <param name="sort_swath_maps" value="false"/>
20028 <param name="use_ms1_traces" value="true"/>
20029 <param name="enable_uis_scoring" value="false"/>
20030 <param name="out_chrom_type" value="mzML"/>
20031 <param name="min_upper_edge_dist" value="0.0"/>
20032 <param name="extra_rt_extraction_window" value="0.0"/>
20033 <param name="mz_extraction_window_unit" value="Th"/>
20034 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20035 <param name="use_ms1_ion_mobility" value="true"/>
20036 <param name="matching_window_only" value="false"/>
20037 <param name="irt_mz_extraction_window" value="0.05"/>
20038 <param name="irt_mz_extraction_window_unit" value="Th"/>
20039 <param name="irt_im_extraction_window" value="-1.0"/>
20040 <param name="min_rsq" value="0.95"/>
20041 <param name="min_coverage" value="0.6"/>
20042 <param name="split_file_input" value="false"/>
20043 <param name="use_elution_model_score" value="false"/>
20044 <param name="readOptions" value="normal"/>
20045 <param name="mz_correction_function" value="none"/>
20046 <param name="extraction_function" value="tophat"/>
20047 <param name="batchSize" value="250"/>
20048 <param name="ms1_isotopes" value="0"/>
20049 <param name="force" value="true"/>
20050 <param name="test" value="true"/>
20051 </conditional>
20052 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20053 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20054 <param name="tr_type" value=""/>
20055 <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20056 <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20057 <param name="sonar" value="false"/>
20058 <param name="rt_extraction_window" value="600.0"/>
20059 <param name="ion_mobility_window" value="-1.0"/>
20060 <param name="mz_extraction_window" value="0.05"/>
20061 <param name="mz_extraction_window_ms1" value="0.05"/>
20062 <param name="im_extraction_window_ms1" value="-1.0"/>
20063 <section name="Debugging"/>
20064 <section name="Calibration">
20065 <param name="ms1_im_calibration" value="false"/>
20066 <param name="im_correction_function" value="linear"/>
20067 <param name="debug_im_file" value=""/>
20068 <param name="debug_mz_file" value=""/>
20069 </section>
20070 <section name="Library">
20071 <param name="retentionTimeInterpretation" value="iRT"/>
20072 <param name="override_group_label_check" value="false"/>
20073 <param name="force_invalid_mods" value="false"/>
20074 </section>
20075 <section name="RTNormalization">
20076 <param name="alignmentMethod" value="linear"/>
20077 <param name="outlierMethod" value="iter_residual"/>
20078 <param name="useIterativeChauvenet" value="false"/>
20079 <param name="RANSACMaxIterations" value="1000"/>
20080 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20081 <param name="RANSACSamplingSize" value="10"/>
20082 <param name="estimateBestPeptides" value="false"/>
20083 <param name="InitialQualityCutoff" value="0.5"/>
20084 <param name="OverallQualityCutoff" value="5.5"/>
20085 <param name="NrRTBins" value="10"/>
20086 <param name="MinPeptidesPerBin" value="1"/>
20087 <param name="MinBinsFilled" value="8"/>
20088 <section name="lowess">
20089 <param name="span" value="0.666666666666667"/>
20090 </section>
20091 <section name="b_spline">
20092 <param name="num_nodes" value="5"/>
20093 </section>
20094 </section>
20095 <section name="Scoring">
20096 <param name="stop_report_after_feature" value="5"/>
20097 <param name="rt_normalization_factor" value="100.0"/>
20098 <param name="quantification_cutoff" value="0.0"/>
20099 <param name="write_convex_hull" value="false"/>
20100 <param name="spectrum_addition_method" value="simple"/>
20101 <param name="add_up_spectra" value="1"/>
20102 <param name="spacing_for_spectra_resampling" value="0.005"/>
20103 <param name="uis_threshold_sn" value="0"/>
20104 <param name="uis_threshold_peak_area" value="0"/>
20105 <param name="scoring_model" value="default"/>
20106 <param name="im_extra_drift" value="0.0"/>
20107 <section name="TransitionGroupPicker">
20108 <param name="stop_after_feature" value="-1"/>
20109 <param name="min_peak_width" value="-1.0"/>
20110 <param name="peak_integration" value="original"/>
20111 <param name="background_subtraction" value="none"/>
20112 <param name="recalculate_peaks" value="true"/>
20113 <param name="use_precursors" value="false"/>
20114 <param name="use_consensus" value="true"/>
20115 <param name="recalculate_peaks_max_z" value="0.75"/>
20116 <param name="minimal_quality" value="-1.5"/>
20117 <param name="resample_boundary" value="15.0"/>
20118 <param name="compute_peak_quality" value="true"/>
20119 <param name="compute_peak_shape_metrics" value="false"/>
20120 <param name="compute_total_mi" value="false"/>
20121 <param name="boundary_selection_method" value="largest"/>
20122 <section name="PeakPickerMRM">
20123 <param name="sgolay_frame_length" value="11"/>
20124 <param name="sgolay_polynomial_order" value="3"/>
20125 <param name="gauss_width" value="30.0"/>
20126 <param name="use_gauss" value="false"/>
20127 <param name="peak_width" value="-1.0"/>
20128 <param name="signal_to_noise" value="0.1"/>
20129 <param name="write_sn_log_messages" value="false"/>
20130 <param name="remove_overlapping_peaks" value="true"/>
20131 <param name="method" value="corrected"/>
20132 </section>
20133 <section name="PeakIntegrator">
20134 <param name="integration_type" value="intensity_sum"/>
20135 <param name="baseline_type" value="base_to_base"/>
20136 <param name="fit_EMG" value="false"/>
20137 </section>
20138 </section>
20139 <section name="DIAScoring">
20140 <param name="dia_extraction_window" value="0.05"/>
20141 <param name="dia_extraction_unit" value="Th"/>
20142 <param name="dia_centroided" value="false"/>
20143 <param name="dia_byseries_intensity_min" value="300.0"/>
20144 <param name="dia_byseries_ppm_diff" value="10.0"/>
20145 <param name="dia_nr_isotopes" value="4"/>
20146 <param name="dia_nr_charges" value="4"/>
20147 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20148 </section>
20149 <section name="EMGScoring">
20150 <param name="max_iteration" value="10"/>
20151 </section>
20152 <section name="Scores">
20153 <param name="use_shape_score" value="true"/>
20154 <param name="use_coelution_score" value="true"/>
20155 <param name="use_rt_score" value="true"/>
20156 <param name="use_library_score" value="true"/>
20157 <param name="use_intensity_score" value="true"/>
20158 <param name="use_nr_peaks_score" value="true"/>
20159 <param name="use_total_xic_score" value="true"/>
20160 <param name="use_total_mi_score" value="false"/>
20161 <param name="use_sn_score" value="true"/>
20162 <param name="use_mi_score" value="false"/>
20163 <param name="use_dia_scores" value="true"/>
20164 <param name="use_ms1_correlation" value="false"/>
20165 <param name="use_sonar_scores" value="false"/>
20166 <param name="use_ion_mobility_scores" value="false"/>
20167 <param name="use_ms1_fullscan" value="false"/>
20168 <param name="use_ms1_mi" value="false"/>
20169 <param name="use_uis_scores" value="false"/>
20170 </section>
20171 </section>
20172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20173 <output name="ctd_out" ftype="xml">
20174 <assert_contents>
20175 <is_valid_xml/>
20176 </assert_contents>
20177 </output>
20178 </test>
20179 <test expect_num_outputs="3">
20180 <conditional name="adv_opts_cond">
20181 <param name="adv_opts_selector" value="advanced"/>
20182 <param name="sort_swath_maps" value="false"/>
20183 <param name="use_ms1_traces" value="false"/>
20184 <param name="enable_uis_scoring" value="false"/>
20185 <param name="out_chrom_type" value="mzML"/>
20186 <param name="min_upper_edge_dist" value="0.0"/>
20187 <param name="extra_rt_extraction_window" value="0.0"/>
20188 <param name="mz_extraction_window_unit" value="Th"/>
20189 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20190 <param name="use_ms1_ion_mobility" value="true"/>
20191 <param name="matching_window_only" value="false"/>
20192 <param name="irt_mz_extraction_window" value="550.0"/>
20193 <param name="irt_mz_extraction_window_unit" value="ppm"/>
20194 <param name="irt_im_extraction_window" value="-1.0"/>
20195 <param name="min_rsq" value="0.95"/>
20196 <param name="min_coverage" value="0.6"/>
20197 <param name="split_file_input" value="false"/>
20198 <param name="use_elution_model_score" value="false"/>
20199 <param name="readOptions" value="normal"/>
20200 <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
20201 <param name="extraction_function" value="tophat"/>
20202 <param name="batchSize" value="250"/>
20203 <param name="ms1_isotopes" value="0"/>
20204 <param name="force" value="false"/>
20205 <param name="test" value="true"/>
20206 </conditional>
20207 <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
20208 <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
20209 <param name="tr_type" value=""/>
20210 <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
20211 <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20212 <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20213 <param name="sonar" value="true"/>
20214 <param name="rt_extraction_window" value="-1.0"/>
20215 <param name="ion_mobility_window" value="-1.0"/>
20216 <param name="mz_extraction_window" value="0.2"/>
20217 <param name="mz_extraction_window_ms1" value="0.05"/>
20218 <param name="im_extraction_window_ms1" value="-1.0"/>
20219 <section name="Debugging"/>
20220 <section name="Calibration">
20221 <param name="ms1_im_calibration" value="false"/>
20222 <param name="im_correction_function" value="linear"/>
20223 <param name="debug_im_file" value=""/>
20224 <param name="debug_mz_file" value=""/>
20225 </section>
20226 <section name="Library">
20227 <param name="retentionTimeInterpretation" value="iRT"/>
20228 <param name="override_group_label_check" value="false"/>
20229 <param name="force_invalid_mods" value="false"/>
20230 </section>
20231 <section name="RTNormalization">
20232 <param name="alignmentMethod" value="linear"/>
20233 <param name="outlierMethod" value="none"/>
20234 <param name="useIterativeChauvenet" value="false"/>
20235 <param name="RANSACMaxIterations" value="1000"/>
20236 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20237 <param name="RANSACSamplingSize" value="10"/>
20238 <param name="estimateBestPeptides" value="false"/>
20239 <param name="InitialQualityCutoff" value="0.5"/>
20240 <param name="OverallQualityCutoff" value="5.5"/>
20241 <param name="NrRTBins" value="10"/>
20242 <param name="MinPeptidesPerBin" value="1"/>
20243 <param name="MinBinsFilled" value="8"/>
20244 <section name="lowess">
20245 <param name="span" value="0.666666666666667"/>
20246 </section>
20247 <section name="b_spline">
20248 <param name="num_nodes" value="5"/>
20249 </section>
20250 </section>
20251 <section name="Scoring">
20252 <param name="stop_report_after_feature" value="5"/>
20253 <param name="rt_normalization_factor" value="100.0"/>
20254 <param name="quantification_cutoff" value="0.0"/>
20255 <param name="write_convex_hull" value="false"/>
20256 <param name="spectrum_addition_method" value="simple"/>
20257 <param name="add_up_spectra" value="1"/>
20258 <param name="spacing_for_spectra_resampling" value="0.005"/>
20259 <param name="uis_threshold_sn" value="0"/>
20260 <param name="uis_threshold_peak_area" value="0"/>
20261 <param name="scoring_model" value="default"/>
20262 <param name="im_extra_drift" value="0.0"/>
20263 <section name="TransitionGroupPicker">
20264 <param name="stop_after_feature" value="-1"/>
20265 <param name="min_peak_width" value="-1.0"/>
20266 <param name="peak_integration" value="original"/>
20267 <param name="background_subtraction" value="none"/>
20268 <param name="recalculate_peaks" value="true"/>
20269 <param name="use_precursors" value="false"/>
20270 <param name="use_consensus" value="true"/>
20271 <param name="recalculate_peaks_max_z" value="0.75"/>
20272 <param name="minimal_quality" value="-1.5"/>
20273 <param name="resample_boundary" value="15.0"/>
20274 <param name="compute_peak_quality" value="true"/>
20275 <param name="compute_peak_shape_metrics" value="false"/>
20276 <param name="compute_total_mi" value="false"/>
20277 <param name="boundary_selection_method" value="largest"/>
20278 <section name="PeakPickerMRM">
20279 <param name="sgolay_frame_length" value="11"/>
20280 <param name="sgolay_polynomial_order" value="3"/>
20281 <param name="gauss_width" value="30.0"/>
20282 <param name="use_gauss" value="false"/>
20283 <param name="peak_width" value="-1.0"/>
20284 <param name="signal_to_noise" value="0.1"/>
20285 <param name="write_sn_log_messages" value="false"/>
20286 <param name="remove_overlapping_peaks" value="true"/>
20287 <param name="method" value="corrected"/>
20288 </section>
20289 <section name="PeakIntegrator">
20290 <param name="integration_type" value="intensity_sum"/>
20291 <param name="baseline_type" value="base_to_base"/>
20292 <param name="fit_EMG" value="false"/>
20293 </section>
20294 </section>
20295 <section name="DIAScoring">
20296 <param name="dia_extraction_window" value="0.05"/>
20297 <param name="dia_extraction_unit" value="Th"/>
20298 <param name="dia_centroided" value="false"/>
20299 <param name="dia_byseries_intensity_min" value="300.0"/>
20300 <param name="dia_byseries_ppm_diff" value="10.0"/>
20301 <param name="dia_nr_isotopes" value="4"/>
20302 <param name="dia_nr_charges" value="4"/>
20303 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20304 </section>
20305 <section name="EMGScoring">
20306 <param name="max_iteration" value="10"/>
20307 </section>
20308 <section name="Scores">
20309 <param name="use_shape_score" value="true"/>
20310 <param name="use_coelution_score" value="true"/>
20311 <param name="use_rt_score" value="true"/>
20312 <param name="use_library_score" value="true"/>
20313 <param name="use_intensity_score" value="true"/>
20314 <param name="use_nr_peaks_score" value="true"/>
20315 <param name="use_total_xic_score" value="true"/>
20316 <param name="use_total_mi_score" value="false"/>
20317 <param name="use_sn_score" value="true"/>
20318 <param name="use_mi_score" value="false"/>
20319 <param name="use_dia_scores" value="true"/>
20320 <param name="use_ms1_correlation" value="false"/>
20321 <param name="use_sonar_scores" value="true"/>
20322 <param name="use_ion_mobility_scores" value="false"/>
20323 <param name="use_ms1_fullscan" value="false"/>
20324 <param name="use_ms1_mi" value="false"/>
20325 <param name="use_uis_scores" value="false"/>
20326 </section>
20327 </section>
20328 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20329 <output name="ctd_out" ftype="xml">
20330 <assert_contents>
20331 <is_valid_xml/>
20332 </assert_contents>
20333 </output>
20334 </test>
20335 <test expect_num_outputs="3">
20336 <conditional name="adv_opts_cond">
20337 <param name="adv_opts_selector" value="advanced"/>
20338 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20339 <param name="sort_swath_maps" value="false"/>
20340 <param name="use_ms1_traces" value="true"/>
20341 <param name="enable_uis_scoring" value="false"/>
20342 <param name="out_chrom_type" value="mzML"/>
20343 <param name="min_upper_edge_dist" value="0.0"/>
20344 <param name="extra_rt_extraction_window" value="0.0"/>
20345 <param name="mz_extraction_window_unit" value="Th"/>
20346 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20347 <param name="use_ms1_ion_mobility" value="true"/>
20348 <param name="matching_window_only" value="false"/>
20349 <param name="irt_mz_extraction_window" value="0.05"/>
20350 <param name="irt_mz_extraction_window_unit" value="Th"/>
20351 <param name="irt_im_extraction_window" value="-1.0"/>
20352 <param name="min_rsq" value="0.95"/>
20353 <param name="min_coverage" value="0.6"/>
20354 <param name="split_file_input" value="false"/>
20355 <param name="use_elution_model_score" value="false"/>
20356 <param name="readOptions" value="normal"/>
20357 <param name="mz_correction_function" value="none"/>
20358 <param name="extraction_function" value="tophat"/>
20359 <param name="batchSize" value="250"/>
20360 <param name="ms1_isotopes" value="0"/>
20361 <param name="force" value="false"/>
20362 <param name="test" value="true"/>
20363 </conditional>
20364 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20365 <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
20366 <param name="tr_type" value="pqp"/>
20367 <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
20368 <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20369 <param name="sonar" value="false"/>
20370 <param name="rt_extraction_window" value="600.0"/>
20371 <param name="ion_mobility_window" value="-1.0"/>
20372 <param name="mz_extraction_window" value="0.05"/>
20373 <param name="mz_extraction_window_ms1" value="0.05"/>
20374 <param name="im_extraction_window_ms1" value="-1.0"/>
20375 <section name="Debugging"/>
20376 <section name="Calibration">
20377 <param name="ms1_im_calibration" value="false"/>
20378 <param name="im_correction_function" value="linear"/>
20379 <param name="debug_im_file" value=""/>
20380 <param name="debug_mz_file" value=""/>
20381 </section>
20382 <section name="Library">
20383 <param name="retentionTimeInterpretation" value="iRT"/>
20384 <param name="override_group_label_check" value="false"/>
20385 <param name="force_invalid_mods" value="false"/>
20386 </section>
20387 <section name="RTNormalization">
20388 <param name="alignmentMethod" value="linear"/>
20389 <param name="outlierMethod" value="iter_residual"/>
20390 <param name="useIterativeChauvenet" value="false"/>
20391 <param name="RANSACMaxIterations" value="1000"/>
20392 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20393 <param name="RANSACSamplingSize" value="10"/>
20394 <param name="estimateBestPeptides" value="false"/>
20395 <param name="InitialQualityCutoff" value="0.5"/>
20396 <param name="OverallQualityCutoff" value="5.5"/>
20397 <param name="NrRTBins" value="10"/>
20398 <param name="MinPeptidesPerBin" value="1"/>
20399 <param name="MinBinsFilled" value="8"/>
20400 <section name="lowess">
20401 <param name="span" value="0.666666666666667"/>
20402 </section>
20403 <section name="b_spline">
20404 <param name="num_nodes" value="5"/>
20405 </section>
20406 </section>
20407 <section name="Scoring">
20408 <param name="stop_report_after_feature" value="5"/>
20409 <param name="rt_normalization_factor" value="100.0"/>
20410 <param name="quantification_cutoff" value="0.0"/>
20411 <param name="write_convex_hull" value="false"/>
20412 <param name="spectrum_addition_method" value="simple"/>
20413 <param name="add_up_spectra" value="1"/>
20414 <param name="spacing_for_spectra_resampling" value="0.005"/>
20415 <param name="uis_threshold_sn" value="0"/>
20416 <param name="uis_threshold_peak_area" value="0"/>
20417 <param name="scoring_model" value="default"/>
20418 <param name="im_extra_drift" value="0.0"/>
20419 <section name="TransitionGroupPicker">
20420 <param name="stop_after_feature" value="-1"/>
20421 <param name="min_peak_width" value="-1.0"/>
20422 <param name="peak_integration" value="original"/>
20423 <param name="background_subtraction" value="none"/>
20424 <param name="recalculate_peaks" value="true"/>
20425 <param name="use_precursors" value="false"/>
20426 <param name="use_consensus" value="true"/>
20427 <param name="recalculate_peaks_max_z" value="0.75"/>
20428 <param name="minimal_quality" value="-1.5"/>
20429 <param name="resample_boundary" value="15.0"/>
20430 <param name="compute_peak_quality" value="true"/>
20431 <param name="compute_peak_shape_metrics" value="false"/>
20432 <param name="compute_total_mi" value="false"/>
20433 <param name="boundary_selection_method" value="largest"/>
20434 <section name="PeakPickerMRM">
20435 <param name="sgolay_frame_length" value="11"/>
20436 <param name="sgolay_polynomial_order" value="3"/>
20437 <param name="gauss_width" value="30.0"/>
20438 <param name="use_gauss" value="false"/>
20439 <param name="peak_width" value="-1.0"/>
20440 <param name="signal_to_noise" value="0.1"/>
20441 <param name="write_sn_log_messages" value="false"/>
20442 <param name="remove_overlapping_peaks" value="true"/>
20443 <param name="method" value="corrected"/>
20444 </section>
20445 <section name="PeakIntegrator">
20446 <param name="integration_type" value="intensity_sum"/>
20447 <param name="baseline_type" value="base_to_base"/>
20448 <param name="fit_EMG" value="false"/>
20449 </section>
20450 </section>
20451 <section name="DIAScoring">
20452 <param name="dia_extraction_window" value="0.05"/>
20453 <param name="dia_extraction_unit" value="Th"/>
20454 <param name="dia_centroided" value="false"/>
20455 <param name="dia_byseries_intensity_min" value="300.0"/>
20456 <param name="dia_byseries_ppm_diff" value="10.0"/>
20457 <param name="dia_nr_isotopes" value="4"/>
20458 <param name="dia_nr_charges" value="4"/>
20459 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20460 </section>
20461 <section name="EMGScoring">
20462 <param name="max_iteration" value="10"/>
20463 </section>
20464 <section name="Scores">
20465 <param name="use_shape_score" value="true"/>
20466 <param name="use_coelution_score" value="true"/>
20467 <param name="use_rt_score" value="true"/>
20468 <param name="use_library_score" value="true"/>
20469 <param name="use_intensity_score" value="true"/>
20470 <param name="use_nr_peaks_score" value="true"/>
20471 <param name="use_total_xic_score" value="true"/>
20472 <param name="use_total_mi_score" value="false"/>
20473 <param name="use_sn_score" value="true"/>
20474 <param name="use_mi_score" value="false"/>
20475 <param name="use_dia_scores" value="true"/>
20476 <param name="use_ms1_correlation" value="false"/>
20477 <param name="use_sonar_scores" value="false"/>
20478 <param name="use_ion_mobility_scores" value="false"/>
20479 <param name="use_ms1_fullscan" value="false"/>
20480 <param name="use_ms1_mi" value="false"/>
20481 <param name="use_uis_scores" value="false"/>
20482 </section>
20483 </section>
20484 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
20485 <output name="ctd_out" ftype="xml">
20486 <assert_contents>
20487 <is_valid_xml/>
20488 </assert_contents>
20489 </output>
20490 </test>
20491 <test expect_num_outputs="3">
20492 <conditional name="adv_opts_cond">
20493 <param name="adv_opts_selector" value="advanced"/>
20494 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20495 <param name="sort_swath_maps" value="false"/>
20496 <param name="use_ms1_traces" value="true"/>
20497 <param name="enable_uis_scoring" value="false"/>
20498 <param name="out_chrom_type" value="sqMass"/>
20499 <param name="min_upper_edge_dist" value="0.0"/>
20500 <param name="extra_rt_extraction_window" value="0.0"/>
20501 <param name="mz_extraction_window_unit" value="Th"/>
20502 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20503 <param name="use_ms1_ion_mobility" value="true"/>
20504 <param name="matching_window_only" value="false"/>
20505 <param name="irt_mz_extraction_window" value="0.05"/>
20506 <param name="irt_mz_extraction_window_unit" value="Th"/>
20507 <param name="irt_im_extraction_window" value="-1.0"/>
20508 <param name="min_rsq" value="0.95"/>
20509 <param name="min_coverage" value="0.6"/>
20510 <param name="split_file_input" value="false"/>
20511 <param name="use_elution_model_score" value="false"/>
20512 <param name="readOptions" value="normal"/>
20513 <param name="mz_correction_function" value="none"/>
20514 <param name="extraction_function" value="tophat"/>
20515 <param name="batchSize" value="250"/>
20516 <param name="ms1_isotopes" value="0"/>
20517 <param name="force" value="false"/>
20518 <param name="test" value="true"/>
20519 </conditional>
20520 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
20521 <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
20522 <param name="tr_type" value="pqp"/>
20523 <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
20524 <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
20525 <param name="sonar" value="false"/>
20526 <param name="rt_extraction_window" value="600.0"/>
20527 <param name="ion_mobility_window" value="-1.0"/>
20528 <param name="mz_extraction_window" value="0.05"/>
20529 <param name="mz_extraction_window_ms1" value="0.05"/>
20530 <param name="im_extraction_window_ms1" value="-1.0"/>
20531 <section name="Debugging"/>
20532 <section name="Calibration">
20533 <param name="ms1_im_calibration" value="false"/>
20534 <param name="im_correction_function" value="linear"/>
20535 <param name="debug_im_file" value=""/>
20536 <param name="debug_mz_file" value=""/>
20537 </section>
20538 <section name="Library">
20539 <param name="retentionTimeInterpretation" value="iRT"/>
20540 <param name="override_group_label_check" value="false"/>
20541 <param name="force_invalid_mods" value="false"/>
20542 </section>
20543 <section name="RTNormalization">
20544 <param name="alignmentMethod" value="linear"/>
20545 <param name="outlierMethod" value="iter_residual"/>
20546 <param name="useIterativeChauvenet" value="false"/>
20547 <param name="RANSACMaxIterations" value="1000"/>
20548 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20549 <param name="RANSACSamplingSize" value="10"/>
20550 <param name="estimateBestPeptides" value="false"/>
20551 <param name="InitialQualityCutoff" value="0.5"/>
20552 <param name="OverallQualityCutoff" value="5.5"/>
20553 <param name="NrRTBins" value="10"/>
20554 <param name="MinPeptidesPerBin" value="1"/>
20555 <param name="MinBinsFilled" value="8"/>
20556 <section name="lowess">
20557 <param name="span" value="0.666666666666667"/>
20558 </section>
20559 <section name="b_spline">
20560 <param name="num_nodes" value="5"/>
20561 </section>
20562 </section>
20563 <section name="Scoring">
20564 <param name="stop_report_after_feature" value="5"/>
20565 <param name="rt_normalization_factor" value="100.0"/>
20566 <param name="quantification_cutoff" value="0.0"/>
20567 <param name="write_convex_hull" value="false"/>
20568 <param name="spectrum_addition_method" value="simple"/>
20569 <param name="add_up_spectra" value="1"/>
20570 <param name="spacing_for_spectra_resampling" value="0.005"/>
20571 <param name="uis_threshold_sn" value="0"/>
20572 <param name="uis_threshold_peak_area" value="0"/>
20573 <param name="scoring_model" value="default"/>
20574 <param name="im_extra_drift" value="0.0"/>
20575 <section name="TransitionGroupPicker">
20576 <param name="stop_after_feature" value="-1"/>
20577 <param name="min_peak_width" value="-1.0"/>
20578 <param name="peak_integration" value="original"/>
20579 <param name="background_subtraction" value="none"/>
20580 <param name="recalculate_peaks" value="true"/>
20581 <param name="use_precursors" value="false"/>
20582 <param name="use_consensus" value="true"/>
20583 <param name="recalculate_peaks_max_z" value="0.75"/>
20584 <param name="minimal_quality" value="-1.5"/>
20585 <param name="resample_boundary" value="15.0"/>
20586 <param name="compute_peak_quality" value="true"/>
20587 <param name="compute_peak_shape_metrics" value="false"/>
20588 <param name="compute_total_mi" value="false"/>
20589 <param name="boundary_selection_method" value="largest"/>
20590 <section name="PeakPickerMRM">
20591 <param name="sgolay_frame_length" value="11"/>
20592 <param name="sgolay_polynomial_order" value="3"/>
20593 <param name="gauss_width" value="30.0"/>
20594 <param name="use_gauss" value="false"/>
20595 <param name="peak_width" value="-1.0"/>
20596 <param name="signal_to_noise" value="0.1"/>
20597 <param name="write_sn_log_messages" value="false"/>
20598 <param name="remove_overlapping_peaks" value="true"/>
20599 <param name="method" value="corrected"/>
20600 </section>
20601 <section name="PeakIntegrator">
20602 <param name="integration_type" value="intensity_sum"/>
20603 <param name="baseline_type" value="base_to_base"/>
20604 <param name="fit_EMG" value="false"/>
20605 </section>
20606 </section>
20607 <section name="DIAScoring">
20608 <param name="dia_extraction_window" value="0.05"/>
20609 <param name="dia_extraction_unit" value="Th"/>
20610 <param name="dia_centroided" value="false"/>
20611 <param name="dia_byseries_intensity_min" value="300.0"/>
20612 <param name="dia_byseries_ppm_diff" value="10.0"/>
20613 <param name="dia_nr_isotopes" value="4"/>
20614 <param name="dia_nr_charges" value="4"/>
20615 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20616 </section>
20617 <section name="EMGScoring">
20618 <param name="max_iteration" value="10"/>
20619 </section>
20620 <section name="Scores">
20621 <param name="use_shape_score" value="true"/>
20622 <param name="use_coelution_score" value="true"/>
20623 <param name="use_rt_score" value="true"/>
20624 <param name="use_library_score" value="true"/>
20625 <param name="use_intensity_score" value="true"/>
20626 <param name="use_nr_peaks_score" value="true"/>
20627 <param name="use_total_xic_score" value="true"/>
20628 <param name="use_total_mi_score" value="false"/>
20629 <param name="use_sn_score" value="true"/>
20630 <param name="use_mi_score" value="false"/>
20631 <param name="use_dia_scores" value="true"/>
20632 <param name="use_ms1_correlation" value="false"/>
20633 <param name="use_sonar_scores" value="false"/>
20634 <param name="use_ion_mobility_scores" value="false"/>
20635 <param name="use_ms1_fullscan" value="false"/>
20636 <param name="use_ms1_mi" value="false"/>
20637 <param name="use_uis_scores" value="false"/>
20638 </section>
20639 </section>
20640 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
20641 <output name="ctd_out" ftype="xml">
20642 <assert_contents>
20643 <is_valid_xml/>
20644 </assert_contents>
20645 </output>
20646 </test>
20647 <test expect_num_outputs="3">
20648 <conditional name="adv_opts_cond">
20649 <param name="adv_opts_selector" value="advanced"/>
20650 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20651 <param name="sort_swath_maps" value="false"/>
20652 <param name="use_ms1_traces" value="true"/>
20653 <param name="enable_uis_scoring" value="false"/>
20654 <param name="out_chrom_type" value="mzML"/>
20655 <param name="min_upper_edge_dist" value="0.0"/>
20656 <param name="extra_rt_extraction_window" value="0.0"/>
20657 <param name="mz_extraction_window_unit" value="Th"/>
20658 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20659 <param name="use_ms1_ion_mobility" value="true"/>
20660 <param name="matching_window_only" value="false"/>
20661 <param name="irt_mz_extraction_window" value="0.05"/>
20662 <param name="irt_mz_extraction_window_unit" value="Th"/>
20663 <param name="irt_im_extraction_window" value="-1.0"/>
20664 <param name="min_rsq" value="0.95"/>
20665 <param name="min_coverage" value="0.6"/>
20666 <param name="split_file_input" value="false"/>
20667 <param name="use_elution_model_score" value="false"/>
20668 <param name="readOptions" value="normal"/>
20669 <param name="mz_correction_function" value="none"/>
20670 <param name="extraction_function" value="tophat"/>
20671 <param name="batchSize" value="250"/>
20672 <param name="ms1_isotopes" value="2"/>
20673 <param name="force" value="false"/>
20674 <param name="test" value="true"/>
20675 </conditional>
20676 <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
20677 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20678 <param name="tr_type" value=""/>
20679 <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20680 <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20681 <param name="sonar" value="false"/>
20682 <param name="rt_extraction_window" value="600.0"/>
20683 <param name="ion_mobility_window" value="-1.0"/>
20684 <param name="mz_extraction_window" value="0.05"/>
20685 <param name="mz_extraction_window_ms1" value="0.05"/>
20686 <param name="im_extraction_window_ms1" value="-1.0"/>
20687 <section name="Debugging"/>
20688 <section name="Calibration">
20689 <param name="ms1_im_calibration" value="false"/>
20690 <param name="im_correction_function" value="linear"/>
20691 <param name="debug_im_file" value=""/>
20692 <param name="debug_mz_file" value=""/>
20693 </section>
20694 <section name="Library">
20695 <param name="retentionTimeInterpretation" value="iRT"/>
20696 <param name="override_group_label_check" value="false"/>
20697 <param name="force_invalid_mods" value="false"/>
20698 </section>
20699 <section name="RTNormalization">
20700 <param name="alignmentMethod" value="linear"/>
20701 <param name="outlierMethod" value="iter_residual"/>
20702 <param name="useIterativeChauvenet" value="false"/>
20703 <param name="RANSACMaxIterations" value="1000"/>
20704 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20705 <param name="RANSACSamplingSize" value="10"/>
20706 <param name="estimateBestPeptides" value="false"/>
20707 <param name="InitialQualityCutoff" value="0.5"/>
20708 <param name="OverallQualityCutoff" value="5.5"/>
20709 <param name="NrRTBins" value="10"/>
20710 <param name="MinPeptidesPerBin" value="1"/>
20711 <param name="MinBinsFilled" value="8"/>
20712 <section name="lowess">
20713 <param name="span" value="0.666666666666667"/>
20714 </section>
20715 <section name="b_spline">
20716 <param name="num_nodes" value="5"/>
20717 </section>
20718 </section>
20719 <section name="Scoring">
20720 <param name="stop_report_after_feature" value="5"/>
20721 <param name="rt_normalization_factor" value="100.0"/>
20722 <param name="quantification_cutoff" value="0.0"/>
20723 <param name="write_convex_hull" value="false"/>
20724 <param name="spectrum_addition_method" value="simple"/>
20725 <param name="add_up_spectra" value="1"/>
20726 <param name="spacing_for_spectra_resampling" value="0.005"/>
20727 <param name="uis_threshold_sn" value="0"/>
20728 <param name="uis_threshold_peak_area" value="0"/>
20729 <param name="scoring_model" value="default"/>
20730 <param name="im_extra_drift" value="0.0"/>
20731 <section name="TransitionGroupPicker">
20732 <param name="stop_after_feature" value="-1"/>
20733 <param name="min_peak_width" value="-1.0"/>
20734 <param name="peak_integration" value="original"/>
20735 <param name="background_subtraction" value="none"/>
20736 <param name="recalculate_peaks" value="true"/>
20737 <param name="use_precursors" value="true"/>
20738 <param name="use_consensus" value="true"/>
20739 <param name="recalculate_peaks_max_z" value="0.75"/>
20740 <param name="minimal_quality" value="-1.5"/>
20741 <param name="resample_boundary" value="15.0"/>
20742 <param name="compute_peak_quality" value="false"/>
20743 <param name="compute_peak_shape_metrics" value="false"/>
20744 <param name="compute_total_mi" value="false"/>
20745 <param name="boundary_selection_method" value="largest"/>
20746 <section name="PeakPickerMRM">
20747 <param name="sgolay_frame_length" value="11"/>
20748 <param name="sgolay_polynomial_order" value="3"/>
20749 <param name="gauss_width" value="30.0"/>
20750 <param name="use_gauss" value="false"/>
20751 <param name="peak_width" value="-1.0"/>
20752 <param name="signal_to_noise" value="0.1"/>
20753 <param name="write_sn_log_messages" value="false"/>
20754 <param name="remove_overlapping_peaks" value="true"/>
20755 <param name="method" value="corrected"/>
20756 </section>
20757 <section name="PeakIntegrator">
20758 <param name="integration_type" value="intensity_sum"/>
20759 <param name="baseline_type" value="base_to_base"/>
20760 <param name="fit_EMG" value="false"/>
20761 </section>
20762 </section>
20763 <section name="DIAScoring">
20764 <param name="dia_extraction_window" value="0.05"/>
20765 <param name="dia_extraction_unit" value="Th"/>
20766 <param name="dia_centroided" value="false"/>
20767 <param name="dia_byseries_intensity_min" value="300.0"/>
20768 <param name="dia_byseries_ppm_diff" value="10.0"/>
20769 <param name="dia_nr_isotopes" value="4"/>
20770 <param name="dia_nr_charges" value="4"/>
20771 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20772 </section>
20773 <section name="EMGScoring">
20774 <param name="max_iteration" value="10"/>
20775 </section>
20776 <section name="Scores">
20777 <param name="use_shape_score" value="true"/>
20778 <param name="use_coelution_score" value="true"/>
20779 <param name="use_rt_score" value="true"/>
20780 <param name="use_library_score" value="true"/>
20781 <param name="use_intensity_score" value="true"/>
20782 <param name="use_nr_peaks_score" value="true"/>
20783 <param name="use_total_xic_score" value="true"/>
20784 <param name="use_total_mi_score" value="false"/>
20785 <param name="use_sn_score" value="true"/>
20786 <param name="use_mi_score" value="false"/>
20787 <param name="use_dia_scores" value="true"/>
20788 <param name="use_ms1_correlation" value="false"/>
20789 <param name="use_sonar_scores" value="false"/>
20790 <param name="use_ion_mobility_scores" value="false"/>
20791 <param name="use_ms1_fullscan" value="false"/>
20792 <param name="use_ms1_mi" value="false"/>
20793 <param name="use_uis_scores" value="false"/>
20794 </section>
20795 </section>
20796 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20797 <output name="ctd_out" ftype="xml">
20798 <assert_contents>
20799 <is_valid_xml/>
20800 </assert_contents>
20801 </output>
20802 </test>
20803 <test expect_num_outputs="3">
20804 <conditional name="adv_opts_cond">
20805 <param name="adv_opts_selector" value="advanced"/>
20806 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
20807 <param name="sort_swath_maps" value="false"/>
20808 <param name="use_ms1_traces" value="true"/>
20809 <param name="enable_uis_scoring" value="false"/>
20810 <param name="out_chrom_type" value="mzML"/>
20811 <param name="min_upper_edge_dist" value="0.0"/>
20812 <param name="extra_rt_extraction_window" value="0.0"/>
20813 <param name="mz_extraction_window_unit" value="Th"/>
20814 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20815 <param name="use_ms1_ion_mobility" value="true"/>
20816 <param name="matching_window_only" value="false"/>
20817 <param name="irt_mz_extraction_window" value="0.05"/>
20818 <param name="irt_mz_extraction_window_unit" value="Th"/>
20819 <param name="irt_im_extraction_window" value="-1.0"/>
20820 <param name="min_rsq" value="0.95"/>
20821 <param name="min_coverage" value="0.6"/>
20822 <param name="split_file_input" value="false"/>
20823 <param name="use_elution_model_score" value="false"/>
20824 <param name="readOptions" value="workingInMemory"/>
20825 <param name="mz_correction_function" value="none"/>
20826 <param name="extraction_function" value="tophat"/>
20827 <param name="batchSize" value="250"/>
20828 <param name="ms1_isotopes" value="2"/>
20829 <param name="force" value="false"/>
20830 <param name="test" value="true"/>
20831 </conditional>
20832 <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
20833 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
20834 <param name="tr_type" value=""/>
20835 <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
20836 <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
20837 <param name="sonar" value="false"/>
20838 <param name="rt_extraction_window" value="600.0"/>
20839 <param name="ion_mobility_window" value="-1.0"/>
20840 <param name="mz_extraction_window" value="0.05"/>
20841 <param name="mz_extraction_window_ms1" value="0.05"/>
20842 <param name="im_extraction_window_ms1" value="-1.0"/>
20843 <section name="Debugging"/>
20844 <section name="Calibration">
20845 <param name="ms1_im_calibration" value="false"/>
20846 <param name="im_correction_function" value="linear"/>
20847 <param name="debug_im_file" value=""/>
20848 <param name="debug_mz_file" value=""/>
20849 </section>
20850 <section name="Library">
20851 <param name="retentionTimeInterpretation" value="iRT"/>
20852 <param name="override_group_label_check" value="false"/>
20853 <param name="force_invalid_mods" value="false"/>
20854 </section>
20855 <section name="RTNormalization">
20856 <param name="alignmentMethod" value="linear"/>
20857 <param name="outlierMethod" value="iter_residual"/>
20858 <param name="useIterativeChauvenet" value="false"/>
20859 <param name="RANSACMaxIterations" value="1000"/>
20860 <param name="RANSACMaxPercentRTThreshold" value="3"/>
20861 <param name="RANSACSamplingSize" value="10"/>
20862 <param name="estimateBestPeptides" value="false"/>
20863 <param name="InitialQualityCutoff" value="0.5"/>
20864 <param name="OverallQualityCutoff" value="5.5"/>
20865 <param name="NrRTBins" value="10"/>
20866 <param name="MinPeptidesPerBin" value="1"/>
20867 <param name="MinBinsFilled" value="8"/>
20868 <section name="lowess">
20869 <param name="span" value="0.666666666666667"/>
20870 </section>
20871 <section name="b_spline">
20872 <param name="num_nodes" value="5"/>
20873 </section>
20874 </section>
20875 <section name="Scoring">
20876 <param name="stop_report_after_feature" value="5"/>
20877 <param name="rt_normalization_factor" value="100.0"/>
20878 <param name="quantification_cutoff" value="0.0"/>
20879 <param name="write_convex_hull" value="false"/>
20880 <param name="spectrum_addition_method" value="simple"/>
20881 <param name="add_up_spectra" value="1"/>
20882 <param name="spacing_for_spectra_resampling" value="0.005"/>
20883 <param name="uis_threshold_sn" value="0"/>
20884 <param name="uis_threshold_peak_area" value="0"/>
20885 <param name="scoring_model" value="default"/>
20886 <param name="im_extra_drift" value="0.0"/>
20887 <section name="TransitionGroupPicker">
20888 <param name="stop_after_feature" value="-1"/>
20889 <param name="min_peak_width" value="-1.0"/>
20890 <param name="peak_integration" value="original"/>
20891 <param name="background_subtraction" value="none"/>
20892 <param name="recalculate_peaks" value="true"/>
20893 <param name="use_precursors" value="false"/>
20894 <param name="use_consensus" value="true"/>
20895 <param name="recalculate_peaks_max_z" value="0.75"/>
20896 <param name="minimal_quality" value="-1.5"/>
20897 <param name="resample_boundary" value="15.0"/>
20898 <param name="compute_peak_quality" value="true"/>
20899 <param name="compute_peak_shape_metrics" value="false"/>
20900 <param name="compute_total_mi" value="false"/>
20901 <param name="boundary_selection_method" value="largest"/>
20902 <section name="PeakPickerMRM">
20903 <param name="sgolay_frame_length" value="11"/>
20904 <param name="sgolay_polynomial_order" value="3"/>
20905 <param name="gauss_width" value="30.0"/>
20906 <param name="use_gauss" value="false"/>
20907 <param name="peak_width" value="-1.0"/>
20908 <param name="signal_to_noise" value="0.1"/>
20909 <param name="write_sn_log_messages" value="false"/>
20910 <param name="remove_overlapping_peaks" value="true"/>
20911 <param name="method" value="corrected"/>
20912 </section>
20913 <section name="PeakIntegrator">
20914 <param name="integration_type" value="intensity_sum"/>
20915 <param name="baseline_type" value="base_to_base"/>
20916 <param name="fit_EMG" value="false"/>
20917 </section>
20918 </section>
20919 <section name="DIAScoring">
20920 <param name="dia_extraction_window" value="0.05"/>
20921 <param name="dia_extraction_unit" value="Th"/>
20922 <param name="dia_centroided" value="false"/>
20923 <param name="dia_byseries_intensity_min" value="300.0"/>
20924 <param name="dia_byseries_ppm_diff" value="10.0"/>
20925 <param name="dia_nr_isotopes" value="4"/>
20926 <param name="dia_nr_charges" value="4"/>
20927 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
20928 </section>
20929 <section name="EMGScoring">
20930 <param name="max_iteration" value="10"/>
20931 </section>
20932 <section name="Scores">
20933 <param name="use_shape_score" value="true"/>
20934 <param name="use_coelution_score" value="true"/>
20935 <param name="use_rt_score" value="true"/>
20936 <param name="use_library_score" value="true"/>
20937 <param name="use_intensity_score" value="true"/>
20938 <param name="use_nr_peaks_score" value="true"/>
20939 <param name="use_total_xic_score" value="true"/>
20940 <param name="use_total_mi_score" value="false"/>
20941 <param name="use_sn_score" value="true"/>
20942 <param name="use_mi_score" value="false"/>
20943 <param name="use_dia_scores" value="true"/>
20944 <param name="use_ms1_correlation" value="false"/>
20945 <param name="use_sonar_scores" value="false"/>
20946 <param name="use_ion_mobility_scores" value="false"/>
20947 <param name="use_ms1_fullscan" value="false"/>
20948 <param name="use_ms1_mi" value="false"/>
20949 <param name="use_uis_scores" value="false"/>
20950 </section>
20951 </section>
20952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
20953 <output name="ctd_out" ftype="xml">
20954 <assert_contents>
20955 <is_valid_xml/>
20956 </assert_contents>
20957 </output>
20958 </test>
20959 <test expect_num_outputs="3">
20960 <conditional name="adv_opts_cond">
20961 <param name="adv_opts_selector" value="advanced"/>
20962 <param name="sort_swath_maps" value="false"/>
20963 <param name="use_ms1_traces" value="true"/>
20964 <param name="enable_uis_scoring" value="false"/>
20965 <param name="out_chrom_type" value="mzML"/>
20966 <param name="min_upper_edge_dist" value="0.0"/>
20967 <param name="extra_rt_extraction_window" value="0.0"/>
20968 <param name="mz_extraction_window_unit" value="Th"/>
20969 <param name="mz_extraction_window_ms1_unit" value="Th"/>
20970 <param name="use_ms1_ion_mobility" value="false"/>
20971 <param name="matching_window_only" value="false"/>
20972 <param name="irt_mz_extraction_window" value="0.05"/>
20973 <param name="irt_mz_extraction_window_unit" value="Th"/>
20974 <param name="irt_im_extraction_window" value="-1.0"/>
20975 <param name="min_rsq" value="0.95"/>
20976 <param name="min_coverage" value="0.6"/>
20977 <param name="split_file_input" value="false"/>
20978 <param name="use_elution_model_score" value="false"/>
20979 <param name="readOptions" value="workingInMemory"/>
20980 <param name="mz_correction_function" value="none"/>
20981 <param name="extraction_function" value="tophat"/>
20982 <param name="batchSize" value="250"/>
20983 <param name="ms1_isotopes" value="0"/>
20984 <param name="force" value="false"/>
20985 <param name="test" value="true"/>
20986 </conditional>
20987 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
20988 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
20989 <param name="tr_type" value=""/>
20990 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
20991 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
20992 <param name="sonar" value="false"/>
20993 <param name="rt_extraction_window" value="600.0"/>
20994 <param name="ion_mobility_window" value="0.05"/>
20995 <param name="mz_extraction_window" value="0.05"/>
20996 <param name="mz_extraction_window_ms1" value="0.05"/>
20997 <param name="im_extraction_window_ms1" value="-1.0"/>
20998 <section name="Debugging"/>
20999 <section name="Calibration">
21000 <param name="ms1_im_calibration" value="false"/>
21001 <param name="im_correction_function" value="linear"/>
21002 <param name="debug_im_file" value=""/>
21003 <param name="debug_mz_file" value=""/>
21004 </section>
21005 <section name="Library">
21006 <param name="retentionTimeInterpretation" value="iRT"/>
21007 <param name="override_group_label_check" value="false"/>
21008 <param name="force_invalid_mods" value="false"/>
21009 </section>
21010 <section name="RTNormalization">
21011 <param name="alignmentMethod" value="linear"/>
21012 <param name="outlierMethod" value="iter_residual"/>
21013 <param name="useIterativeChauvenet" value="false"/>
21014 <param name="RANSACMaxIterations" value="1000"/>
21015 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21016 <param name="RANSACSamplingSize" value="10"/>
21017 <param name="estimateBestPeptides" value="false"/>
21018 <param name="InitialQualityCutoff" value="0.5"/>
21019 <param name="OverallQualityCutoff" value="5.5"/>
21020 <param name="NrRTBins" value="10"/>
21021 <param name="MinPeptidesPerBin" value="1"/>
21022 <param name="MinBinsFilled" value="8"/>
21023 <section name="lowess">
21024 <param name="span" value="0.666666666666667"/>
21025 </section>
21026 <section name="b_spline">
21027 <param name="num_nodes" value="5"/>
21028 </section>
21029 </section>
21030 <section name="Scoring">
21031 <param name="stop_report_after_feature" value="5"/>
21032 <param name="rt_normalization_factor" value="100.0"/>
21033 <param name="quantification_cutoff" value="0.0"/>
21034 <param name="write_convex_hull" value="false"/>
21035 <param name="spectrum_addition_method" value="simple"/>
21036 <param name="add_up_spectra" value="1"/>
21037 <param name="spacing_for_spectra_resampling" value="0.005"/>
21038 <param name="uis_threshold_sn" value="0"/>
21039 <param name="uis_threshold_peak_area" value="0"/>
21040 <param name="scoring_model" value="default"/>
21041 <param name="im_extra_drift" value="0.0"/>
21042 <section name="TransitionGroupPicker">
21043 <param name="stop_after_feature" value="-1"/>
21044 <param name="min_peak_width" value="-1.0"/>
21045 <param name="peak_integration" value="original"/>
21046 <param name="background_subtraction" value="none"/>
21047 <param name="recalculate_peaks" value="true"/>
21048 <param name="use_precursors" value="false"/>
21049 <param name="use_consensus" value="true"/>
21050 <param name="recalculate_peaks_max_z" value="0.75"/>
21051 <param name="minimal_quality" value="-1.5"/>
21052 <param name="resample_boundary" value="15.0"/>
21053 <param name="compute_peak_quality" value="true"/>
21054 <param name="compute_peak_shape_metrics" value="false"/>
21055 <param name="compute_total_mi" value="false"/>
21056 <param name="boundary_selection_method" value="largest"/>
21057 <section name="PeakPickerMRM">
21058 <param name="sgolay_frame_length" value="11"/>
21059 <param name="sgolay_polynomial_order" value="3"/>
21060 <param name="gauss_width" value="30.0"/>
21061 <param name="use_gauss" value="false"/>
21062 <param name="peak_width" value="-1.0"/>
21063 <param name="signal_to_noise" value="0.1"/>
21064 <param name="write_sn_log_messages" value="false"/>
21065 <param name="remove_overlapping_peaks" value="true"/>
21066 <param name="method" value="corrected"/>
21067 </section>
21068 <section name="PeakIntegrator">
21069 <param name="integration_type" value="intensity_sum"/>
21070 <param name="baseline_type" value="base_to_base"/>
21071 <param name="fit_EMG" value="false"/>
21072 </section>
21073 </section>
21074 <section name="DIAScoring">
21075 <param name="dia_extraction_window" value="0.05"/>
21076 <param name="dia_extraction_unit" value="Th"/>
21077 <param name="dia_centroided" value="false"/>
21078 <param name="dia_byseries_intensity_min" value="300.0"/>
21079 <param name="dia_byseries_ppm_diff" value="10.0"/>
21080 <param name="dia_nr_isotopes" value="4"/>
21081 <param name="dia_nr_charges" value="4"/>
21082 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21083 </section>
21084 <section name="EMGScoring">
21085 <param name="max_iteration" value="10"/>
21086 </section>
21087 <section name="Scores">
21088 <param name="use_shape_score" value="true"/>
21089 <param name="use_coelution_score" value="true"/>
21090 <param name="use_rt_score" value="true"/>
21091 <param name="use_library_score" value="true"/>
21092 <param name="use_intensity_score" value="true"/>
21093 <param name="use_nr_peaks_score" value="true"/>
21094 <param name="use_total_xic_score" value="true"/>
21095 <param name="use_total_mi_score" value="false"/>
21096 <param name="use_sn_score" value="true"/>
21097 <param name="use_mi_score" value="false"/>
21098 <param name="use_dia_scores" value="true"/>
21099 <param name="use_ms1_correlation" value="false"/>
21100 <param name="use_sonar_scores" value="false"/>
21101 <param name="use_ion_mobility_scores" value="true"/>
21102 <param name="use_ms1_fullscan" value="false"/>
21103 <param name="use_ms1_mi" value="false"/>
21104 <param name="use_uis_scores" value="false"/>
21105 </section>
21106 </section>
21107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21108 <output name="ctd_out" ftype="xml">
21109 <assert_contents>
21110 <is_valid_xml/>
21111 </assert_contents>
21112 </output>
21113 </test>
21114 <test expect_num_outputs="3">
21115 <conditional name="adv_opts_cond">
21116 <param name="adv_opts_selector" value="advanced"/>
21117 <param name="sort_swath_maps" value="false"/>
21118 <param name="use_ms1_traces" value="true"/>
21119 <param name="enable_uis_scoring" value="false"/>
21120 <param name="out_chrom_type" value="mzML"/>
21121 <param name="min_upper_edge_dist" value="0.0"/>
21122 <param name="extra_rt_extraction_window" value="0.0"/>
21123 <param name="mz_extraction_window_unit" value="Th"/>
21124 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21125 <param name="use_ms1_ion_mobility" value="false"/>
21126 <param name="matching_window_only" value="false"/>
21127 <param name="irt_mz_extraction_window" value="0.05"/>
21128 <param name="irt_mz_extraction_window_unit" value="Th"/>
21129 <param name="irt_im_extraction_window" value="-1.0"/>
21130 <param name="min_rsq" value="0.95"/>
21131 <param name="min_coverage" value="0.6"/>
21132 <param name="split_file_input" value="false"/>
21133 <param name="use_elution_model_score" value="false"/>
21134 <param name="readOptions" value="cache"/>
21135 <param name="mz_correction_function" value="none"/>
21136 <param name="extraction_function" value="tophat"/>
21137 <param name="batchSize" value="250"/>
21138 <param name="ms1_isotopes" value="0"/>
21139 <param name="force" value="false"/>
21140 <param name="test" value="true"/>
21141 </conditional>
21142 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21143 <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
21144 <param name="tr_type" value=""/>
21145 <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
21146 <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
21147 <param name="sonar" value="false"/>
21148 <param name="rt_extraction_window" value="600.0"/>
21149 <param name="ion_mobility_window" value="0.05"/>
21150 <param name="mz_extraction_window" value="0.05"/>
21151 <param name="mz_extraction_window_ms1" value="0.05"/>
21152 <param name="im_extraction_window_ms1" value="-1.0"/>
21153 <section name="Debugging"/>
21154 <section name="Calibration">
21155 <param name="ms1_im_calibration" value="false"/>
21156 <param name="im_correction_function" value="linear"/>
21157 <param name="debug_im_file" value=""/>
21158 <param name="debug_mz_file" value=""/>
21159 </section>
21160 <section name="Library">
21161 <param name="retentionTimeInterpretation" value="iRT"/>
21162 <param name="override_group_label_check" value="false"/>
21163 <param name="force_invalid_mods" value="false"/>
21164 </section>
21165 <section name="RTNormalization">
21166 <param name="alignmentMethod" value="linear"/>
21167 <param name="outlierMethod" value="iter_residual"/>
21168 <param name="useIterativeChauvenet" value="false"/>
21169 <param name="RANSACMaxIterations" value="1000"/>
21170 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21171 <param name="RANSACSamplingSize" value="10"/>
21172 <param name="estimateBestPeptides" value="false"/>
21173 <param name="InitialQualityCutoff" value="0.5"/>
21174 <param name="OverallQualityCutoff" value="5.5"/>
21175 <param name="NrRTBins" value="10"/>
21176 <param name="MinPeptidesPerBin" value="1"/>
21177 <param name="MinBinsFilled" value="8"/>
21178 <section name="lowess">
21179 <param name="span" value="0.666666666666667"/>
21180 </section>
21181 <section name="b_spline">
21182 <param name="num_nodes" value="5"/>
21183 </section>
21184 </section>
21185 <section name="Scoring">
21186 <param name="stop_report_after_feature" value="5"/>
21187 <param name="rt_normalization_factor" value="100.0"/>
21188 <param name="quantification_cutoff" value="0.0"/>
21189 <param name="write_convex_hull" value="false"/>
21190 <param name="spectrum_addition_method" value="simple"/>
21191 <param name="add_up_spectra" value="1"/>
21192 <param name="spacing_for_spectra_resampling" value="0.005"/>
21193 <param name="uis_threshold_sn" value="0"/>
21194 <param name="uis_threshold_peak_area" value="0"/>
21195 <param name="scoring_model" value="default"/>
21196 <param name="im_extra_drift" value="0.0"/>
21197 <section name="TransitionGroupPicker">
21198 <param name="stop_after_feature" value="-1"/>
21199 <param name="min_peak_width" value="-1.0"/>
21200 <param name="peak_integration" value="original"/>
21201 <param name="background_subtraction" value="none"/>
21202 <param name="recalculate_peaks" value="true"/>
21203 <param name="use_precursors" value="false"/>
21204 <param name="use_consensus" value="true"/>
21205 <param name="recalculate_peaks_max_z" value="0.75"/>
21206 <param name="minimal_quality" value="-1.5"/>
21207 <param name="resample_boundary" value="15.0"/>
21208 <param name="compute_peak_quality" value="true"/>
21209 <param name="compute_peak_shape_metrics" value="false"/>
21210 <param name="compute_total_mi" value="false"/>
21211 <param name="boundary_selection_method" value="largest"/>
21212 <section name="PeakPickerMRM">
21213 <param name="sgolay_frame_length" value="11"/>
21214 <param name="sgolay_polynomial_order" value="3"/>
21215 <param name="gauss_width" value="30.0"/>
21216 <param name="use_gauss" value="false"/>
21217 <param name="peak_width" value="-1.0"/>
21218 <param name="signal_to_noise" value="0.1"/>
21219 <param name="write_sn_log_messages" value="false"/>
21220 <param name="remove_overlapping_peaks" value="true"/>
21221 <param name="method" value="corrected"/>
21222 </section>
21223 <section name="PeakIntegrator">
21224 <param name="integration_type" value="intensity_sum"/>
21225 <param name="baseline_type" value="base_to_base"/>
21226 <param name="fit_EMG" value="false"/>
21227 </section>
21228 </section>
21229 <section name="DIAScoring">
21230 <param name="dia_extraction_window" value="0.05"/>
21231 <param name="dia_extraction_unit" value="Th"/>
21232 <param name="dia_centroided" value="false"/>
21233 <param name="dia_byseries_intensity_min" value="300.0"/>
21234 <param name="dia_byseries_ppm_diff" value="10.0"/>
21235 <param name="dia_nr_isotopes" value="4"/>
21236 <param name="dia_nr_charges" value="4"/>
21237 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21238 </section>
21239 <section name="EMGScoring">
21240 <param name="max_iteration" value="10"/>
21241 </section>
21242 <section name="Scores">
21243 <param name="use_shape_score" value="true"/>
21244 <param name="use_coelution_score" value="true"/>
21245 <param name="use_rt_score" value="true"/>
21246 <param name="use_library_score" value="true"/>
21247 <param name="use_intensity_score" value="true"/>
21248 <param name="use_nr_peaks_score" value="true"/>
21249 <param name="use_total_xic_score" value="true"/>
21250 <param name="use_total_mi_score" value="false"/>
21251 <param name="use_sn_score" value="true"/>
21252 <param name="use_mi_score" value="false"/>
21253 <param name="use_dia_scores" value="true"/>
21254 <param name="use_ms1_correlation" value="false"/>
21255 <param name="use_sonar_scores" value="false"/>
21256 <param name="use_ion_mobility_scores" value="true"/>
21257 <param name="use_ms1_fullscan" value="false"/>
21258 <param name="use_ms1_mi" value="false"/>
21259 <param name="use_uis_scores" value="false"/>
21260 </section>
21261 </section>
21262 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21263 <output name="ctd_out" ftype="xml">
21264 <assert_contents>
21265 <is_valid_xml/>
21266 </assert_contents>
21267 </output>
21268 </test>
21269 <test expect_num_outputs="3">
21270 <conditional name="adv_opts_cond">
21271 <param name="adv_opts_selector" value="advanced"/>
21272 <param name="sort_swath_maps" value="false"/>
21273 <param name="use_ms1_traces" value="true"/>
21274 <param name="enable_uis_scoring" value="false"/>
21275 <param name="out_chrom_type" value="mzML"/>
21276 <param name="min_upper_edge_dist" value="0.0"/>
21277 <param name="extra_rt_extraction_window" value="0.0"/>
21278 <param name="mz_extraction_window_unit" value="Th"/>
21279 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21280 <param name="use_ms1_ion_mobility" value="false"/>
21281 <param name="matching_window_only" value="false"/>
21282 <param name="irt_mz_extraction_window" value="0.05"/>
21283 <param name="irt_mz_extraction_window_unit" value="Th"/>
21284 <param name="irt_im_extraction_window" value="-1.0"/>
21285 <param name="min_rsq" value="0.95"/>
21286 <param name="min_coverage" value="0.6"/>
21287 <param name="split_file_input" value="false"/>
21288 <param name="use_elution_model_score" value="false"/>
21289 <param name="readOptions" value="workingInMemory"/>
21290 <param name="mz_correction_function" value="none"/>
21291 <param name="extraction_function" value="tophat"/>
21292 <param name="batchSize" value="250"/>
21293 <param name="ms1_isotopes" value="0"/>
21294 <param name="force" value="false"/>
21295 <param name="test" value="true"/>
21296 </conditional>
21297 <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
21298 <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
21299 <param name="tr_type" value="pqp"/>
21300 <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21301 <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21302 <param name="sonar" value="false"/>
21303 <param name="rt_extraction_window" value="600.0"/>
21304 <param name="ion_mobility_window" value="0.05"/>
21305 <param name="mz_extraction_window" value="0.05"/>
21306 <param name="mz_extraction_window_ms1" value="0.05"/>
21307 <param name="im_extraction_window_ms1" value="-1.0"/>
21308 <section name="Debugging"/>
21309 <section name="Calibration">
21310 <param name="ms1_im_calibration" value="false"/>
21311 <param name="im_correction_function" value="linear"/>
21312 <param name="debug_im_file" value=""/>
21313 <param name="debug_mz_file" value=""/>
21314 </section>
21315 <section name="Library">
21316 <param name="retentionTimeInterpretation" value="iRT"/>
21317 <param name="override_group_label_check" value="false"/>
21318 <param name="force_invalid_mods" value="false"/>
21319 </section>
21320 <section name="RTNormalization">
21321 <param name="alignmentMethod" value="linear"/>
21322 <param name="outlierMethod" value="iter_residual"/>
21323 <param name="useIterativeChauvenet" value="false"/>
21324 <param name="RANSACMaxIterations" value="1000"/>
21325 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21326 <param name="RANSACSamplingSize" value="10"/>
21327 <param name="estimateBestPeptides" value="false"/>
21328 <param name="InitialQualityCutoff" value="0.5"/>
21329 <param name="OverallQualityCutoff" value="5.5"/>
21330 <param name="NrRTBins" value="10"/>
21331 <param name="MinPeptidesPerBin" value="1"/>
21332 <param name="MinBinsFilled" value="8"/>
21333 <section name="lowess">
21334 <param name="span" value="0.666666666666667"/>
21335 </section>
21336 <section name="b_spline">
21337 <param name="num_nodes" value="5"/>
21338 </section>
21339 </section>
21340 <section name="Scoring">
21341 <param name="stop_report_after_feature" value="5"/>
21342 <param name="rt_normalization_factor" value="100.0"/>
21343 <param name="quantification_cutoff" value="0.0"/>
21344 <param name="write_convex_hull" value="false"/>
21345 <param name="spectrum_addition_method" value="simple"/>
21346 <param name="add_up_spectra" value="1"/>
21347 <param name="spacing_for_spectra_resampling" value="0.005"/>
21348 <param name="uis_threshold_sn" value="0"/>
21349 <param name="uis_threshold_peak_area" value="0"/>
21350 <param name="scoring_model" value="default"/>
21351 <param name="im_extra_drift" value="0.0"/>
21352 <section name="TransitionGroupPicker">
21353 <param name="stop_after_feature" value="-1"/>
21354 <param name="min_peak_width" value="-1.0"/>
21355 <param name="peak_integration" value="original"/>
21356 <param name="background_subtraction" value="none"/>
21357 <param name="recalculate_peaks" value="true"/>
21358 <param name="use_precursors" value="false"/>
21359 <param name="use_consensus" value="true"/>
21360 <param name="recalculate_peaks_max_z" value="0.75"/>
21361 <param name="minimal_quality" value="-1.5"/>
21362 <param name="resample_boundary" value="15.0"/>
21363 <param name="compute_peak_quality" value="true"/>
21364 <param name="compute_peak_shape_metrics" value="false"/>
21365 <param name="compute_total_mi" value="false"/>
21366 <param name="boundary_selection_method" value="largest"/>
21367 <section name="PeakPickerMRM">
21368 <param name="sgolay_frame_length" value="11"/>
21369 <param name="sgolay_polynomial_order" value="3"/>
21370 <param name="gauss_width" value="30.0"/>
21371 <param name="use_gauss" value="false"/>
21372 <param name="peak_width" value="-1.0"/>
21373 <param name="signal_to_noise" value="0.1"/>
21374 <param name="write_sn_log_messages" value="false"/>
21375 <param name="remove_overlapping_peaks" value="true"/>
21376 <param name="method" value="corrected"/>
21377 </section>
21378 <section name="PeakIntegrator">
21379 <param name="integration_type" value="intensity_sum"/>
21380 <param name="baseline_type" value="base_to_base"/>
21381 <param name="fit_EMG" value="false"/>
21382 </section>
21383 </section>
21384 <section name="DIAScoring">
21385 <param name="dia_extraction_window" value="0.05"/>
21386 <param name="dia_extraction_unit" value="Th"/>
21387 <param name="dia_centroided" value="false"/>
21388 <param name="dia_byseries_intensity_min" value="300.0"/>
21389 <param name="dia_byseries_ppm_diff" value="10.0"/>
21390 <param name="dia_nr_isotopes" value="4"/>
21391 <param name="dia_nr_charges" value="4"/>
21392 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21393 </section>
21394 <section name="EMGScoring">
21395 <param name="max_iteration" value="10"/>
21396 </section>
21397 <section name="Scores">
21398 <param name="use_shape_score" value="true"/>
21399 <param name="use_coelution_score" value="true"/>
21400 <param name="use_rt_score" value="true"/>
21401 <param name="use_library_score" value="true"/>
21402 <param name="use_intensity_score" value="true"/>
21403 <param name="use_nr_peaks_score" value="true"/>
21404 <param name="use_total_xic_score" value="true"/>
21405 <param name="use_total_mi_score" value="false"/>
21406 <param name="use_sn_score" value="true"/>
21407 <param name="use_mi_score" value="false"/>
21408 <param name="use_dia_scores" value="true"/>
21409 <param name="use_ms1_correlation" value="false"/>
21410 <param name="use_sonar_scores" value="false"/>
21411 <param name="use_ion_mobility_scores" value="false"/>
21412 <param name="use_ms1_fullscan" value="false"/>
21413 <param name="use_ms1_mi" value="false"/>
21414 <param name="use_uis_scores" value="false"/>
21415 </section>
21416 </section>
21417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
21418 <output name="ctd_out" ftype="xml">
21419 <assert_contents>
21420 <is_valid_xml/>
21421 </assert_contents>
21422 </output>
21423 </test>
21424 <test expect_num_outputs="2">
21425 <conditional name="adv_opts_cond">
21426 <param name="adv_opts_selector" value="advanced"/>
21427 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21428 <param name="sort_swath_maps" value="false"/>
21429 <param name="use_ms1_traces" value="true"/>
21430 <param name="enable_uis_scoring" value="false"/>
21431 <param name="min_upper_edge_dist" value="0.0"/>
21432 <param name="extra_rt_extraction_window" value="0.0"/>
21433 <param name="mz_extraction_window_unit" value="Th"/>
21434 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21435 <param name="use_ms1_ion_mobility" value="true"/>
21436 <param name="matching_window_only" value="false"/>
21437 <param name="irt_mz_extraction_window" value="0.05"/>
21438 <param name="irt_mz_extraction_window_unit" value="Th"/>
21439 <param name="irt_im_extraction_window" value="-1.0"/>
21440 <param name="min_rsq" value="0.95"/>
21441 <param name="min_coverage" value="0.6"/>
21442 <param name="split_file_input" value="false"/>
21443 <param name="use_elution_model_score" value="false"/>
21444 <param name="readOptions" value="normal"/>
21445 <param name="mz_correction_function" value="none"/>
21446 <param name="extraction_function" value="tophat"/>
21447 <param name="batchSize" value="250"/>
21448 <param name="ms1_isotopes" value="0"/>
21449 <param name="force" value="false"/>
21450 <param name="test" value="true"/>
21451 </conditional>
21452 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21453 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21454 <param name="tr_type" value=""/>
21455 <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21456 <param name="sonar" value="false"/>
21457 <param name="rt_extraction_window" value="600.0"/>
21458 <param name="ion_mobility_window" value="-1.0"/>
21459 <param name="mz_extraction_window" value="0.05"/>
21460 <param name="mz_extraction_window_ms1" value="0.05"/>
21461 <param name="im_extraction_window_ms1" value="-1.0"/>
21462 <section name="Debugging"/>
21463 <section name="Calibration">
21464 <param name="ms1_im_calibration" value="false"/>
21465 <param name="im_correction_function" value="linear"/>
21466 <param name="debug_im_file" value=""/>
21467 <param name="debug_mz_file" value=""/>
21468 </section>
21469 <section name="Library">
21470 <param name="retentionTimeInterpretation" value="iRT"/>
21471 <param name="override_group_label_check" value="false"/>
21472 <param name="force_invalid_mods" value="false"/>
21473 </section>
21474 <section name="RTNormalization">
21475 <param name="alignmentMethod" value="linear"/>
21476 <param name="outlierMethod" value="iter_residual"/>
21477 <param name="useIterativeChauvenet" value="false"/>
21478 <param name="RANSACMaxIterations" value="1000"/>
21479 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21480 <param name="RANSACSamplingSize" value="10"/>
21481 <param name="estimateBestPeptides" value="false"/>
21482 <param name="InitialQualityCutoff" value="0.5"/>
21483 <param name="OverallQualityCutoff" value="5.5"/>
21484 <param name="NrRTBins" value="10"/>
21485 <param name="MinPeptidesPerBin" value="1"/>
21486 <param name="MinBinsFilled" value="8"/>
21487 <section name="lowess">
21488 <param name="span" value="0.666666666666667"/>
21489 </section>
21490 <section name="b_spline">
21491 <param name="num_nodes" value="5"/>
21492 </section>
21493 </section>
21494 <section name="Scoring">
21495 <param name="stop_report_after_feature" value="5"/>
21496 <param name="rt_normalization_factor" value="100.0"/>
21497 <param name="quantification_cutoff" value="0.0"/>
21498 <param name="write_convex_hull" value="false"/>
21499 <param name="spectrum_addition_method" value="simple"/>
21500 <param name="add_up_spectra" value="1"/>
21501 <param name="spacing_for_spectra_resampling" value="0.005"/>
21502 <param name="uis_threshold_sn" value="0"/>
21503 <param name="uis_threshold_peak_area" value="0"/>
21504 <param name="scoring_model" value="default"/>
21505 <param name="im_extra_drift" value="0.0"/>
21506 <section name="TransitionGroupPicker">
21507 <param name="stop_after_feature" value="-1"/>
21508 <param name="min_peak_width" value="-1.0"/>
21509 <param name="peak_integration" value="original"/>
21510 <param name="background_subtraction" value="none"/>
21511 <param name="recalculate_peaks" value="true"/>
21512 <param name="use_precursors" value="false"/>
21513 <param name="use_consensus" value="true"/>
21514 <param name="recalculate_peaks_max_z" value="0.75"/>
21515 <param name="minimal_quality" value="-1.5"/>
21516 <param name="resample_boundary" value="15.0"/>
21517 <param name="compute_peak_quality" value="true"/>
21518 <param name="compute_peak_shape_metrics" value="false"/>
21519 <param name="compute_total_mi" value="false"/>
21520 <param name="boundary_selection_method" value="largest"/>
21521 <section name="PeakPickerMRM">
21522 <param name="sgolay_frame_length" value="11"/>
21523 <param name="sgolay_polynomial_order" value="3"/>
21524 <param name="gauss_width" value="30.0"/>
21525 <param name="use_gauss" value="false"/>
21526 <param name="peak_width" value="-1.0"/>
21527 <param name="signal_to_noise" value="0.1"/>
21528 <param name="write_sn_log_messages" value="false"/>
21529 <param name="remove_overlapping_peaks" value="true"/>
21530 <param name="method" value="corrected"/>
21531 </section>
21532 <section name="PeakIntegrator">
21533 <param name="integration_type" value="intensity_sum"/>
21534 <param name="baseline_type" value="base_to_base"/>
21535 <param name="fit_EMG" value="false"/>
21536 </section>
21537 </section>
21538 <section name="DIAScoring">
21539 <param name="dia_extraction_window" value="0.05"/>
21540 <param name="dia_extraction_unit" value="Th"/>
21541 <param name="dia_centroided" value="false"/>
21542 <param name="dia_byseries_intensity_min" value="300.0"/>
21543 <param name="dia_byseries_ppm_diff" value="10.0"/>
21544 <param name="dia_nr_isotopes" value="4"/>
21545 <param name="dia_nr_charges" value="4"/>
21546 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21547 </section>
21548 <section name="EMGScoring">
21549 <param name="max_iteration" value="10"/>
21550 </section>
21551 <section name="Scores">
21552 <param name="use_shape_score" value="true"/>
21553 <param name="use_coelution_score" value="true"/>
21554 <param name="use_rt_score" value="true"/>
21555 <param name="use_library_score" value="true"/>
21556 <param name="use_intensity_score" value="true"/>
21557 <param name="use_nr_peaks_score" value="true"/>
21558 <param name="use_total_xic_score" value="true"/>
21559 <param name="use_total_mi_score" value="false"/>
21560 <param name="use_sn_score" value="true"/>
21561 <param name="use_mi_score" value="false"/>
21562 <param name="use_dia_scores" value="true"/>
21563 <param name="use_ms1_correlation" value="false"/>
21564 <param name="use_sonar_scores" value="false"/>
21565 <param name="use_ion_mobility_scores" value="false"/>
21566 <param name="use_ms1_fullscan" value="false"/>
21567 <param name="use_ms1_mi" value="true"/>
21568 <param name="use_uis_scores" value="false"/>
21569 </section>
21570 </section>
21571 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21572 <output name="ctd_out" ftype="xml">
21573 <assert_contents>
21574 <is_valid_xml/>
21575 </assert_contents>
21576 </output>
21577 </test>
21578 <test expect_num_outputs="2">
21579 <conditional name="adv_opts_cond">
21580 <param name="adv_opts_selector" value="advanced"/>
21581 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21582 <param name="sort_swath_maps" value="false"/>
21583 <param name="use_ms1_traces" value="true"/>
21584 <param name="enable_uis_scoring" value="false"/>
21585 <param name="min_upper_edge_dist" value="0.0"/>
21586 <param name="extra_rt_extraction_window" value="0.0"/>
21587 <param name="mz_extraction_window_unit" value="Th"/>
21588 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21589 <param name="use_ms1_ion_mobility" value="true"/>
21590 <param name="matching_window_only" value="false"/>
21591 <param name="irt_mz_extraction_window" value="0.05"/>
21592 <param name="irt_mz_extraction_window_unit" value="Th"/>
21593 <param name="irt_im_extraction_window" value="-1.0"/>
21594 <param name="min_rsq" value="0.95"/>
21595 <param name="min_coverage" value="0.6"/>
21596 <param name="split_file_input" value="false"/>
21597 <param name="use_elution_model_score" value="false"/>
21598 <param name="readOptions" value="normal"/>
21599 <param name="mz_correction_function" value="none"/>
21600 <param name="extraction_function" value="tophat"/>
21601 <param name="batchSize" value="250"/>
21602 <param name="ms1_isotopes" value="0"/>
21603 <param name="force" value="false"/>
21604 <param name="test" value="true"/>
21605 </conditional>
21606 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21607 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21608 <param name="tr_type" value=""/>
21609 <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21610 <param name="sonar" value="false"/>
21611 <param name="rt_extraction_window" value="600.0"/>
21612 <param name="ion_mobility_window" value="-1.0"/>
21613 <param name="mz_extraction_window" value="0.05"/>
21614 <param name="mz_extraction_window_ms1" value="0.05"/>
21615 <param name="im_extraction_window_ms1" value="-1.0"/>
21616 <section name="Debugging"/>
21617 <section name="Calibration">
21618 <param name="ms1_im_calibration" value="false"/>
21619 <param name="im_correction_function" value="linear"/>
21620 <param name="debug_im_file" value=""/>
21621 <param name="debug_mz_file" value=""/>
21622 </section>
21623 <section name="Library">
21624 <param name="retentionTimeInterpretation" value="iRT"/>
21625 <param name="override_group_label_check" value="false"/>
21626 <param name="force_invalid_mods" value="false"/>
21627 </section>
21628 <section name="RTNormalization">
21629 <param name="alignmentMethod" value="linear"/>
21630 <param name="outlierMethod" value="iter_residual"/>
21631 <param name="useIterativeChauvenet" value="false"/>
21632 <param name="RANSACMaxIterations" value="1000"/>
21633 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21634 <param name="RANSACSamplingSize" value="10"/>
21635 <param name="estimateBestPeptides" value="false"/>
21636 <param name="InitialQualityCutoff" value="0.5"/>
21637 <param name="OverallQualityCutoff" value="5.5"/>
21638 <param name="NrRTBins" value="10"/>
21639 <param name="MinPeptidesPerBin" value="1"/>
21640 <param name="MinBinsFilled" value="8"/>
21641 <section name="lowess">
21642 <param name="span" value="0.666666666666667"/>
21643 </section>
21644 <section name="b_spline">
21645 <param name="num_nodes" value="5"/>
21646 </section>
21647 </section>
21648 <section name="Scoring">
21649 <param name="stop_report_after_feature" value="5"/>
21650 <param name="rt_normalization_factor" value="100.0"/>
21651 <param name="quantification_cutoff" value="0.0"/>
21652 <param name="write_convex_hull" value="false"/>
21653 <param name="spectrum_addition_method" value="simple"/>
21654 <param name="add_up_spectra" value="1"/>
21655 <param name="spacing_for_spectra_resampling" value="0.005"/>
21656 <param name="uis_threshold_sn" value="0"/>
21657 <param name="uis_threshold_peak_area" value="0"/>
21658 <param name="scoring_model" value="default"/>
21659 <param name="im_extra_drift" value="0.0"/>
21660 <section name="TransitionGroupPicker">
21661 <param name="stop_after_feature" value="-1"/>
21662 <param name="min_peak_width" value="-1.0"/>
21663 <param name="peak_integration" value="original"/>
21664 <param name="background_subtraction" value="none"/>
21665 <param name="recalculate_peaks" value="true"/>
21666 <param name="use_precursors" value="false"/>
21667 <param name="use_consensus" value="true"/>
21668 <param name="recalculate_peaks_max_z" value="0.75"/>
21669 <param name="minimal_quality" value="-1.5"/>
21670 <param name="resample_boundary" value="15.0"/>
21671 <param name="compute_peak_quality" value="true"/>
21672 <param name="compute_peak_shape_metrics" value="false"/>
21673 <param name="compute_total_mi" value="false"/>
21674 <param name="boundary_selection_method" value="largest"/>
21675 <section name="PeakPickerMRM">
21676 <param name="sgolay_frame_length" value="11"/>
21677 <param name="sgolay_polynomial_order" value="3"/>
21678 <param name="gauss_width" value="30.0"/>
21679 <param name="use_gauss" value="false"/>
21680 <param name="peak_width" value="-1.0"/>
21681 <param name="signal_to_noise" value="0.1"/>
21682 <param name="write_sn_log_messages" value="false"/>
21683 <param name="remove_overlapping_peaks" value="true"/>
21684 <param name="method" value="corrected"/>
21685 </section>
21686 <section name="PeakIntegrator">
21687 <param name="integration_type" value="intensity_sum"/>
21688 <param name="baseline_type" value="base_to_base"/>
21689 <param name="fit_EMG" value="false"/>
21690 </section>
21691 </section>
21692 <section name="DIAScoring">
21693 <param name="dia_extraction_window" value="0.05"/>
21694 <param name="dia_extraction_unit" value="Th"/>
21695 <param name="dia_centroided" value="false"/>
21696 <param name="dia_byseries_intensity_min" value="300.0"/>
21697 <param name="dia_byseries_ppm_diff" value="10.0"/>
21698 <param name="dia_nr_isotopes" value="4"/>
21699 <param name="dia_nr_charges" value="4"/>
21700 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21701 </section>
21702 <section name="EMGScoring">
21703 <param name="max_iteration" value="10"/>
21704 </section>
21705 <section name="Scores">
21706 <param name="use_shape_score" value="true"/>
21707 <param name="use_coelution_score" value="true"/>
21708 <param name="use_rt_score" value="true"/>
21709 <param name="use_library_score" value="true"/>
21710 <param name="use_intensity_score" value="true"/>
21711 <param name="use_nr_peaks_score" value="true"/>
21712 <param name="use_total_xic_score" value="true"/>
21713 <param name="use_total_mi_score" value="false"/>
21714 <param name="use_sn_score" value="true"/>
21715 <param name="use_mi_score" value="true"/>
21716 <param name="use_dia_scores" value="true"/>
21717 <param name="use_ms1_correlation" value="false"/>
21718 <param name="use_sonar_scores" value="false"/>
21719 <param name="use_ion_mobility_scores" value="false"/>
21720 <param name="use_ms1_fullscan" value="false"/>
21721 <param name="use_ms1_mi" value="false"/>
21722 <param name="use_uis_scores" value="false"/>
21723 </section>
21724 </section>
21725 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21726 <output name="ctd_out" ftype="xml">
21727 <assert_contents>
21728 <is_valid_xml/>
21729 </assert_contents>
21730 </output>
21731 </test>
21732 <test expect_num_outputs="2">
21733 <conditional name="adv_opts_cond">
21734 <param name="adv_opts_selector" value="advanced"/>
21735 <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
21736 <param name="sort_swath_maps" value="false"/>
21737 <param name="use_ms1_traces" value="true"/>
21738 <param name="enable_uis_scoring" value="false"/>
21739 <param name="min_upper_edge_dist" value="0.0"/>
21740 <param name="extra_rt_extraction_window" value="0.0"/>
21741 <param name="mz_extraction_window_unit" value="Th"/>
21742 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21743 <param name="use_ms1_ion_mobility" value="true"/>
21744 <param name="matching_window_only" value="false"/>
21745 <param name="irt_mz_extraction_window" value="0.05"/>
21746 <param name="irt_mz_extraction_window_unit" value="Th"/>
21747 <param name="irt_im_extraction_window" value="-1.0"/>
21748 <param name="min_rsq" value="0.95"/>
21749 <param name="min_coverage" value="0.6"/>
21750 <param name="split_file_input" value="false"/>
21751 <param name="use_elution_model_score" value="false"/>
21752 <param name="readOptions" value="normal"/>
21753 <param name="mz_correction_function" value="none"/>
21754 <param name="extraction_function" value="tophat"/>
21755 <param name="batchSize" value="250"/>
21756 <param name="ms1_isotopes" value="0"/>
21757 <param name="force" value="false"/>
21758 <param name="test" value="true"/>
21759 </conditional>
21760 <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
21761 <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
21762 <param name="tr_type" value=""/>
21763 <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21764 <param name="sonar" value="false"/>
21765 <param name="rt_extraction_window" value="600.0"/>
21766 <param name="ion_mobility_window" value="-1.0"/>
21767 <param name="mz_extraction_window" value="0.05"/>
21768 <param name="mz_extraction_window_ms1" value="0.05"/>
21769 <param name="im_extraction_window_ms1" value="-1.0"/>
21770 <section name="Debugging"/>
21771 <section name="Calibration">
21772 <param name="ms1_im_calibration" value="false"/>
21773 <param name="im_correction_function" value="linear"/>
21774 <param name="debug_im_file" value=""/>
21775 <param name="debug_mz_file" value=""/>
21776 </section>
21777 <section name="Library">
21778 <param name="retentionTimeInterpretation" value="iRT"/>
21779 <param name="override_group_label_check" value="false"/>
21780 <param name="force_invalid_mods" value="false"/>
21781 </section>
21782 <section name="RTNormalization">
21783 <param name="alignmentMethod" value="linear"/>
21784 <param name="outlierMethod" value="iter_residual"/>
21785 <param name="useIterativeChauvenet" value="false"/>
21786 <param name="RANSACMaxIterations" value="1000"/>
21787 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21788 <param name="RANSACSamplingSize" value="10"/>
21789 <param name="estimateBestPeptides" value="false"/>
21790 <param name="InitialQualityCutoff" value="0.5"/>
21791 <param name="OverallQualityCutoff" value="5.5"/>
21792 <param name="NrRTBins" value="10"/>
21793 <param name="MinPeptidesPerBin" value="1"/>
21794 <param name="MinBinsFilled" value="8"/>
21795 <section name="lowess">
21796 <param name="span" value="0.666666666666667"/>
21797 </section>
21798 <section name="b_spline">
21799 <param name="num_nodes" value="5"/>
21800 </section>
21801 </section>
21802 <section name="Scoring">
21803 <param name="stop_report_after_feature" value="5"/>
21804 <param name="rt_normalization_factor" value="100.0"/>
21805 <param name="quantification_cutoff" value="0.0"/>
21806 <param name="write_convex_hull" value="false"/>
21807 <param name="spectrum_addition_method" value="simple"/>
21808 <param name="add_up_spectra" value="1"/>
21809 <param name="spacing_for_spectra_resampling" value="0.005"/>
21810 <param name="uis_threshold_sn" value="0"/>
21811 <param name="uis_threshold_peak_area" value="0"/>
21812 <param name="scoring_model" value="default"/>
21813 <param name="im_extra_drift" value="0.0"/>
21814 <section name="TransitionGroupPicker">
21815 <param name="stop_after_feature" value="-1"/>
21816 <param name="min_peak_width" value="-1.0"/>
21817 <param name="peak_integration" value="original"/>
21818 <param name="background_subtraction" value="none"/>
21819 <param name="recalculate_peaks" value="true"/>
21820 <param name="use_precursors" value="false"/>
21821 <param name="use_consensus" value="true"/>
21822 <param name="recalculate_peaks_max_z" value="0.75"/>
21823 <param name="minimal_quality" value="-1.5"/>
21824 <param name="resample_boundary" value="15.0"/>
21825 <param name="compute_peak_quality" value="true"/>
21826 <param name="compute_peak_shape_metrics" value="false"/>
21827 <param name="compute_total_mi" value="false"/>
21828 <param name="boundary_selection_method" value="largest"/>
21829 <section name="PeakPickerMRM">
21830 <param name="sgolay_frame_length" value="11"/>
21831 <param name="sgolay_polynomial_order" value="3"/>
21832 <param name="gauss_width" value="30.0"/>
21833 <param name="use_gauss" value="false"/>
21834 <param name="peak_width" value="-1.0"/>
21835 <param name="signal_to_noise" value="0.1"/>
21836 <param name="write_sn_log_messages" value="false"/>
21837 <param name="remove_overlapping_peaks" value="true"/>
21838 <param name="method" value="corrected"/>
21839 </section>
21840 <section name="PeakIntegrator">
21841 <param name="integration_type" value="intensity_sum"/>
21842 <param name="baseline_type" value="base_to_base"/>
21843 <param name="fit_EMG" value="false"/>
21844 </section>
21845 </section>
21846 <section name="DIAScoring">
21847 <param name="dia_extraction_window" value="0.05"/>
21848 <param name="dia_extraction_unit" value="Th"/>
21849 <param name="dia_centroided" value="false"/>
21850 <param name="dia_byseries_intensity_min" value="300.0"/>
21851 <param name="dia_byseries_ppm_diff" value="10.0"/>
21852 <param name="dia_nr_isotopes" value="4"/>
21853 <param name="dia_nr_charges" value="4"/>
21854 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
21855 </section>
21856 <section name="EMGScoring">
21857 <param name="max_iteration" value="10"/>
21858 </section>
21859 <section name="Scores">
21860 <param name="use_shape_score" value="true"/>
21861 <param name="use_coelution_score" value="true"/>
21862 <param name="use_rt_score" value="true"/>
21863 <param name="use_library_score" value="true"/>
21864 <param name="use_intensity_score" value="true"/>
21865 <param name="use_nr_peaks_score" value="true"/>
21866 <param name="use_total_xic_score" value="true"/>
21867 <param name="use_total_mi_score" value="true"/>
21868 <param name="use_sn_score" value="true"/>
21869 <param name="use_mi_score" value="true"/>
21870 <param name="use_dia_scores" value="true"/>
21871 <param name="use_ms1_correlation" value="false"/>
21872 <param name="use_sonar_scores" value="false"/>
21873 <param name="use_ion_mobility_scores" value="false"/>
21874 <param name="use_ms1_fullscan" value="false"/>
21875 <param name="use_ms1_mi" value="false"/>
21876 <param name="use_uis_scores" value="false"/>
21877 </section>
21878 </section>
21879 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
21880 <output name="ctd_out" ftype="xml">
21881 <assert_contents>
21882 <is_valid_xml/>
21883 </assert_contents>
21884 </output>
21885 </test>
21886 <test expect_num_outputs="4">
21887 <conditional name="adv_opts_cond">
21888 <param name="adv_opts_selector" value="advanced"/>
21889 <param name="sort_swath_maps" value="false"/>
21890 <param name="use_ms1_traces" value="true"/>
21891 <param name="enable_uis_scoring" value="false"/>
21892 <param name="out_chrom_type" value="mzML"/>
21893 <param name="min_upper_edge_dist" value="0.0"/>
21894 <param name="extra_rt_extraction_window" value="0.0"/>
21895 <param name="mz_extraction_window_unit" value="Th"/>
21896 <param name="mz_extraction_window_ms1_unit" value="Th"/>
21897 <param name="use_ms1_ion_mobility" value="true"/>
21898 <param name="matching_window_only" value="false"/>
21899 <param name="irt_mz_extraction_window" value="0.05"/>
21900 <param name="irt_mz_extraction_window_unit" value="Th"/>
21901 <param name="irt_im_extraction_window" value="-1.0"/>
21902 <param name="min_rsq" value="0.95"/>
21903 <param name="min_coverage" value="0.6"/>
21904 <param name="split_file_input" value="false"/>
21905 <param name="use_elution_model_score" value="false"/>
21906 <param name="readOptions" value="normal"/>
21907 <param name="mz_correction_function" value="none"/>
21908 <param name="extraction_function" value="tophat"/>
21909 <param name="batchSize" value="250"/>
21910 <param name="ms1_isotopes" value="0"/>
21911 <param name="force" value="false"/>
21912 <param name="test" value="true"/>
21913 </conditional>
21914 <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
21915 <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
21916 <param name="tr_type" value=""/>
21917 <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
21918 <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
21919 <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
21920 <param name="sonar" value="false"/>
21921 <param name="rt_extraction_window" value="600.0"/>
21922 <param name="ion_mobility_window" value="-1.0"/>
21923 <param name="mz_extraction_window" value="0.05"/>
21924 <param name="mz_extraction_window_ms1" value="0.05"/>
21925 <param name="im_extraction_window_ms1" value="-1.0"/>
21926 <section name="Debugging"/>
21927 <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
21928 <section name="Calibration">
21929 <param name="ms1_im_calibration" value="false"/>
21930 <param name="im_correction_function" value="linear"/>
21931 <param name="debug_im_file" value=""/>
21932 <param name="debug_mz_file" value=""/>
21933 </section>
21934 <section name="Library">
21935 <param name="retentionTimeInterpretation" value="iRT"/>
21936 <param name="override_group_label_check" value="false"/>
21937 <param name="force_invalid_mods" value="false"/>
21938 </section>
21939 <section name="RTNormalization">
21940 <param name="alignmentMethod" value="linear"/>
21941 <param name="outlierMethod" value="iter_residual"/>
21942 <param name="useIterativeChauvenet" value="false"/>
21943 <param name="RANSACMaxIterations" value="1000"/>
21944 <param name="RANSACMaxPercentRTThreshold" value="3"/>
21945 <param name="RANSACSamplingSize" value="10"/>
21946 <param name="estimateBestPeptides" value="false"/>
21947 <param name="InitialQualityCutoff" value="0.5"/>
21948 <param name="OverallQualityCutoff" value="5.5"/>
21949 <param name="NrRTBins" value="10"/>
21950 <param name="MinPeptidesPerBin" value="1"/>
21951 <param name="MinBinsFilled" value="8"/>
21952 <section name="lowess">
21953 <param name="span" value="0.666666666666667"/>
21954 </section>
21955 <section name="b_spline">
21956 <param name="num_nodes" value="5"/>
21957 </section>
21958 </section>
21959 <section name="Scoring">
21960 <param name="stop_report_after_feature" value="5"/>
21961 <param name="rt_normalization_factor" value="100.0"/>
21962 <param name="quantification_cutoff" value="0.0"/>
21963 <param name="write_convex_hull" value="false"/>
21964 <param name="spectrum_addition_method" value="simple"/>
21965 <param name="add_up_spectra" value="1"/>
21966 <param name="spacing_for_spectra_resampling" value="0.005"/>
21967 <param name="uis_threshold_sn" value="0"/>
21968 <param name="uis_threshold_peak_area" value="0"/>
21969 <param name="scoring_model" value="default"/>
21970 <param name="im_extra_drift" value="0.0"/>
21971 <section name="TransitionGroupPicker">
21972 <param name="stop_after_feature" value="-1"/>
21973 <param name="min_peak_width" value="-1.0"/>
21974 <param name="peak_integration" value="original"/>
21975 <param name="background_subtraction" value="none"/>
21976 <param name="recalculate_peaks" value="true"/>
21977 <param name="use_precursors" value="false"/>
21978 <param name="use_consensus" value="true"/>
21979 <param name="recalculate_peaks_max_z" value="0.75"/>
21980 <param name="minimal_quality" value="-1.5"/>
21981 <param name="resample_boundary" value="15.0"/>
21982 <param name="compute_peak_quality" value="true"/>
21983 <param name="compute_peak_shape_metrics" value="false"/>
21984 <param name="compute_total_mi" value="false"/>
21985 <param name="boundary_selection_method" value="largest"/>
21986 <section name="PeakPickerMRM">
21987 <param name="sgolay_frame_length" value="11"/>
21988 <param name="sgolay_polynomial_order" value="3"/>
21989 <param name="gauss_width" value="30.0"/>
21990 <param name="use_gauss" value="false"/>
21991 <param name="peak_width" value="-1.0"/>
21992 <param name="signal_to_noise" value="0.1"/>
21993 <param name="write_sn_log_messages" value="false"/>
21994 <param name="remove_overlapping_peaks" value="true"/>
21995 <param name="method" value="corrected"/>
21996 </section>
21997 <section name="PeakIntegrator">
21998 <param name="integration_type" value="intensity_sum"/>
21999 <param name="baseline_type" value="base_to_base"/>
22000 <param name="fit_EMG" value="false"/>
22001 </section>
22002 </section>
22003 <section name="DIAScoring">
22004 <param name="dia_extraction_window" value="0.05"/>
22005 <param name="dia_extraction_unit" value="Th"/>
22006 <param name="dia_centroided" value="false"/>
22007 <param name="dia_byseries_intensity_min" value="300.0"/>
22008 <param name="dia_byseries_ppm_diff" value="10.0"/>
22009 <param name="dia_nr_isotopes" value="4"/>
22010 <param name="dia_nr_charges" value="4"/>
22011 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22012 </section>
22013 <section name="EMGScoring">
22014 <param name="max_iteration" value="10"/>
22015 </section>
22016 <section name="Scores">
22017 <param name="use_shape_score" value="true"/>
22018 <param name="use_coelution_score" value="true"/>
22019 <param name="use_rt_score" value="true"/>
22020 <param name="use_library_score" value="true"/>
22021 <param name="use_intensity_score" value="true"/>
22022 <param name="use_nr_peaks_score" value="true"/>
22023 <param name="use_total_xic_score" value="true"/>
22024 <param name="use_total_mi_score" value="true"/>
22025 <param name="use_sn_score" value="true"/>
22026 <param name="use_mi_score" value="true"/>
22027 <param name="use_dia_scores" value="true"/>
22028 <param name="use_ms1_correlation" value="false"/>
22029 <param name="use_sonar_scores" value="false"/>
22030 <param name="use_ion_mobility_scores" value="false"/>
22031 <param name="use_ms1_fullscan" value="false"/>
22032 <param name="use_ms1_mi" value="false"/>
22033 <param name="use_uis_scores" value="false"/>
22034 </section>
22035 </section>
22036 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
22037 <output name="ctd_out" ftype="xml">
22038 <assert_contents>
22039 <is_valid_xml/>
22040 </assert_contents>
22041 </output>
22042 </test>
22043 <test expect_num_outputs="3">
22044 <conditional name="adv_opts_cond">
22045 <param name="adv_opts_selector" value="advanced"/>
22046 <param name="sort_swath_maps" value="false"/>
22047 <param name="use_ms1_traces" value="true"/>
22048 <param name="enable_uis_scoring" value="false"/>
22049 <param name="out_chrom_type" value="mzML"/>
22050 <param name="min_upper_edge_dist" value="0.0"/>
22051 <param name="extra_rt_extraction_window" value="0.0"/>
22052 <param name="mz_extraction_window_unit" value="Th"/>
22053 <param name="mz_extraction_window_ms1_unit" value="Th"/>
22054 <param name="use_ms1_ion_mobility" value="true"/>
22055 <param name="matching_window_only" value="true"/>
22056 <param name="irt_mz_extraction_window" value="0.05"/>
22057 <param name="irt_mz_extraction_window_unit" value="Th"/>
22058 <param name="irt_im_extraction_window" value="-1.0"/>
22059 <param name="min_rsq" value="0.95"/>
22060 <param name="min_coverage" value="0.6"/>
22061 <param name="split_file_input" value="false"/>
22062 <param name="use_elution_model_score" value="false"/>
22063 <param name="readOptions" value="workingInMemory"/>
22064 <param name="mz_correction_function" value="none"/>
22065 <param name="extraction_function" value="tophat"/>
22066 <param name="batchSize" value="250"/>
22067 <param name="ms1_isotopes" value="3"/>
22068 <param name="force" value="false"/>
22069 <param name="test" value="true"/>
22070 </conditional>
22071 <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
22072 <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
22073 <param name="tr_type" value=""/>
22074 <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
22075 <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22076 <param name="sonar" value="false"/>
22077 <param name="rt_extraction_window" value="600.0"/>
22078 <param name="ion_mobility_window" value="-1.0"/>
22079 <param name="mz_extraction_window" value="0.05"/>
22080 <param name="mz_extraction_window_ms1" value="0.05"/>
22081 <param name="im_extraction_window_ms1" value="-1.0"/>
22082 <section name="Debugging"/>
22083 <section name="Calibration">
22084 <param name="ms1_im_calibration" value="false"/>
22085 <param name="im_correction_function" value="linear"/>
22086 <param name="debug_im_file" value=""/>
22087 <param name="debug_mz_file" value=""/>
22088 </section>
22089 <section name="Library">
22090 <param name="retentionTimeInterpretation" value="iRT"/>
22091 <param name="override_group_label_check" value="false"/>
22092 <param name="force_invalid_mods" value="false"/>
22093 </section>
22094 <section name="RTNormalization">
22095 <param name="alignmentMethod" value="linear"/>
22096 <param name="outlierMethod" value="iter_residual"/>
22097 <param name="useIterativeChauvenet" value="false"/>
22098 <param name="RANSACMaxIterations" value="1000"/>
22099 <param name="RANSACMaxPercentRTThreshold" value="3"/>
22100 <param name="RANSACSamplingSize" value="10"/>
22101 <param name="estimateBestPeptides" value="false"/>
22102 <param name="InitialQualityCutoff" value="0.5"/>
22103 <param name="OverallQualityCutoff" value="5.5"/>
22104 <param name="NrRTBins" value="10"/>
22105 <param name="MinPeptidesPerBin" value="1"/>
22106 <param name="MinBinsFilled" value="8"/>
22107 <section name="lowess">
22108 <param name="span" value="0.666666666666667"/>
22109 </section>
22110 <section name="b_spline">
22111 <param name="num_nodes" value="5"/>
22112 </section>
22113 </section>
22114 <section name="Scoring">
22115 <param name="stop_report_after_feature" value="5"/>
22116 <param name="rt_normalization_factor" value="100.0"/>
22117 <param name="quantification_cutoff" value="0.0"/>
22118 <param name="write_convex_hull" value="false"/>
22119 <param name="spectrum_addition_method" value="simple"/>
22120 <param name="add_up_spectra" value="1"/>
22121 <param name="spacing_for_spectra_resampling" value="0.005"/>
22122 <param name="uis_threshold_sn" value="0"/>
22123 <param name="uis_threshold_peak_area" value="0"/>
22124 <param name="scoring_model" value="default"/>
22125 <param name="im_extra_drift" value="0.0"/>
22126 <section name="TransitionGroupPicker">
22127 <param name="stop_after_feature" value="-1"/>
22128 <param name="min_peak_width" value="-1.0"/>
22129 <param name="peak_integration" value="original"/>
22130 <param name="background_subtraction" value="none"/>
22131 <param name="recalculate_peaks" value="true"/>
22132 <param name="use_precursors" value="false"/>
22133 <param name="use_consensus" value="true"/>
22134 <param name="recalculate_peaks_max_z" value="0.75"/>
22135 <param name="minimal_quality" value="-1.5"/>
22136 <param name="resample_boundary" value="15.0"/>
22137 <param name="compute_peak_quality" value="true"/>
22138 <param name="compute_peak_shape_metrics" value="false"/>
22139 <param name="compute_total_mi" value="false"/>
22140 <param name="boundary_selection_method" value="largest"/>
22141 <section name="PeakPickerMRM">
22142 <param name="sgolay_frame_length" value="11"/>
22143 <param name="sgolay_polynomial_order" value="3"/>
22144 <param name="gauss_width" value="30.0"/>
22145 <param name="use_gauss" value="false"/>
22146 <param name="peak_width" value="-1.0"/>
22147 <param name="signal_to_noise" value="0.1"/>
22148 <param name="write_sn_log_messages" value="false"/>
22149 <param name="remove_overlapping_peaks" value="true"/>
22150 <param name="method" value="corrected"/>
22151 </section>
22152 <section name="PeakIntegrator">
22153 <param name="integration_type" value="intensity_sum"/>
22154 <param name="baseline_type" value="base_to_base"/>
22155 <param name="fit_EMG" value="false"/>
22156 </section>
22157 </section>
22158 <section name="DIAScoring">
22159 <param name="dia_extraction_window" value="0.05"/>
22160 <param name="dia_extraction_unit" value="Th"/>
22161 <param name="dia_centroided" value="false"/>
22162 <param name="dia_byseries_intensity_min" value="300.0"/>
22163 <param name="dia_byseries_ppm_diff" value="10.0"/>
22164 <param name="dia_nr_isotopes" value="4"/>
22165 <param name="dia_nr_charges" value="4"/>
22166 <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
22167 </section>
22168 <section name="EMGScoring">
22169 <param name="max_iteration" value="10"/>
22170 </section>
22171 <section name="Scores">
22172 <param name="use_shape_score" value="true"/>
22173 <param name="use_coelution_score" value="true"/>
22174 <param name="use_rt_score" value="true"/>
22175 <param name="use_library_score" value="true"/>
22176 <param name="use_intensity_score" value="true"/>
22177 <param name="use_nr_peaks_score" value="true"/>
22178 <param name="use_total_xic_score" value="true"/>
22179 <param name="use_total_mi_score" value="false"/>
22180 <param name="use_sn_score" value="true"/>
22181 <param name="use_mi_score" value="false"/>
22182 <param name="use_dia_scores" value="true"/>
22183 <param name="use_ms1_correlation" value="false"/>
22184 <param name="use_sonar_scores" value="false"/>
22185 <param name="use_ion_mobility_scores" value="false"/>
22186 <param name="use_ms1_fullscan" value="false"/>
22187 <param name="use_ms1_mi" value="false"/>
22188 <param name="use_uis_scores" value="false"/>
22189 </section>
22190 </section>
22191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
22192 <output name="ctd_out" ftype="xml">
22193 <assert_contents>
22194 <is_valid_xml/>
22195 </assert_contents>
22196 </output>
22197 </test>
22198 </xml>
22199 <xml name="autotest_PeakPickerHiRes">
22200 <test expect_num_outputs="2">
22201 <conditional name="adv_opts_cond">
22202 <param name="adv_opts_selector" value="advanced"/>
22203 <param name="processOption" value="inmemory"/>
22204 <param name="force" value="false"/>
22205 <param name="test" value="true"/>
22206 </conditional>
22207 <param name="in" value="PeakPickerHiRes_input.mzML"/>
22208 <output name="out" file="PeakPickerHiRes_1.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
22209 <section name="algorithm">
22210 <param name="signal_to_noise" value="1.0"/>
22211 <param name="spacing_difference_gap" value="4.0"/>
22212 <param name="spacing_difference" value="1.5"/>
22213 <param name="missing" value="1"/>
22214 <param name="ms_levels" value="1"/>
22215 <param name="report_FWHM" value="true"/>
22216 <param name="report_FWHM_unit" value="relative"/>
22217 <section name="SignalToNoise">
22218 <param name="max_intensity" value="-1"/>
22219 <param name="auto_max_stdev_factor" value="3.0"/>
22220 <param name="auto_max_percentile" value="95"/>
22221 <param name="auto_mode" value="0"/>
22222 <param name="win_len" value="200.0"/>
22223 <param name="bin_count" value="30"/>
22224 <param name="min_required_elements" value="10"/>
22225 <param name="noise_for_empty_window" value="1e+20"/>
22226 <param name="write_log_messages" value="true"/>
22227 </section>
22228 </section>
22229 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22230 <output name="ctd_out" ftype="xml">
22231 <assert_contents>
22232 <is_valid_xml/>
22233 </assert_contents>
22234 </output>
22235 </test>
22236 <test expect_num_outputs="2">
22237 <conditional name="adv_opts_cond">
22238 <param name="adv_opts_selector" value="advanced"/>
22239 <param name="processOption" value="inmemory"/>
22240 <param name="force" value="false"/>
22241 <param name="test" value="true"/>
22242 </conditional>
22243 <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
22244 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22245 <section name="algorithm">
22246 <param name="signal_to_noise" value="1.0"/>
22247 <param name="spacing_difference_gap" value="4.0"/>
22248 <param name="spacing_difference" value="1.5"/>
22249 <param name="missing" value="1"/>
22250 <param name="ms_levels" value="1"/>
22251 <param name="report_FWHM" value="true"/>
22252 <param name="report_FWHM_unit" value="relative"/>
22253 <section name="SignalToNoise">
22254 <param name="max_intensity" value="-1"/>
22255 <param name="auto_max_stdev_factor" value="3.0"/>
22256 <param name="auto_max_percentile" value="95"/>
22257 <param name="auto_mode" value="0"/>
22258 <param name="win_len" value="200.0"/>
22259 <param name="bin_count" value="30"/>
22260 <param name="min_required_elements" value="10"/>
22261 <param name="noise_for_empty_window" value="1e+20"/>
22262 <param name="write_log_messages" value="true"/>
22263 </section>
22264 </section>
22265 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22266 <output name="ctd_out" ftype="xml">
22267 <assert_contents>
22268 <is_valid_xml/>
22269 </assert_contents>
22270 </output>
22271 </test>
22272 <test expect_num_outputs="2">
22273 <conditional name="adv_opts_cond">
22274 <param name="adv_opts_selector" value="advanced"/>
22275 <param name="processOption" value="lowmemory"/>
22276 <param name="force" value="false"/>
22277 <param name="test" value="true"/>
22278 </conditional>
22279 <param name="in" value="PeakPickerHiRes_input.mzML"/>
22280 <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22281 <section name="algorithm">
22282 <param name="signal_to_noise" value="1.0"/>
22283 <param name="spacing_difference_gap" value="4.0"/>
22284 <param name="spacing_difference" value="1.5"/>
22285 <param name="missing" value="1"/>
22286 <param name="ms_levels" value="1"/>
22287 <param name="report_FWHM" value="true"/>
22288 <param name="report_FWHM_unit" value="relative"/>
22289 <section name="SignalToNoise">
22290 <param name="max_intensity" value="-1"/>
22291 <param name="auto_max_stdev_factor" value="3.0"/>
22292 <param name="auto_max_percentile" value="95"/>
22293 <param name="auto_mode" value="0"/>
22294 <param name="win_len" value="200.0"/>
22295 <param name="bin_count" value="30"/>
22296 <param name="min_required_elements" value="10"/>
22297 <param name="noise_for_empty_window" value="1e+20"/>
22298 <param name="write_log_messages" value="true"/>
22299 </section>
22300 </section>
22301 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22302 <output name="ctd_out" ftype="xml">
22303 <assert_contents>
22304 <is_valid_xml/>
22305 </assert_contents>
22306 </output>
22307 </test>
22308 <test expect_num_outputs="2">
22309 <conditional name="adv_opts_cond">
22310 <param name="adv_opts_selector" value="advanced"/>
22311 <param name="processOption" value="lowmemory"/>
22312 <param name="force" value="false"/>
22313 <param name="test" value="true"/>
22314 </conditional>
22315 <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
22316 <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22317 <section name="algorithm">
22318 <param name="signal_to_noise" value="1.0"/>
22319 <param name="spacing_difference_gap" value="4.0"/>
22320 <param name="spacing_difference" value="1.5"/>
22321 <param name="missing" value="1"/>
22322 <param name="ms_levels" value="1"/>
22323 <param name="report_FWHM" value="true"/>
22324 <param name="report_FWHM_unit" value="relative"/>
22325 <section name="SignalToNoise">
22326 <param name="max_intensity" value="-1"/>
22327 <param name="auto_max_stdev_factor" value="3.0"/>
22328 <param name="auto_max_percentile" value="95"/>
22329 <param name="auto_mode" value="0"/>
22330 <param name="win_len" value="200.0"/>
22331 <param name="bin_count" value="30"/>
22332 <param name="min_required_elements" value="10"/>
22333 <param name="noise_for_empty_window" value="1e+20"/>
22334 <param name="write_log_messages" value="true"/>
22335 </section>
22336 </section>
22337 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22338 <output name="ctd_out" ftype="xml">
22339 <assert_contents>
22340 <is_valid_xml/>
22341 </assert_contents>
22342 </output>
22343 </test>
22344 <test expect_num_outputs="2">
22345 <conditional name="adv_opts_cond">
22346 <param name="adv_opts_selector" value="advanced"/>
22347 <param name="processOption" value="inmemory"/>
22348 <param name="force" value="false"/>
22349 <param name="test" value="true"/>
22350 </conditional>
22351 <param name="in" value="PeakPickerHiRes_5_input.mzML"/>
22352 <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22353 <section name="algorithm">
22354 <param name="signal_to_noise" value="0.0"/>
22355 <param name="spacing_difference_gap" value="4.0"/>
22356 <param name="spacing_difference" value="1.5"/>
22357 <param name="missing" value="1"/>
22358 <param name="ms_levels" value=""/>
22359 <param name="report_FWHM" value="false"/>
22360 <param name="report_FWHM_unit" value="relative"/>
22361 <section name="SignalToNoise">
22362 <param name="max_intensity" value="-1"/>
22363 <param name="auto_max_stdev_factor" value="3.0"/>
22364 <param name="auto_max_percentile" value="95"/>
22365 <param name="auto_mode" value="0"/>
22366 <param name="win_len" value="200.0"/>
22367 <param name="bin_count" value="30"/>
22368 <param name="min_required_elements" value="10"/>
22369 <param name="noise_for_empty_window" value="1e+20"/>
22370 <param name="write_log_messages" value="true"/>
22371 </section>
22372 </section>
22373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22374 <output name="ctd_out" ftype="xml">
22375 <assert_contents>
22376 <is_valid_xml/>
22377 </assert_contents>
22378 </output>
22379 </test>
22380 </xml>
22381 <xml name="autotest_PeakPickerIterative">
22382 <test expect_num_outputs="2">
22383 <conditional name="adv_opts_cond">
22384 <param name="adv_opts_selector" value="advanced"/>
22385 <param name="force" value="false"/>
22386 <param name="test" value="true"/>
22387 </conditional>
22388 <param name="in" value="PeakPickerIterative_1_input.mzML"/>
22389 <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22390 <section name="algorithm">
22391 <param name="signal_to_noise_" value="1.0"/>
22392 <param name="peak_width" value="0.04"/>
22393 <param name="spacing_difference" value="1.5"/>
22394 <param name="sn_bin_count_" value="30"/>
22395 <param name="nr_iterations_" value="5"/>
22396 <param name="sn_win_len_" value="20.0"/>
22397 <param name="check_width_internally" value="false"/>
22398 <param name="ms1_only" value="false"/>
22399 <param name="clear_meta_data" value="false"/>
22400 </section>
22401 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22402 <output name="ctd_out" ftype="xml">
22403 <assert_contents>
22404 <is_valid_xml/>
22405 </assert_contents>
22406 </output>
22407 </test>
22408 <test expect_num_outputs="2">
22409 <conditional name="adv_opts_cond">
22410 <param name="adv_opts_selector" value="advanced"/>
22411 <param name="force" value="false"/>
22412 <param name="test" value="true"/>
22413 </conditional>
22414 <param name="in" value="PeakPickerIterative_2_input.mzML"/>
22415 <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22416 <section name="algorithm">
22417 <param name="signal_to_noise_" value="0.0"/>
22418 <param name="peak_width" value="0.04"/>
22419 <param name="spacing_difference" value="2.5"/>
22420 <param name="sn_bin_count_" value="30"/>
22421 <param name="nr_iterations_" value="5"/>
22422 <param name="sn_win_len_" value="20.0"/>
22423 <param name="check_width_internally" value="true"/>
22424 <param name="ms1_only" value="false"/>
22425 <param name="clear_meta_data" value="false"/>
22426 </section>
22427 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22428 <output name="ctd_out" ftype="xml">
22429 <assert_contents>
22430 <is_valid_xml/>
22431 </assert_contents>
22432 </output>
22433 </test>
22434 </xml>
22435 <xml name="autotest_PeakPickerWavelet">
22436 <test expect_num_outputs="2">
22437 <conditional name="adv_opts_cond">
22438 <param name="adv_opts_selector" value="advanced"/>
22439 <param name="write_peak_meta_data" value="true"/>
22440 <param name="force" value="false"/>
22441 <param name="test" value="true"/>
22442 </conditional>
22443 <param name="in" value="PeakPickerWavelet_input.mzML"/>
22444 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22445 <section name="algorithm">
22446 <param name="signal_to_noise" value="3.0"/>
22447 <param name="centroid_percentage" value="0.6"/>
22448 <param name="peak_width" value="0.2"/>
22449 <param name="estimate_peak_width" value="false"/>
22450 <param name="fwhm_lower_bound_factor" value="0.5"/>
22451 <param name="fwhm_upper_bound_factor" value="20.0"/>
22452 <section name="optimization">
22453 <param name="iterations" value="400"/>
22454 <section name="penalties">
22455 <param name="position" value="0.0"/>
22456 <param name="left_width" value="1.0"/>
22457 <param name="right_width" value="1.0"/>
22458 <param name="height" value="1.0"/>
22459 </section>
22460 <section name="2d">
22461 <param name="tolerance_mz" value="2.2"/>
22462 <param name="max_peak_distance" value="1.2"/>
22463 </section>
22464 </section>
22465 <section name="thresholds">
22466 <param name="peak_bound" value="100.0"/>
22467 <param name="peak_bound_ms2_level" value="10.0"/>
22468 <param name="correlation" value="0.5"/>
22469 <param name="noise_level" value="0.1"/>
22470 <param name="search_radius" value="3"/>
22471 </section>
22472 <section name="wavelet_transform">
22473 <param name="spacing" value="0.001"/>
22474 </section>
22475 <section name="deconvolution">
22476 <param name="deconvolution" value="false"/>
22477 <param name="asym_threshold" value="0.3"/>
22478 <param name="left_width" value="2.0"/>
22479 <param name="right_width" value="2.0"/>
22480 <param name="scaling" value="0.12"/>
22481 <section name="fitting">
22482 <param name="fwhm_threshold" value="0.7"/>
22483 <param name="eps_abs" value="9.999999747378752e-06"/>
22484 <param name="eps_rel" value="9.999999747378752e-06"/>
22485 <param name="max_iteration" value="10"/>
22486 <section name="penalties">
22487 <param name="position" value="0.0"/>
22488 <param name="height" value="1.0"/>
22489 <param name="left_width" value="0.0"/>
22490 <param name="right_width" value="0.0"/>
22491 </section>
22492 </section>
22493 </section>
22494 <section name="SignalToNoiseEstimationParameter">
22495 <param name="max_intensity" value="-1"/>
22496 <param name="auto_max_stdev_factor" value="3.0"/>
22497 <param name="auto_max_percentile" value="95"/>
22498 <param name="auto_mode" value="0"/>
22499 <param name="win_len" value="200.0"/>
22500 <param name="bin_count" value="30"/>
22501 <param name="stdev_mp" value="3.0"/>
22502 <param name="min_required_elements" value="10"/>
22503 <param name="noise_for_empty_window" value="1e+20"/>
22504 </section>
22505 </section>
22506 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22507 <output name="ctd_out" ftype="xml">
22508 <assert_contents>
22509 <is_valid_xml/>
22510 </assert_contents>
22511 </output>
22512 </test>
22513 <test expect_num_outputs="2">
22514 <conditional name="adv_opts_cond">
22515 <param name="adv_opts_selector" value="advanced"/>
22516 <param name="write_peak_meta_data" value="true"/>
22517 <param name="force" value="false"/>
22518 <param name="test" value="true"/>
22519 </conditional>
22520 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
22521 <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22522 <section name="algorithm">
22523 <param name="signal_to_noise" value="2.0"/>
22524 <param name="centroid_percentage" value="0.8"/>
22525 <param name="peak_width" value="0.15"/>
22526 <param name="estimate_peak_width" value="false"/>
22527 <param name="fwhm_lower_bound_factor" value="1.0"/>
22528 <param name="fwhm_upper_bound_factor" value="20.0"/>
22529 <section name="optimization">
22530 <param name="iterations" value="400"/>
22531 <section name="penalties">
22532 <param name="position" value="0.0"/>
22533 <param name="left_width" value="1.0"/>
22534 <param name="right_width" value="1.0"/>
22535 <param name="height" value="1.0"/>
22536 </section>
22537 <section name="2d">
22538 <param name="tolerance_mz" value="2.2"/>
22539 <param name="max_peak_distance" value="1.2"/>
22540 </section>
22541 </section>
22542 <section name="thresholds">
22543 <param name="peak_bound" value="200.0"/>
22544 <param name="peak_bound_ms2_level" value="50.0"/>
22545 <param name="correlation" value="0.5"/>
22546 <param name="noise_level" value="0.1"/>
22547 <param name="search_radius" value="3"/>
22548 </section>
22549 <section name="wavelet_transform">
22550 <param name="spacing" value="0.001"/>
22551 </section>
22552 <section name="deconvolution">
22553 <param name="deconvolution" value="true"/>
22554 <param name="asym_threshold" value="0.3"/>
22555 <param name="left_width" value="2.0"/>
22556 <param name="right_width" value="2.0"/>
22557 <param name="scaling" value="0.1"/>
22558 <section name="fitting">
22559 <param name="fwhm_threshold" value="0.7"/>
22560 <param name="eps_abs" value="9.999999747378752e-06"/>
22561 <param name="eps_rel" value="9.999999747378752e-06"/>
22562 <param name="max_iteration" value="100"/>
22563 <section name="penalties">
22564 <param name="position" value="1.0"/>
22565 <param name="height" value="1.0"/>
22566 <param name="left_width" value="0.0"/>
22567 <param name="right_width" value="0.0"/>
22568 </section>
22569 </section>
22570 </section>
22571 <section name="SignalToNoiseEstimationParameter">
22572 <param name="max_intensity" value="-1"/>
22573 <param name="auto_max_stdev_factor" value="3.0"/>
22574 <param name="auto_max_percentile" value="95"/>
22575 <param name="auto_mode" value="0"/>
22576 <param name="win_len" value="200.0"/>
22577 <param name="bin_count" value="30"/>
22578 <param name="stdev_mp" value="3.0"/>
22579 <param name="min_required_elements" value="10"/>
22580 <param name="noise_for_empty_window" value="1e+20"/>
22581 </section>
22582 </section>
22583 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22584 <output name="ctd_out" ftype="xml">
22585 <assert_contents>
22586 <is_valid_xml/>
22587 </assert_contents>
22588 </output>
22589 </test>
22590 <test expect_num_outputs="2">
22591 <conditional name="adv_opts_cond">
22592 <param name="adv_opts_selector" value="advanced"/>
22593 <param name="write_peak_meta_data" value="true"/>
22594 <param name="force" value="false"/>
22595 <param name="test" value="true"/>
22596 </conditional>
22597 <param name="in" value="PeakPickerWavelet_input.mzML"/>
22598 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22599 <section name="algorithm">
22600 <param name="signal_to_noise" value="3.0"/>
22601 <param name="centroid_percentage" value="0.6"/>
22602 <param name="peak_width" value="0.2"/>
22603 <param name="estimate_peak_width" value="false"/>
22604 <param name="fwhm_lower_bound_factor" value="0.5"/>
22605 <param name="fwhm_upper_bound_factor" value="20.0"/>
22606 <section name="optimization">
22607 <param name="iterations" value="400"/>
22608 <section name="penalties">
22609 <param name="position" value="0.0"/>
22610 <param name="left_width" value="1.0"/>
22611 <param name="right_width" value="1.0"/>
22612 <param name="height" value="1.0"/>
22613 </section>
22614 <section name="2d">
22615 <param name="tolerance_mz" value="2.2"/>
22616 <param name="max_peak_distance" value="1.2"/>
22617 </section>
22618 </section>
22619 <section name="thresholds">
22620 <param name="peak_bound" value="100.0"/>
22621 <param name="peak_bound_ms2_level" value="10.0"/>
22622 <param name="correlation" value="0.5"/>
22623 <param name="noise_level" value="0.1"/>
22624 <param name="search_radius" value="3"/>
22625 </section>
22626 <section name="wavelet_transform">
22627 <param name="spacing" value="0.001"/>
22628 </section>
22629 <section name="deconvolution">
22630 <param name="deconvolution" value="false"/>
22631 <param name="asym_threshold" value="0.3"/>
22632 <param name="left_width" value="2.0"/>
22633 <param name="right_width" value="2.0"/>
22634 <param name="scaling" value="0.12"/>
22635 <section name="fitting">
22636 <param name="fwhm_threshold" value="0.7"/>
22637 <param name="eps_abs" value="9.999999747378752e-06"/>
22638 <param name="eps_rel" value="9.999999747378752e-06"/>
22639 <param name="max_iteration" value="10"/>
22640 <section name="penalties">
22641 <param name="position" value="0.0"/>
22642 <param name="height" value="1.0"/>
22643 <param name="left_width" value="0.0"/>
22644 <param name="right_width" value="0.0"/>
22645 </section>
22646 </section>
22647 </section>
22648 <section name="SignalToNoiseEstimationParameter">
22649 <param name="max_intensity" value="-1"/>
22650 <param name="auto_max_stdev_factor" value="3.0"/>
22651 <param name="auto_max_percentile" value="95"/>
22652 <param name="auto_mode" value="0"/>
22653 <param name="win_len" value="200.0"/>
22654 <param name="bin_count" value="30"/>
22655 <param name="stdev_mp" value="3.0"/>
22656 <param name="min_required_elements" value="10"/>
22657 <param name="noise_for_empty_window" value="1e+20"/>
22658 </section>
22659 </section>
22660 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22661 <output name="ctd_out" ftype="xml">
22662 <assert_contents>
22663 <is_valid_xml/>
22664 </assert_contents>
22665 </output>
22666 </test>
22667 <test expect_num_outputs="2">
22668 <conditional name="adv_opts_cond">
22669 <param name="adv_opts_selector" value="advanced"/>
22670 <param name="write_peak_meta_data" value="false"/>
22671 <param name="force" value="false"/>
22672 <param name="test" value="true"/>
22673 </conditional>
22674 <param name="in" value="PeakPickerWavelet_input.mzML"/>
22675 <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
22676 <section name="algorithm">
22677 <param name="signal_to_noise" value="3.0"/>
22678 <param name="centroid_percentage" value="0.6"/>
22679 <param name="peak_width" value="0.2"/>
22680 <param name="estimate_peak_width" value="false"/>
22681 <param name="fwhm_lower_bound_factor" value="0.5"/>
22682 <param name="fwhm_upper_bound_factor" value="20.0"/>
22683 <section name="optimization">
22684 <param name="iterations" value="400"/>
22685 <section name="penalties">
22686 <param name="position" value="0.0"/>
22687 <param name="left_width" value="1.0"/>
22688 <param name="right_width" value="1.0"/>
22689 <param name="height" value="1.0"/>
22690 </section>
22691 <section name="2d">
22692 <param name="tolerance_mz" value="2.2"/>
22693 <param name="max_peak_distance" value="1.2"/>
22694 </section>
22695 </section>
22696 <section name="thresholds">
22697 <param name="peak_bound" value="100.0"/>
22698 <param name="peak_bound_ms2_level" value="10.0"/>
22699 <param name="correlation" value="0.5"/>
22700 <param name="noise_level" value="0.1"/>
22701 <param name="search_radius" value="3"/>
22702 </section>
22703 <section name="wavelet_transform">
22704 <param name="spacing" value="0.001"/>
22705 </section>
22706 <section name="deconvolution">
22707 <param name="deconvolution" value="false"/>
22708 <param name="asym_threshold" value="0.3"/>
22709 <param name="left_width" value="2.0"/>
22710 <param name="right_width" value="2.0"/>
22711 <param name="scaling" value="0.12"/>
22712 <section name="fitting">
22713 <param name="fwhm_threshold" value="0.7"/>
22714 <param name="eps_abs" value="9.999999747378752e-06"/>
22715 <param name="eps_rel" value="9.999999747378752e-06"/>
22716 <param name="max_iteration" value="10"/>
22717 <section name="penalties">
22718 <param name="position" value="0.0"/>
22719 <param name="height" value="1.0"/>
22720 <param name="left_width" value="0.0"/>
22721 <param name="right_width" value="0.0"/>
22722 </section>
22723 </section>
22724 </section>
22725 <section name="SignalToNoiseEstimationParameter">
22726 <param name="max_intensity" value="-1"/>
22727 <param name="auto_max_stdev_factor" value="3.0"/>
22728 <param name="auto_max_percentile" value="95"/>
22729 <param name="auto_mode" value="0"/>
22730 <param name="win_len" value="200.0"/>
22731 <param name="bin_count" value="30"/>
22732 <param name="stdev_mp" value="3.0"/>
22733 <param name="min_required_elements" value="10"/>
22734 <param name="noise_for_empty_window" value="1e+20"/>
22735 </section>
22736 </section>
22737 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22738 <output name="ctd_out" ftype="xml">
22739 <assert_contents>
22740 <is_valid_xml/>
22741 </assert_contents>
22742 </output>
22743 </test>
22744 </xml>
22745 <xml name="autotest_PepNovoAdapter">
22746 </xml>
22747 <xml name="autotest_PeptideIndexer">
22748 <test expect_num_outputs="2">
22749 <conditional name="adv_opts_cond">
22750 <param name="adv_opts_selector" value="advanced"/>
22751 <param name="force" value="false"/>
22752 <param name="test" value="true"/>
22753 </conditional>
22754 <param name="in" value="PeptideIndexer_1.idXML"/>
22755 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22756 <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22757 <param name="decoy_string" value=""/>
22758 <param name="decoy_string_position" value="prefix"/>
22759 <param name="missing_decoy_action" value="error"/>
22760 <param name="write_protein_sequence" value="false"/>
22761 <param name="write_protein_description" value="false"/>
22762 <param name="keep_unreferenced_proteins" value="false"/>
22763 <param name="allow_unmatched" value="true"/>
22764 <param name="aaa_max" value="4"/>
22765 <param name="mismatches_max" value="0"/>
22766 <param name="IL_equivalent" value="false"/>
22767 <section name="enzyme">
22768 <param name="name" value="Trypsin"/>
22769 <param name="specificity" value="none"/>
22770 </section>
22771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22772 <output name="ctd_out" ftype="xml">
22773 <assert_contents>
22774 <is_valid_xml/>
22775 </assert_contents>
22776 </output>
22777 </test>
22778 <test expect_num_outputs="2">
22779 <conditional name="adv_opts_cond">
22780 <param name="adv_opts_selector" value="advanced"/>
22781 <param name="force" value="false"/>
22782 <param name="test" value="true"/>
22783 </conditional>
22784 <param name="in" value="PeptideIndexer_1.idXML"/>
22785 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22786 <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22787 <param name="decoy_string" value=""/>
22788 <param name="decoy_string_position" value="prefix"/>
22789 <param name="missing_decoy_action" value="error"/>
22790 <param name="write_protein_sequence" value="true"/>
22791 <param name="write_protein_description" value="false"/>
22792 <param name="keep_unreferenced_proteins" value="false"/>
22793 <param name="allow_unmatched" value="true"/>
22794 <param name="aaa_max" value="4"/>
22795 <param name="mismatches_max" value="0"/>
22796 <param name="IL_equivalent" value="false"/>
22797 <section name="enzyme">
22798 <param name="name" value="Trypsin"/>
22799 <param name="specificity" value="none"/>
22800 </section>
22801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22802 <output name="ctd_out" ftype="xml">
22803 <assert_contents>
22804 <is_valid_xml/>
22805 </assert_contents>
22806 </output>
22807 </test>
22808 <test expect_num_outputs="2">
22809 <conditional name="adv_opts_cond">
22810 <param name="adv_opts_selector" value="advanced"/>
22811 <param name="force" value="false"/>
22812 <param name="test" value="true"/>
22813 </conditional>
22814 <param name="in" value="PeptideIndexer_1.idXML"/>
22815 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22816 <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22817 <param name="decoy_string" value=""/>
22818 <param name="decoy_string_position" value="prefix"/>
22819 <param name="missing_decoy_action" value="error"/>
22820 <param name="write_protein_sequence" value="false"/>
22821 <param name="write_protein_description" value="false"/>
22822 <param name="keep_unreferenced_proteins" value="true"/>
22823 <param name="allow_unmatched" value="true"/>
22824 <param name="aaa_max" value="4"/>
22825 <param name="mismatches_max" value="0"/>
22826 <param name="IL_equivalent" value="false"/>
22827 <section name="enzyme">
22828 <param name="name" value="Trypsin"/>
22829 <param name="specificity" value="none"/>
22830 </section>
22831 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22832 <output name="ctd_out" ftype="xml">
22833 <assert_contents>
22834 <is_valid_xml/>
22835 </assert_contents>
22836 </output>
22837 </test>
22838 <test expect_num_outputs="2">
22839 <conditional name="adv_opts_cond">
22840 <param name="adv_opts_selector" value="advanced"/>
22841 <param name="force" value="false"/>
22842 <param name="test" value="true"/>
22843 </conditional>
22844 <param name="in" value="PeptideIndexer_1.idXML"/>
22845 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22846 <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22847 <param name="decoy_string" value=""/>
22848 <param name="decoy_string_position" value="prefix"/>
22849 <param name="missing_decoy_action" value="error"/>
22850 <param name="write_protein_sequence" value="true"/>
22851 <param name="write_protein_description" value="false"/>
22852 <param name="keep_unreferenced_proteins" value="false"/>
22853 <param name="allow_unmatched" value="true"/>
22854 <param name="aaa_max" value="0"/>
22855 <param name="mismatches_max" value="0"/>
22856 <param name="IL_equivalent" value="false"/>
22857 <section name="enzyme">
22858 <param name="name" value="Trypsin"/>
22859 <param name="specificity" value="none"/>
22860 </section>
22861 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22862 <output name="ctd_out" ftype="xml">
22863 <assert_contents>
22864 <is_valid_xml/>
22865 </assert_contents>
22866 </output>
22867 </test>
22868 <test expect_num_outputs="2">
22869 <conditional name="adv_opts_cond">
22870 <param name="adv_opts_selector" value="advanced"/>
22871 <param name="force" value="false"/>
22872 <param name="test" value="true"/>
22873 </conditional>
22874 <param name="in" value="PeptideIndexer_1.idXML"/>
22875 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22876 <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22877 <param name="decoy_string" value=""/>
22878 <param name="decoy_string_position" value="prefix"/>
22879 <param name="missing_decoy_action" value="error"/>
22880 <param name="write_protein_sequence" value="false"/>
22881 <param name="write_protein_description" value="false"/>
22882 <param name="keep_unreferenced_proteins" value="false"/>
22883 <param name="allow_unmatched" value="true"/>
22884 <param name="aaa_max" value="4"/>
22885 <param name="mismatches_max" value="0"/>
22886 <param name="IL_equivalent" value="false"/>
22887 <section name="enzyme">
22888 <param name="name" value="Trypsin"/>
22889 <param name="specificity" value="none"/>
22890 </section>
22891 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22892 <output name="ctd_out" ftype="xml">
22893 <assert_contents>
22894 <is_valid_xml/>
22895 </assert_contents>
22896 </output>
22897 </test>
22898 <test expect_num_outputs="2">
22899 <conditional name="adv_opts_cond">
22900 <param name="adv_opts_selector" value="advanced"/>
22901 <param name="force" value="false"/>
22902 <param name="test" value="true"/>
22903 </conditional>
22904 <param name="in" value="PeptideIndexer_2.idXML"/>
22905 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22906 <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22907 <param name="decoy_string" value=""/>
22908 <param name="decoy_string_position" value="prefix"/>
22909 <param name="missing_decoy_action" value="error"/>
22910 <param name="write_protein_sequence" value="false"/>
22911 <param name="write_protein_description" value="false"/>
22912 <param name="keep_unreferenced_proteins" value="false"/>
22913 <param name="allow_unmatched" value="true"/>
22914 <param name="aaa_max" value="3"/>
22915 <param name="mismatches_max" value="0"/>
22916 <param name="IL_equivalent" value="false"/>
22917 <section name="enzyme">
22918 <param name="name" value="Trypsin"/>
22919 <param name="specificity" value="none"/>
22920 </section>
22921 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22922 <output name="ctd_out" ftype="xml">
22923 <assert_contents>
22924 <is_valid_xml/>
22925 </assert_contents>
22926 </output>
22927 </test>
22928 <test expect_num_outputs="2">
22929 <conditional name="adv_opts_cond">
22930 <param name="adv_opts_selector" value="advanced"/>
22931 <param name="force" value="false"/>
22932 <param name="test" value="true"/>
22933 </conditional>
22934 <param name="in" value="PeptideIndexer_3.idXML"/>
22935 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22936 <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22937 <param name="decoy_string" value="DECOY_"/>
22938 <param name="decoy_string_position" value="prefix"/>
22939 <param name="missing_decoy_action" value="error"/>
22940 <param name="write_protein_sequence" value="false"/>
22941 <param name="write_protein_description" value="false"/>
22942 <param name="keep_unreferenced_proteins" value="false"/>
22943 <param name="allow_unmatched" value="true"/>
22944 <param name="aaa_max" value="4"/>
22945 <param name="mismatches_max" value="0"/>
22946 <param name="IL_equivalent" value="false"/>
22947 <section name="enzyme">
22948 <param name="name" value="Trypsin"/>
22949 <param name="specificity" value="full"/>
22950 </section>
22951 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22952 <output name="ctd_out" ftype="xml">
22953 <assert_contents>
22954 <is_valid_xml/>
22955 </assert_contents>
22956 </output>
22957 </test>
22958 <test expect_num_outputs="2">
22959 <conditional name="adv_opts_cond">
22960 <param name="adv_opts_selector" value="advanced"/>
22961 <param name="force" value="false"/>
22962 <param name="test" value="true"/>
22963 </conditional>
22964 <param name="in" value="PeptideIndexer_3.idXML"/>
22965 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22966 <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22967 <param name="decoy_string" value=""/>
22968 <param name="decoy_string_position" value="prefix"/>
22969 <param name="missing_decoy_action" value="error"/>
22970 <param name="write_protein_sequence" value="false"/>
22971 <param name="write_protein_description" value="false"/>
22972 <param name="keep_unreferenced_proteins" value="false"/>
22973 <param name="allow_unmatched" value="true"/>
22974 <param name="aaa_max" value="4"/>
22975 <param name="mismatches_max" value="0"/>
22976 <param name="IL_equivalent" value="false"/>
22977 <section name="enzyme">
22978 <param name="name" value="Trypsin"/>
22979 <param name="specificity" value="semi"/>
22980 </section>
22981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
22982 <output name="ctd_out" ftype="xml">
22983 <assert_contents>
22984 <is_valid_xml/>
22985 </assert_contents>
22986 </output>
22987 </test>
22988 <test expect_num_outputs="2">
22989 <conditional name="adv_opts_cond">
22990 <param name="adv_opts_selector" value="advanced"/>
22991 <param name="force" value="false"/>
22992 <param name="test" value="true"/>
22993 </conditional>
22994 <param name="in" value="PeptideIndexer_3.idXML"/>
22995 <param name="fasta" value="PeptideIndexer_1.fasta"/>
22996 <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
22997 <param name="decoy_string" value=""/>
22998 <param name="decoy_string_position" value="prefix"/>
22999 <param name="missing_decoy_action" value="error"/>
23000 <param name="write_protein_sequence" value="false"/>
23001 <param name="write_protein_description" value="false"/>
23002 <param name="keep_unreferenced_proteins" value="false"/>
23003 <param name="allow_unmatched" value="true"/>
23004 <param name="aaa_max" value="4"/>
23005 <param name="mismatches_max" value="0"/>
23006 <param name="IL_equivalent" value="false"/>
23007 <section name="enzyme">
23008 <param name="name" value="Trypsin"/>
23009 <param name="specificity" value="none"/>
23010 </section>
23011 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23012 <output name="ctd_out" ftype="xml">
23013 <assert_contents>
23014 <is_valid_xml/>
23015 </assert_contents>
23016 </output>
23017 </test>
23018 <test expect_num_outputs="2">
23019 <conditional name="adv_opts_cond">
23020 <param name="adv_opts_selector" value="advanced"/>
23021 <param name="force" value="false"/>
23022 <param name="test" value="true"/>
23023 </conditional>
23024 <param name="in" value="PeptideIndexer_10_input.idXML"/>
23025 <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
23026 <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23027 <param name="decoy_string" value=""/>
23028 <param name="decoy_string_position" value="prefix"/>
23029 <param name="missing_decoy_action" value="error"/>
23030 <param name="write_protein_sequence" value="true"/>
23031 <param name="write_protein_description" value="false"/>
23032 <param name="keep_unreferenced_proteins" value="false"/>
23033 <param name="allow_unmatched" value="false"/>
23034 <param name="aaa_max" value="3"/>
23035 <param name="mismatches_max" value="0"/>
23036 <param name="IL_equivalent" value="true"/>
23037 <section name="enzyme">
23038 <param name="name" value="Trypsin"/>
23039 <param name="specificity" value="full"/>
23040 </section>
23041 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23042 <output name="ctd_out" ftype="xml">
23043 <assert_contents>
23044 <is_valid_xml/>
23045 </assert_contents>
23046 </output>
23047 </test>
23048 <test expect_num_outputs="2">
23049 <conditional name="adv_opts_cond">
23050 <param name="adv_opts_selector" value="advanced"/>
23051 <param name="force" value="false"/>
23052 <param name="test" value="true"/>
23053 </conditional>
23054 <param name="in" value="PeptideIndexer_1.idXML"/>
23055 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23056 <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23057 <param name="decoy_string" value=""/>
23058 <param name="decoy_string_position" value="prefix"/>
23059 <param name="missing_decoy_action" value="error"/>
23060 <param name="write_protein_sequence" value="false"/>
23061 <param name="write_protein_description" value="false"/>
23062 <param name="keep_unreferenced_proteins" value="false"/>
23063 <param name="allow_unmatched" value="true"/>
23064 <param name="aaa_max" value="4"/>
23065 <param name="mismatches_max" value="0"/>
23066 <param name="IL_equivalent" value="false"/>
23067 <section name="enzyme">
23068 <param name="name" value="Trypsin"/>
23069 <param name="specificity" value="none"/>
23070 </section>
23071 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23072 <output name="ctd_out" ftype="xml">
23073 <assert_contents>
23074 <is_valid_xml/>
23075 </assert_contents>
23076 </output>
23077 </test>
23078 <test expect_num_outputs="2">
23079 <conditional name="adv_opts_cond">
23080 <param name="adv_opts_selector" value="advanced"/>
23081 <param name="force" value="false"/>
23082 <param name="test" value="true"/>
23083 </conditional>
23084 <param name="in" value="empty.idXML"/>
23085 <param name="fasta" value="PeptideIndexer_1.fasta"/>
23086 <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23087 <param name="decoy_string" value=""/>
23088 <param name="decoy_string_position" value="prefix"/>
23089 <param name="missing_decoy_action" value="error"/>
23090 <param name="write_protein_sequence" value="false"/>
23091 <param name="write_protein_description" value="false"/>
23092 <param name="keep_unreferenced_proteins" value="false"/>
23093 <param name="allow_unmatched" value="false"/>
23094 <param name="aaa_max" value="4"/>
23095 <param name="mismatches_max" value="0"/>
23096 <param name="IL_equivalent" value="false"/>
23097 <section name="enzyme">
23098 <param name="name" value="Trypsin"/>
23099 <param name="specificity" value="full"/>
23100 </section>
23101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23102 <output name="ctd_out" ftype="xml">
23103 <assert_contents>
23104 <is_valid_xml/>
23105 </assert_contents>
23106 </output>
23107 </test>
23108 <test expect_num_outputs="2">
23109 <conditional name="adv_opts_cond">
23110 <param name="adv_opts_selector" value="advanced"/>
23111 <param name="force" value="false"/>
23112 <param name="test" value="true"/>
23113 </conditional>
23114 <param name="in" value="PeptideIndexer_14.idXML"/>
23115 <param name="fasta" value="PeptideIndexer_2.fasta"/>
23116 <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23117 <param name="decoy_string" value=""/>
23118 <param name="decoy_string_position" value="prefix"/>
23119 <param name="missing_decoy_action" value="error"/>
23120 <param name="write_protein_sequence" value="true"/>
23121 <param name="write_protein_description" value="false"/>
23122 <param name="keep_unreferenced_proteins" value="false"/>
23123 <param name="allow_unmatched" value="false"/>
23124 <param name="aaa_max" value="4"/>
23125 <param name="mismatches_max" value="0"/>
23126 <param name="IL_equivalent" value="false"/>
23127 <section name="enzyme">
23128 <param name="name" value="Trypsin"/>
23129 <param name="specificity" value="none"/>
23130 </section>
23131 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23132 <output name="ctd_out" ftype="xml">
23133 <assert_contents>
23134 <is_valid_xml/>
23135 </assert_contents>
23136 </output>
23137 </test>
23138 </xml>
23139 <xml name="autotest_PercolatorAdapter">
23140 <test expect_num_outputs="2">
23141 <conditional name="adv_opts_cond">
23142 <param name="adv_opts_selector" value="advanced"/>
23143 <param name="generic_feature_set" value="false"/>
23144 <param name="subset_max_train" value="0"/>
23145 <param name="cpos" value="0.0"/>
23146 <param name="cneg" value="0.0"/>
23147 <param name="testFDR" value="0.5"/>
23148 <param name="trainFDR" value="0.5"/>
23149 <param name="maxiter" value="10"/>
23150 <param name="quick_validation" value="false"/>
23151 <param name="default_direction" value=""/>
23152 <param name="verbose" value="2"/>
23153 <param name="unitnorm" value="false"/>
23154 <param name="test_each_iteration" value="false"/>
23155 <param name="override" value="false"/>
23156 <param name="seed" value="1"/>
23157 <param name="doc" value="0"/>
23158 <param name="klammer" value="false"/>
23159 <param name="decoy_pattern" value="random"/>
23160 <param name="post_processing_tdc" value="false"/>
23161 <param name="train_best_positive" value="false"/>
23162 <param name="ipf_max_peakgroup_pep" value="0.7"/>
23163 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
23164 <param name="ipf_min_transition_sn" value="0.0"/>
23165 <param name="force" value="false"/>
23166 <param name="test" value="true"/>
23167 </conditional>
23168 <param name="in" value="PercolatorAdapter_1.idXML"/>
23169 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23170 <param name="out_type" value="idXML"/>
23171 <param name="enzyme" value="trypsin"/>
23172 <param name="peptide_level_fdrs" value="false"/>
23173 <param name="protein_level_fdrs" value="false"/>
23174 <param name="osw_level" value="ms2"/>
23175 <param name="score_type" value="q-value"/>
23176 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23177 <output name="ctd_out" ftype="xml">
23178 <assert_contents>
23179 <is_valid_xml/>
23180 </assert_contents>
23181 </output>
23182 </test>
23183 <test expect_num_outputs="2">
23184 <conditional name="adv_opts_cond">
23185 <param name="adv_opts_selector" value="advanced"/>
23186 <param name="generic_feature_set" value="false"/>
23187 <param name="subset_max_train" value="0"/>
23188 <param name="cpos" value="0.0"/>
23189 <param name="cneg" value="0.0"/>
23190 <param name="testFDR" value="0.01"/>
23191 <param name="trainFDR" value="0.01"/>
23192 <param name="maxiter" value="10"/>
23193 <param name="quick_validation" value="false"/>
23194 <param name="default_direction" value=""/>
23195 <param name="verbose" value="2"/>
23196 <param name="unitnorm" value="false"/>
23197 <param name="test_each_iteration" value="false"/>
23198 <param name="override" value="false"/>
23199 <param name="seed" value="1"/>
23200 <param name="doc" value="0"/>
23201 <param name="klammer" value="false"/>
23202 <param name="decoy_pattern" value="random"/>
23203 <param name="post_processing_tdc" value="false"/>
23204 <param name="train_best_positive" value="false"/>
23205 <param name="ipf_max_peakgroup_pep" value="0.7"/>
23206 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
23207 <param name="ipf_min_transition_sn" value="0.0"/>
23208 <param name="force" value="false"/>
23209 <param name="test" value="true"/>
23210 </conditional>
23211 <param name="in_osw" value="PercolatorAdapter_2.osw"/>
23212 <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
23213 <param name="out_type" value="osw"/>
23214 <param name="enzyme" value="trypsin"/>
23215 <param name="peptide_level_fdrs" value="false"/>
23216 <param name="protein_level_fdrs" value="false"/>
23217 <param name="osw_level" value="ms1"/>
23218 <param name="score_type" value="q-value"/>
23219 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23220 <output name="ctd_out" ftype="xml">
23221 <assert_contents>
23222 <is_valid_xml/>
23223 </assert_contents>
23224 </output>
23225 </test>
23226 <test expect_num_outputs="2">
23227 <conditional name="adv_opts_cond">
23228 <param name="adv_opts_selector" value="advanced"/>
23229 <param name="generic_feature_set" value="false"/>
23230 <param name="subset_max_train" value="0"/>
23231 <param name="cpos" value="0.0"/>
23232 <param name="cneg" value="0.0"/>
23233 <param name="testFDR" value="0.01"/>
23234 <param name="trainFDR" value="0.01"/>
23235 <param name="maxiter" value="10"/>
23236 <param name="quick_validation" value="false"/>
23237 <param name="default_direction" value=""/>
23238 <param name="verbose" value="2"/>
23239 <param name="unitnorm" value="false"/>
23240 <param name="test_each_iteration" value="false"/>
23241 <param name="override" value="false"/>
23242 <param name="seed" value="1"/>
23243 <param name="doc" value="0"/>
23244 <param name="klammer" value="false"/>
23245 <param name="decoy_pattern" value="random"/>
23246 <param name="post_processing_tdc" value="false"/>
23247 <param name="train_best_positive" value="false"/>
23248 <param name="ipf_max_peakgroup_pep" value="0.7"/>
23249 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
23250 <param name="ipf_min_transition_sn" value="0.0"/>
23251 <param name="force" value="false"/>
23252 <param name="test" value="true"/>
23253 </conditional>
23254 <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
23255 <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
23256 <param name="out_type" value="osw"/>
23257 <param name="enzyme" value="trypsin"/>
23258 <param name="peptide_level_fdrs" value="false"/>
23259 <param name="protein_level_fdrs" value="false"/>
23260 <param name="osw_level" value="ms2"/>
23261 <param name="score_type" value="q-value"/>
23262 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23263 <output name="ctd_out" ftype="xml">
23264 <assert_contents>
23265 <is_valid_xml/>
23266 </assert_contents>
23267 </output>
23268 </test>
23269 <test expect_num_outputs="2">
23270 <conditional name="adv_opts_cond">
23271 <param name="adv_opts_selector" value="advanced"/>
23272 <param name="generic_feature_set" value="false"/>
23273 <param name="subset_max_train" value="0"/>
23274 <param name="cpos" value="0.0"/>
23275 <param name="cneg" value="0.0"/>
23276 <param name="testFDR" value="0.01"/>
23277 <param name="trainFDR" value="0.01"/>
23278 <param name="maxiter" value="10"/>
23279 <param name="quick_validation" value="false"/>
23280 <param name="default_direction" value=""/>
23281 <param name="verbose" value="2"/>
23282 <param name="unitnorm" value="false"/>
23283 <param name="test_each_iteration" value="false"/>
23284 <param name="override" value="false"/>
23285 <param name="seed" value="1"/>
23286 <param name="doc" value="0"/>
23287 <param name="klammer" value="false"/>
23288 <param name="decoy_pattern" value="random"/>
23289 <param name="post_processing_tdc" value="false"/>
23290 <param name="train_best_positive" value="false"/>
23291 <param name="ipf_max_peakgroup_pep" value="0.7"/>
23292 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
23293 <param name="ipf_min_transition_sn" value="0.0"/>
23294 <param name="force" value="false"/>
23295 <param name="test" value="true"/>
23296 </conditional>
23297 <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
23298 <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
23299 <param name="out_type" value="osw"/>
23300 <param name="enzyme" value="trypsin"/>
23301 <param name="peptide_level_fdrs" value="false"/>
23302 <param name="protein_level_fdrs" value="false"/>
23303 <param name="osw_level" value="transition"/>
23304 <param name="score_type" value="q-value"/>
23305 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23306 <output name="ctd_out" ftype="xml">
23307 <assert_contents>
23308 <is_valid_xml/>
23309 </assert_contents>
23310 </output>
23311 </test>
23312 <test expect_num_outputs="3">
23313 <conditional name="adv_opts_cond">
23314 <param name="adv_opts_selector" value="advanced"/>
23315 <param name="generic_feature_set" value="false"/>
23316 <param name="subset_max_train" value="0"/>
23317 <param name="cpos" value="0.0"/>
23318 <param name="cneg" value="0.0"/>
23319 <param name="testFDR" value="0.5"/>
23320 <param name="trainFDR" value="0.5"/>
23321 <param name="maxiter" value="10"/>
23322 <param name="quick_validation" value="false"/>
23323 <param name="default_direction" value=""/>
23324 <param name="verbose" value="2"/>
23325 <param name="unitnorm" value="false"/>
23326 <param name="test_each_iteration" value="false"/>
23327 <param name="override" value="false"/>
23328 <param name="seed" value="1"/>
23329 <param name="doc" value="0"/>
23330 <param name="klammer" value="false"/>
23331 <param name="decoy_pattern" value="random"/>
23332 <param name="post_processing_tdc" value="false"/>
23333 <param name="train_best_positive" value="false"/>
23334 <param name="ipf_max_peakgroup_pep" value="0.7"/>
23335 <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
23336 <param name="ipf_min_transition_sn" value="0.0"/>
23337 <param name="force" value="false"/>
23338 <param name="test" value="true"/>
23339 </conditional>
23340 <param name="in" value="PercolatorAdapter_1.idXML"/>
23341 <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23342 <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
23343 <param name="out_type" value="idXML"/>
23344 <param name="enzyme" value="trypsin"/>
23345 <param name="peptide_level_fdrs" value="false"/>
23346 <param name="protein_level_fdrs" value="false"/>
23347 <param name="osw_level" value="ms2"/>
23348 <param name="score_type" value="q-value"/>
23349 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
23350 <output name="ctd_out" ftype="xml">
23351 <assert_contents>
23352 <is_valid_xml/>
23353 </assert_contents>
23354 </output>
23355 </test>
23356 </xml>
23357 <xml name="autotest_PhosphoScoring">
23358 </xml>
23359 <xml name="autotest_PrecursorIonSelector">
23360 <test expect_num_outputs="2">
23361 <conditional name="adv_opts_cond">
23362 <param name="adv_opts_selector" value="advanced"/>
23363 <param name="solver" value="GLPK"/>
23364 <param name="force" value="false"/>
23365 <param name="test" value="true"/>
23366 </conditional>
23367 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
23368 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
23369 <param name="num_precursors" value="1"/>
23370 <param name="load_preprocessing" value="false"/>
23371 <param name="store_preprocessing" value="false"/>
23372 <param name="simulation" value="true"/>
23373 <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
23374 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
23375 <param name="fixed_modifications" value=""/>
23376 <section name="algorithm">
23377 <param name="type" value="IPS"/>
23378 <param name="max_iteration" value="10"/>
23379 <param name="rt_bin_capacity" value="10"/>
23380 <param name="step_size" value="1"/>
23381 <param name="peptide_min_prob" value="0.2"/>
23382 <param name="sequential_spectrum_order" value="false"/>
23383 <section name="MIPFormulation">
23384 <section name="thresholds">
23385 <param name="min_protein_probability" value="0.2"/>
23386 <param name="min_protein_id_probability" value="0.95"/>
23387 <param name="min_pt_weight" value="0.5"/>
23388 <param name="min_mz" value="500.0"/>
23389 <param name="max_mz" value="5000.0"/>
23390 <param name="min_pred_pep_prob" value="0.5"/>
23391 <param name="min_rt_weight" value="0.5"/>
23392 <param name="use_peptide_rule" value="true"/>
23393 <param name="min_peptide_ids" value="2"/>
23394 <param name="min_peptide_probability" value="0.95"/>
23395 </section>
23396 <section name="combined_ilp">
23397 <param name="k1" value="0.2"/>
23398 <param name="k2" value="0.2"/>
23399 <param name="k3" value="0.4"/>
23400 <param name="scale_matching_probs" value="true"/>
23401 </section>
23402 <section name="feature_based">
23403 <param name="no_intensity_normalization" value="false"/>
23404 <param name="max_number_precursors_per_feature" value="1"/>
23405 </section>
23406 </section>
23407 <section name="Preprocessing">
23408 <param name="precursor_mass_tolerance" value="0.9"/>
23409 <param name="precursor_mass_tolerance_unit" value="Da"/>
23410 <param name="preprocessed_db_path" value=""/>
23411 <param name="preprocessed_db_pred_rt_path" value=""/>
23412 <param name="preprocessed_db_pred_dt_path" value=""/>
23413 <param name="max_peptides_per_run" value="100000"/>
23414 <param name="missed_cleavages" value="1"/>
23415 <param name="taxonomy" value=""/>
23416 <param name="store_peptide_sequences" value="false"/>
23417 <section name="rt_settings">
23418 <param name="min_rt" value="960.0"/>
23419 <param name="max_rt" value="3840.0"/>
23420 <param name="rt_step_size" value="30.0"/>
23421 <param name="gauss_mean" value="-1.0"/>
23422 <param name="gauss_sigma" value="3.0"/>
23423 </section>
23424 </section>
23425 </section>
23426 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
23427 <output name="ctd_out" ftype="xml">
23428 <assert_contents>
23429 <is_valid_xml/>
23430 </assert_contents>
23431 </output>
23432 </test>
23433 <test expect_num_outputs="2">
23434 <conditional name="adv_opts_cond">
23435 <param name="adv_opts_selector" value="advanced"/>
23436 <param name="solver" value="GLPK"/>
23437 <param name="force" value="false"/>
23438 <param name="test" value="true"/>
23439 </conditional>
23440 <param name="in" value="PrecursorIonSelector_features.featureXML"/>
23441 <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
23442 <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
23443 <param name="num_precursors" value="1"/>
23444 <param name="load_preprocessing" value="false"/>
23445 <param name="store_preprocessing" value="false"/>
23446 <param name="simulation" value="false"/>
23447 <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
23448 <param name="fixed_modifications" value=""/>
23449 <section name="algorithm">
23450 <param name="type" value="IPS"/>
23451 <param name="max_iteration" value="10"/>
23452 <param name="rt_bin_capacity" value="10"/>
23453 <param name="step_size" value="1"/>
23454 <param name="peptide_min_prob" value="0.2"/>
23455 <param name="sequential_spectrum_order" value="false"/>
23456 <section name="MIPFormulation">
23457 <section name="thresholds">
23458 <param name="min_protein_probability" value="0.2"/>
23459 <param name="min_protein_id_probability" value="0.95"/>
23460 <param name="min_pt_weight" value="0.5"/>
23461 <param name="min_mz" value="500.0"/>
23462 <param name="max_mz" value="5000.0"/>
23463 <param name="min_pred_pep_prob" value="0.5"/>
23464 <param name="min_rt_weight" value="0.5"/>
23465 <param name="use_peptide_rule" value="true"/>
23466 <param name="min_peptide_ids" value="2"/>
23467 <param name="min_peptide_probability" value="0.95"/>
23468 </section>
23469 <section name="combined_ilp">
23470 <param name="k1" value="0.2"/>
23471 <param name="k2" value="0.2"/>
23472 <param name="k3" value="0.4"/>
23473 <param name="scale_matching_probs" value="true"/>
23474 </section>
23475 <section name="feature_based">
23476 <param name="no_intensity_normalization" value="false"/>
23477 <param name="max_number_precursors_per_feature" value="1"/>
23478 </section>
23479 </section>
23480 <section name="Preprocessing">
23481 <param name="precursor_mass_tolerance" value="0.9"/>
23482 <param name="precursor_mass_tolerance_unit" value="Da"/>
23483 <param name="preprocessed_db_path" value=""/>
23484 <param name="preprocessed_db_pred_rt_path" value=""/>
23485 <param name="preprocessed_db_pred_dt_path" value=""/>
23486 <param name="max_peptides_per_run" value="100000"/>
23487 <param name="missed_cleavages" value="1"/>
23488 <param name="taxonomy" value=""/>
23489 <param name="store_peptide_sequences" value="false"/>
23490 <section name="rt_settings">
23491 <param name="min_rt" value="960.0"/>
23492 <param name="max_rt" value="3840.0"/>
23493 <param name="rt_step_size" value="30.0"/>
23494 <param name="gauss_mean" value="-1.0"/>
23495 <param name="gauss_sigma" value="3.0"/>
23496 </section>
23497 </section>
23498 </section>
23499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23500 <output name="ctd_out" ftype="xml">
23501 <assert_contents>
23502 <is_valid_xml/>
23503 </assert_contents>
23504 </output>
23505 </test>
23506 </xml>
23507 <xml name="autotest_PrecursorMassCorrector">
23508 <test expect_num_outputs="2">
23509 <conditional name="adv_opts_cond">
23510 <param name="adv_opts_selector" value="advanced"/>
23511 <param name="max_charge" value="3"/>
23512 <param name="intensity_threshold" value="-1.0"/>
23513 <param name="force" value="false"/>
23514 <param name="test" value="true"/>
23515 </conditional>
23516 <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
23517 <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
23518 <param name="precursor_mass_tolerance" value="1.5"/>
23519 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23520 <output name="ctd_out" ftype="xml">
23521 <assert_contents>
23522 <is_valid_xml/>
23523 </assert_contents>
23524 </output>
23525 </test>
23526 </xml>
23527 <xml name="autotest_ProteinInference">
23528 <test expect_num_outputs="2">
23529 <conditional name="adv_opts_cond">
23530 <param name="adv_opts_selector" value="advanced"/>
23531 <param name="force" value="false"/>
23532 <param name="test" value="true"/>
23533 </conditional>
23534 <param name="in" value="ProteinInference_1_input.idXML"/>
23535 <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
23536 <param name="merge_runs" value="all"/>
23537 <param name="annotate_indist_groups" value="true"/>
23538 <section name="Merging">
23539 <param name="annotate_origin" value="false"/>
23540 </section>
23541 <section name="Algorithm">
23542 <param name="min_peptides_per_protein" value="1"/>
23543 <param name="score_aggregation_method" value="maximum"/>
23544 <param name="treat_charge_variants_separately" value="true"/>
23545 <param name="treat_modification_variants_separately" value="true"/>
23546 <param name="use_shared_peptides" value="false"/>
23547 <param name="skip_count_annotation" value="false"/>
23548 </section>
23549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
23550 <output name="ctd_out" ftype="xml">
23551 <assert_contents>
23552 <is_valid_xml/>
23553 </assert_contents>
23554 </output>
23555 </test>
23556 </xml>
23557 <xml name="autotest_ProteinQuantifier">
23558 <test expect_num_outputs="3">
23559 <conditional name="adv_opts_cond">
23560 <param name="adv_opts_selector" value="advanced"/>
23561 <param name="force" value="false"/>
23562 <param name="test" value="true"/>
23563 </conditional>
23564 <param name="in" value="ProteinQuantifier_input.featureXML"/>
23565 <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
23566 <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
23567 <param name="top" value="3"/>
23568 <param name="average" value="median"/>
23569 <param name="include_all" value="false"/>
23570 <param name="best_charge_and_fraction" value="false"/>
23571 <param name="greedy_group_resolution" value="false"/>
23572 <param name="ratios" value="false"/>
23573 <param name="ratiosSILAC" value="false"/>
23574 <section name="consensus">
23575 <param name="normalize" value="false"/>
23576 <param name="fix_peptides" value="false"/>
23577 </section>
23578 <section name="format">
23579 <param name="separator" value=""/>
23580 <param name="quoting" value="double"/>
23581 <param name="replacement" value="_"/>
23582 </section>
23583 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
23584 <output name="ctd_out" ftype="xml">
23585 <assert_contents>
23586 <is_valid_xml/>
23587 </assert_contents>
23588 </output>
23589 </test>
23590 <test expect_num_outputs="3">
23591 <conditional name="adv_opts_cond">
23592 <param name="adv_opts_selector" value="advanced"/>
23593 <param name="force" value="false"/>
23594 <param name="test" value="true"/>
23595 </conditional>
23596 <param name="in" value="ProteinQuantifier_input.featureXML"/>
23597 <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
23598 <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
23599 <param name="top" value="2"/>
23600 <param name="average" value="sum"/>
23601 <param name="include_all" value="true"/>
23602 <param name="best_charge_and_fraction" value="true"/>
23603 <param name="greedy_group_resolution" value="false"/>
23604 <param name="ratios" value="false"/>
23605 <param name="ratiosSILAC" value="false"/>
23606 <section name="consensus">
23607 <param name="normalize" value="false"/>
23608 <param name="fix_peptides" value="false"/>
23609 </section>
23610 <section name="format">
23611 <param name="separator" value=""/>
23612 <param name="quoting" value="double"/>
23613 <param name="replacement" value="_"/>
23614 </section>
23615 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
23616 <output name="ctd_out" ftype="xml">
23617 <assert_contents>
23618 <is_valid_xml/>
23619 </assert_contents>
23620 </output>
23621 </test>
23622 <test expect_num_outputs="3">
23623 <conditional name="adv_opts_cond">
23624 <param name="adv_opts_selector" value="advanced"/>
23625 <param name="force" value="false"/>
23626 <param name="test" value="true"/>
23627 </conditional>
23628 <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
23629 <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
23630 <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
23631 <param name="top" value="2"/>
23632 <param name="average" value="mean"/>
23633 <param name="include_all" value="true"/>
23634 <param name="best_charge_and_fraction" value="false"/>
23635 <param name="greedy_group_resolution" value="false"/>
23636 <param name="ratios" value="false"/>
23637 <param name="ratiosSILAC" value="false"/>
23638 <section name="consensus">
23639 <param name="normalize" value="false"/>
23640 <param name="fix_peptides" value="false"/>
23641 </section>
23642 <section name="format">
23643 <param name="separator" value=""/>
23644 <param name="quoting" value="double"/>
23645 <param name="replacement" value="_"/>
23646 </section>
23647 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
23648 <output name="ctd_out" ftype="xml">
23649 <assert_contents>
23650 <is_valid_xml/>
23651 </assert_contents>
23652 </output>
23653 </test>
23654 <test expect_num_outputs="2">
23655 <conditional name="adv_opts_cond">
23656 <param name="adv_opts_selector" value="advanced"/>
23657 <param name="force" value="false"/>
23658 <param name="test" value="true"/>
23659 </conditional>
23660 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23661 <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23662 <param name="top" value="0"/>
23663 <param name="average" value="sum"/>
23664 <param name="include_all" value="false"/>
23665 <param name="best_charge_and_fraction" value="false"/>
23666 <param name="greedy_group_resolution" value="false"/>
23667 <param name="ratios" value="false"/>
23668 <param name="ratiosSILAC" value="false"/>
23669 <section name="consensus">
23670 <param name="normalize" value="false"/>
23671 <param name="fix_peptides" value="false"/>
23672 </section>
23673 <section name="format">
23674 <param name="separator" value=""/>
23675 <param name="quoting" value="double"/>
23676 <param name="replacement" value="_"/>
23677 </section>
23678 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23679 <output name="ctd_out" ftype="xml">
23680 <assert_contents>
23681 <is_valid_xml/>
23682 </assert_contents>
23683 </output>
23684 </test>
23685 <test expect_num_outputs="2">
23686 <conditional name="adv_opts_cond">
23687 <param name="adv_opts_selector" value="advanced"/>
23688 <param name="force" value="false"/>
23689 <param name="test" value="true"/>
23690 </conditional>
23691 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23692 <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23693 <param name="top" value="3"/>
23694 <param name="average" value="sum"/>
23695 <param name="include_all" value="false"/>
23696 <param name="best_charge_and_fraction" value="false"/>
23697 <param name="greedy_group_resolution" value="false"/>
23698 <param name="ratios" value="false"/>
23699 <param name="ratiosSILAC" value="false"/>
23700 <section name="consensus">
23701 <param name="normalize" value="false"/>
23702 <param name="fix_peptides" value="false"/>
23703 </section>
23704 <section name="format">
23705 <param name="separator" value=""/>
23706 <param name="quoting" value="double"/>
23707 <param name="replacement" value="_"/>
23708 </section>
23709 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23710 <output name="ctd_out" ftype="xml">
23711 <assert_contents>
23712 <is_valid_xml/>
23713 </assert_contents>
23714 </output>
23715 </test>
23716 <test expect_num_outputs="2">
23717 <conditional name="adv_opts_cond">
23718 <param name="adv_opts_selector" value="advanced"/>
23719 <param name="force" value="false"/>
23720 <param name="test" value="true"/>
23721 </conditional>
23722 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23723 <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23724 <param name="top" value="3"/>
23725 <param name="average" value="sum"/>
23726 <param name="include_all" value="true"/>
23727 <param name="best_charge_and_fraction" value="false"/>
23728 <param name="greedy_group_resolution" value="false"/>
23729 <param name="ratios" value="false"/>
23730 <param name="ratiosSILAC" value="false"/>
23731 <section name="consensus">
23732 <param name="normalize" value="false"/>
23733 <param name="fix_peptides" value="false"/>
23734 </section>
23735 <section name="format">
23736 <param name="separator" value=""/>
23737 <param name="quoting" value="double"/>
23738 <param name="replacement" value="_"/>
23739 </section>
23740 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23741 <output name="ctd_out" ftype="xml">
23742 <assert_contents>
23743 <is_valid_xml/>
23744 </assert_contents>
23745 </output>
23746 </test>
23747 <test expect_num_outputs="2">
23748 <conditional name="adv_opts_cond">
23749 <param name="adv_opts_selector" value="advanced"/>
23750 <param name="force" value="false"/>
23751 <param name="test" value="true"/>
23752 </conditional>
23753 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23754 <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23755 <param name="top" value="0"/>
23756 <param name="average" value="sum"/>
23757 <param name="include_all" value="false"/>
23758 <param name="best_charge_and_fraction" value="false"/>
23759 <param name="greedy_group_resolution" value="false"/>
23760 <param name="ratios" value="false"/>
23761 <param name="ratiosSILAC" value="false"/>
23762 <section name="consensus">
23763 <param name="normalize" value="false"/>
23764 <param name="fix_peptides" value="true"/>
23765 </section>
23766 <section name="format">
23767 <param name="separator" value=""/>
23768 <param name="quoting" value="double"/>
23769 <param name="replacement" value="_"/>
23770 </section>
23771 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23772 <output name="ctd_out" ftype="xml">
23773 <assert_contents>
23774 <is_valid_xml/>
23775 </assert_contents>
23776 </output>
23777 </test>
23778 <test expect_num_outputs="2">
23779 <conditional name="adv_opts_cond">
23780 <param name="adv_opts_selector" value="advanced"/>
23781 <param name="force" value="false"/>
23782 <param name="test" value="true"/>
23783 </conditional>
23784 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23785 <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23786 <param name="top" value="3"/>
23787 <param name="average" value="sum"/>
23788 <param name="include_all" value="false"/>
23789 <param name="best_charge_and_fraction" value="false"/>
23790 <param name="greedy_group_resolution" value="false"/>
23791 <param name="ratios" value="false"/>
23792 <param name="ratiosSILAC" value="false"/>
23793 <section name="consensus">
23794 <param name="normalize" value="false"/>
23795 <param name="fix_peptides" value="true"/>
23796 </section>
23797 <section name="format">
23798 <param name="separator" value=""/>
23799 <param name="quoting" value="double"/>
23800 <param name="replacement" value="_"/>
23801 </section>
23802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23803 <output name="ctd_out" ftype="xml">
23804 <assert_contents>
23805 <is_valid_xml/>
23806 </assert_contents>
23807 </output>
23808 </test>
23809 <test expect_num_outputs="2">
23810 <conditional name="adv_opts_cond">
23811 <param name="adv_opts_selector" value="advanced"/>
23812 <param name="force" value="false"/>
23813 <param name="test" value="true"/>
23814 </conditional>
23815 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23816 <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23817 <param name="top" value="3"/>
23818 <param name="average" value="sum"/>
23819 <param name="include_all" value="true"/>
23820 <param name="best_charge_and_fraction" value="false"/>
23821 <param name="greedy_group_resolution" value="false"/>
23822 <param name="ratios" value="false"/>
23823 <param name="ratiosSILAC" value="false"/>
23824 <section name="consensus">
23825 <param name="normalize" value="false"/>
23826 <param name="fix_peptides" value="true"/>
23827 </section>
23828 <section name="format">
23829 <param name="separator" value=""/>
23830 <param name="quoting" value="double"/>
23831 <param name="replacement" value="_"/>
23832 </section>
23833 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23834 <output name="ctd_out" ftype="xml">
23835 <assert_contents>
23836 <is_valid_xml/>
23837 </assert_contents>
23838 </output>
23839 </test>
23840 <test expect_num_outputs="2">
23841 <conditional name="adv_opts_cond">
23842 <param name="adv_opts_selector" value="advanced"/>
23843 <param name="force" value="false"/>
23844 <param name="test" value="true"/>
23845 </conditional>
23846 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23847 <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23848 <param name="top" value="3"/>
23849 <param name="average" value="sum"/>
23850 <param name="include_all" value="true"/>
23851 <param name="best_charge_and_fraction" value="false"/>
23852 <param name="greedy_group_resolution" value="false"/>
23853 <param name="ratios" value="true"/>
23854 <param name="ratiosSILAC" value="false"/>
23855 <section name="consensus">
23856 <param name="normalize" value="false"/>
23857 <param name="fix_peptides" value="true"/>
23858 </section>
23859 <section name="format">
23860 <param name="separator" value=""/>
23861 <param name="quoting" value="double"/>
23862 <param name="replacement" value="_"/>
23863 </section>
23864 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23865 <output name="ctd_out" ftype="xml">
23866 <assert_contents>
23867 <is_valid_xml/>
23868 </assert_contents>
23869 </output>
23870 </test>
23871 <test expect_num_outputs="2">
23872 <conditional name="adv_opts_cond">
23873 <param name="adv_opts_selector" value="advanced"/>
23874 <param name="force" value="false"/>
23875 <param name="test" value="true"/>
23876 </conditional>
23877 <param name="in" value="ProteinQuantifier_input.consensusXML"/>
23878 <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
23879 <param name="top" value="3"/>
23880 <param name="average" value="sum"/>
23881 <param name="include_all" value="true"/>
23882 <param name="best_charge_and_fraction" value="false"/>
23883 <param name="greedy_group_resolution" value="false"/>
23884 <param name="ratios" value="false"/>
23885 <param name="ratiosSILAC" value="true"/>
23886 <section name="consensus">
23887 <param name="normalize" value="false"/>
23888 <param name="fix_peptides" value="true"/>
23889 </section>
23890 <section name="format">
23891 <param name="separator" value=""/>
23892 <param name="quoting" value="double"/>
23893 <param name="replacement" value="_"/>
23894 </section>
23895 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
23896 <output name="ctd_out" ftype="xml">
23897 <assert_contents>
23898 <is_valid_xml/>
23899 </assert_contents>
23900 </output>
23901 </test>
23902 <test expect_num_outputs="3">
23903 <conditional name="adv_opts_cond">
23904 <param name="adv_opts_selector" value="advanced"/>
23905 <param name="force" value="false"/>
23906 <param name="test" value="true"/>
23907 </conditional>
23908 <param name="in" value="ProteinQuantifier_input.idXML"/>
23909 <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
23910 <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
23911 <param name="top" value="0"/>
23912 <param name="average" value="sum"/>
23913 <param name="include_all" value="false"/>
23914 <param name="best_charge_and_fraction" value="false"/>
23915 <param name="greedy_group_resolution" value="false"/>
23916 <param name="ratios" value="false"/>
23917 <param name="ratiosSILAC" value="false"/>
23918 <section name="consensus">
23919 <param name="normalize" value="false"/>
23920 <param name="fix_peptides" value="false"/>
23921 </section>
23922 <section name="format">
23923 <param name="separator" value=""/>
23924 <param name="quoting" value="double"/>
23925 <param name="replacement" value="_"/>
23926 </section>
23927 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
23928 <output name="ctd_out" ftype="xml">
23929 <assert_contents>
23930 <is_valid_xml/>
23931 </assert_contents>
23932 </output>
23933 </test>
23934 </xml>
23935 <xml name="autotest_ProteinResolver">
23936 <test expect_num_outputs="4">
23937 <conditional name="adv_opts_cond">
23938 <param name="adv_opts_selector" value="advanced"/>
23939 <param name="force" value="false"/>
23940 <param name="test" value="true"/>
23941 </conditional>
23942 <param name="fasta" value="ProteinResolver_1_input.fasta"/>
23943 <param name="in" value="ProteinResolver_1_input.consensusXML"/>
23944 <param name="in_path" value=""/>
23945 <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
23946 <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
23947 <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/>
23948 <section name="resolver">
23949 <param name="missed_cleavages" value="2"/>
23950 <param name="min_length" value="6"/>
23951 <param name="enzyme" value="Trypsin"/>
23952 </section>
23953 <section name="designer">
23954 <param name="experiment" value="ExperimentalSetting"/>
23955 <param name="file" value="File"/>
23956 <param name="separator" value="tab"/>
23957 </section>
23958 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/>
23959 <output name="ctd_out" ftype="xml">
23960 <assert_contents>
23961 <is_valid_xml/>
23962 </assert_contents>
23963 </output>
23964 </test>
23965 </xml>
23966 <xml name="autotest_PSMFeatureExtractor">
23967 </xml>
23968 <xml name="autotest_PTModel">
23969 <test expect_num_outputs="2">
23970 <conditional name="adv_opts_cond">
23971 <param name="adv_opts_selector" value="advanced"/>
23972 <param name="force" value="false"/>
23973 <param name="test" value="true"/>
23974 </conditional>
23975 <param name="in_positive" value="PTModel_1_input_positive.idXML"/>
23976 <param name="in_negative" value="PTModel_1_input_negative.idXML"/>
23977 <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
23978 <param name="c" value="0.5"/>
23979 <param name="svm_type" value="C_SVC"/>
23980 <param name="nu" value="0.5"/>
23981 <param name="kernel_type" value="OLIGO"/>
23982 <param name="degree" value="1"/>
23983 <param name="border_length" value="22"/>
23984 <param name="k_mer_length" value="1"/>
23985 <param name="sigma" value="5.0"/>
23986 <param name="max_positive_count" value="1000"/>
23987 <param name="max_negative_count" value="1000"/>
23988 <param name="redundant" value="false"/>
23989 <param name="additive_cv" value="false"/>
23990 <section name="cv">
23991 <param name="skip_cv" value="true"/>
23992 <param name="number_of_runs" value="10"/>
23993 <param name="number_of_partitions" value="10"/>
23994 <param name="degree_start" value="1"/>
23995 <param name="degree_step_size" value="2"/>
23996 <param name="degree_stop" value="4"/>
23997 <param name="c_start" value="1.0"/>
23998 <param name="c_step_size" value="100.0"/>
23999 <param name="c_stop" value="1000.0"/>
24000 <param name="nu_start" value="0.1"/>
24001 <param name="nu_step_size" value="1.3"/>
24002 <param name="nu_stop" value="0.9"/>
24003 <param name="sigma_start" value="1.0"/>
24004 <param name="sigma_step_size" value="1.3"/>
24005 <param name="sigma_stop" value="15.0"/>
24006 </section>
24007 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24008 <output name="ctd_out" ftype="xml">
24009 <assert_contents>
24010 <is_valid_xml/>
24011 </assert_contents>
24012 </output>
24013 </test>
24014 </xml>
24015 <xml name="autotest_QCCalculator">
24016 </xml>
24017 <xml name="autotest_QCEmbedder">
24018 </xml>
24019 <xml name="autotest_QCExporter">
24020 </xml>
24021 <xml name="autotest_QCExtractor">
24022 </xml>
24023 <xml name="autotest_QCImporter">
24024 </xml>
24025 <xml name="autotest_QCMerger">
24026 </xml>
24027 <xml name="autotest_QCShrinker">
24028 </xml>
24029 <xml name="autotest_QualityControl">
24030 <test expect_num_outputs="3">
24031 <conditional name="adv_opts_cond">
24032 <param name="adv_opts_selector" value="advanced"/>
24033 <param name="force" value="false"/>
24034 <param name="test" value="true"/>
24035 </conditional>
24036 <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
24037 <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
24038 <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
24039 <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24040 <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
24041 <param name="in_contaminants" value="QualityControl_1.fasta"/>
24042 <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
24043 <section name="FragmentMassError">
24044 <param name="unit" value="auto"/>
24045 <param name="tolerance" value="20.0"/>
24046 </section>
24047 <section name="MS2_id_rate">
24048 <param name="force_no_fdr" value="false"/>
24049 </section>
24050 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG"/>
24051 <output name="ctd_out" ftype="xml">
24052 <assert_contents>
24053 <is_valid_xml/>
24054 </assert_contents>
24055 </output>
24056 </test>
24057 </xml>
24058 <xml name="autotest_RNADigestor">
24059 </xml>
24060 <xml name="autotest_RNAMassCalculator">
24061 <test expect_num_outputs="2">
24062 <conditional name="adv_opts_cond">
24063 <param name="adv_opts_selector" value="advanced"/>
24064 <param name="force" value="false"/>
24065 <param name="test" value="true"/>
24066 </conditional>
24067 <param name="in_seq" value="&quot;AUCGGC&quot;"/>
24068 <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/>
24069 <param name="charge" value="-1 -2"/>
24070 <param name="format" value="list"/>
24071 <param name="average_mass" value="false"/>
24072 <param name="fragment_type" value="full"/>
24073 <param name="separator" value=""/>
24074 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
24075 <output name="ctd_out" ftype="xml">
24076 <assert_contents>
24077 <is_valid_xml/>
24078 </assert_contents>
24079 </output>
24080 </test>
24081 </xml>
24082 <xml name="autotest_RNPxlSearch">
24083 <test expect_num_outputs="2">
24084 <conditional name="adv_opts_cond">
24085 <param name="adv_opts_selector" value="advanced"/>
24086 <param name="force" value="false"/>
24087 <param name="test" value="true"/>
24088 </conditional>
24089 <param name="in" value="RNPxlSearch_1_input.mzML"/>
24090 <param name="database" value="RNPxlSearch_1_input.fasta"/>
24091 <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24092 <section name="precursor">
24093 <param name="mass_tolerance" value="20.0"/>
24094 <param name="mass_tolerance_unit" value="ppm"/>
24095 <param name="min_charge" value="2"/>
24096 <param name="max_charge" value="5"/>
24097 <param name="isotopes" value="0 1"/>
24098 </section>
24099 <section name="fragment">
24100 <param name="mass_tolerance" value="20.0"/>
24101 <param name="mass_tolerance_unit" value="ppm"/>
24102 </section>
24103 <section name="modifications">
24104 <param name="fixed" value=""/>
24105 <param name="variable" value="Oxidation (M)"/>
24106 <param name="variable_max_per_peptide" value="2"/>
24107 </section>
24108 <section name="peptide">
24109 <param name="min_size" value="6"/>
24110 <param name="max_size" value="1000000"/>
24111 <param name="missed_cleavages" value="1"/>
24112 <param name="enzyme" value="Trypsin"/>
24113 </section>
24114 <section name="report">
24115 <param name="top_hits" value="1"/>
24116 </section>
24117 <section name="RNPxl">
24118 <param name="length" value="2"/>
24119 <param name="sequence" value="GUA"/>
24120 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
24121 <param name="nt_groups" value=""/>
24122 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
24123 <param name="can_cross_link" value="U"/>
24124 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
24125 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
24126 <param name="scoring" value="fast"/>
24127 <param name="decoys" value="false"/>
24128 <param name="CysteineAdduct" value="false"/>
24129 <param name="filter_fractional_mass" value="false"/>
24130 <param name="carbon_labeled_fragments" value="false"/>
24131 <param name="only_xl" value="false"/>
24132 <param name="filter_small_peptide_mass" value="600.0"/>
24133 <param name="marker_ions_tolerance" value="0.05"/>
24134 </section>
24135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24136 <output name="ctd_out" ftype="xml">
24137 <assert_contents>
24138 <is_valid_xml/>
24139 </assert_contents>
24140 </output>
24141 </test>
24142 <test expect_num_outputs="2">
24143 <conditional name="adv_opts_cond">
24144 <param name="adv_opts_selector" value="advanced"/>
24145 <param name="force" value="false"/>
24146 <param name="test" value="true"/>
24147 </conditional>
24148 <param name="in" value="RNPxlSearch_1_input.mzML"/>
24149 <param name="database" value="RNPxlSearch_1_input.fasta"/>
24150 <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24151 <section name="precursor">
24152 <param name="mass_tolerance" value="20.0"/>
24153 <param name="mass_tolerance_unit" value="ppm"/>
24154 <param name="min_charge" value="2"/>
24155 <param name="max_charge" value="5"/>
24156 <param name="isotopes" value="0 1"/>
24157 </section>
24158 <section name="fragment">
24159 <param name="mass_tolerance" value="20.0"/>
24160 <param name="mass_tolerance_unit" value="ppm"/>
24161 </section>
24162 <section name="modifications">
24163 <param name="fixed" value=""/>
24164 <param name="variable" value="Oxidation (M)"/>
24165 <param name="variable_max_per_peptide" value="2"/>
24166 </section>
24167 <section name="peptide">
24168 <param name="min_size" value="6"/>
24169 <param name="max_size" value="1000000"/>
24170 <param name="missed_cleavages" value="1"/>
24171 <param name="enzyme" value="Trypsin"/>
24172 </section>
24173 <section name="report">
24174 <param name="top_hits" value="1"/>
24175 </section>
24176 <section name="RNPxl">
24177 <param name="length" value="2"/>
24178 <param name="sequence" value="GUA"/>
24179 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
24180 <param name="nt_groups" value=""/>
24181 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
24182 <param name="can_cross_link" value="U"/>
24183 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
24184 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
24185 <param name="scoring" value="fast"/>
24186 <param name="decoys" value="true"/>
24187 <param name="CysteineAdduct" value="false"/>
24188 <param name="filter_fractional_mass" value="false"/>
24189 <param name="carbon_labeled_fragments" value="false"/>
24190 <param name="only_xl" value="false"/>
24191 <param name="filter_small_peptide_mass" value="600.0"/>
24192 <param name="marker_ions_tolerance" value="0.05"/>
24193 </section>
24194 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24195 <output name="ctd_out" ftype="xml">
24196 <assert_contents>
24197 <is_valid_xml/>
24198 </assert_contents>
24199 </output>
24200 </test>
24201 <test expect_num_outputs="3">
24202 <conditional name="adv_opts_cond">
24203 <param name="adv_opts_selector" value="advanced"/>
24204 <param name="force" value="false"/>
24205 <param name="test" value="true"/>
24206 </conditional>
24207 <param name="in" value="RNPxlSearch_1_input.mzML"/>
24208 <param name="database" value="RNPxlSearch_1_input.fasta"/>
24209 <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24210 <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
24211 <section name="precursor">
24212 <param name="mass_tolerance" value="10.0"/>
24213 <param name="mass_tolerance_unit" value="ppm"/>
24214 <param name="min_charge" value="2"/>
24215 <param name="max_charge" value="5"/>
24216 <param name="isotopes" value="0 1"/>
24217 </section>
24218 <section name="fragment">
24219 <param name="mass_tolerance" value="10.0"/>
24220 <param name="mass_tolerance_unit" value="ppm"/>
24221 </section>
24222 <section name="modifications">
24223 <param name="fixed" value=""/>
24224 <param name="variable" value=""/>
24225 <param name="variable_max_per_peptide" value="2"/>
24226 </section>
24227 <section name="peptide">
24228 <param name="min_size" value="6"/>
24229 <param name="max_size" value="1000000"/>
24230 <param name="missed_cleavages" value="1"/>
24231 <param name="enzyme" value="Trypsin"/>
24232 </section>
24233 <section name="report">
24234 <param name="top_hits" value="3"/>
24235 </section>
24236 <section name="RNPxl">
24237 <param name="length" value="2"/>
24238 <param name="sequence" value=""/>
24239 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
24240 <param name="nt_groups" value=""/>
24241 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
24242 <param name="can_cross_link" value="U"/>
24243 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
24244 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
24245 <param name="scoring" value="fast"/>
24246 <param name="decoys" value="false"/>
24247 <param name="CysteineAdduct" value="false"/>
24248 <param name="filter_fractional_mass" value="false"/>
24249 <param name="carbon_labeled_fragments" value="false"/>
24250 <param name="only_xl" value="false"/>
24251 <param name="filter_small_peptide_mass" value="600.0"/>
24252 <param name="marker_ions_tolerance" value="0.05"/>
24253 </section>
24254 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
24255 <output name="ctd_out" ftype="xml">
24256 <assert_contents>
24257 <is_valid_xml/>
24258 </assert_contents>
24259 </output>
24260 </test>
24261 <test expect_num_outputs="3">
24262 <conditional name="adv_opts_cond">
24263 <param name="adv_opts_selector" value="advanced"/>
24264 <param name="force" value="false"/>
24265 <param name="test" value="true"/>
24266 </conditional>
24267 <param name="in" value="RNPxlSearch_1_input.mzML"/>
24268 <param name="database" value="RNPxlSearch_1_input.fasta"/>
24269 <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24270 <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
24271 <section name="precursor">
24272 <param name="mass_tolerance" value="10.0"/>
24273 <param name="mass_tolerance_unit" value="ppm"/>
24274 <param name="min_charge" value="2"/>
24275 <param name="max_charge" value="5"/>
24276 <param name="isotopes" value="0 1"/>
24277 </section>
24278 <section name="fragment">
24279 <param name="mass_tolerance" value="10.0"/>
24280 <param name="mass_tolerance_unit" value="ppm"/>
24281 </section>
24282 <section name="modifications">
24283 <param name="fixed" value=""/>
24284 <param name="variable" value=""/>
24285 <param name="variable_max_per_peptide" value="2"/>
24286 </section>
24287 <section name="peptide">
24288 <param name="min_size" value="6"/>
24289 <param name="max_size" value="1000000"/>
24290 <param name="missed_cleavages" value="1"/>
24291 <param name="enzyme" value="Trypsin"/>
24292 </section>
24293 <section name="report">
24294 <param name="top_hits" value="2"/>
24295 </section>
24296 <section name="RNPxl">
24297 <param name="length" value="2"/>
24298 <param name="sequence" value=""/>
24299 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
24300 <param name="nt_groups" value=""/>
24301 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
24302 <param name="can_cross_link" value="U"/>
24303 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
24304 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
24305 <param name="scoring" value="fast"/>
24306 <param name="decoys" value="true"/>
24307 <param name="CysteineAdduct" value="false"/>
24308 <param name="filter_fractional_mass" value="false"/>
24309 <param name="carbon_labeled_fragments" value="false"/>
24310 <param name="only_xl" value="false"/>
24311 <param name="filter_small_peptide_mass" value="600.0"/>
24312 <param name="marker_ions_tolerance" value="0.05"/>
24313 </section>
24314 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
24315 <output name="ctd_out" ftype="xml">
24316 <assert_contents>
24317 <is_valid_xml/>
24318 </assert_contents>
24319 </output>
24320 </test>
24321 </xml>
24322 <xml name="autotest_RNPxlXICFilter">
24323 </xml>
24324 <xml name="autotest_RTEvaluation">
24325 </xml>
24326 <xml name="autotest_RTModel">
24327 <test expect_num_outputs="2">
24328 <conditional name="adv_opts_cond">
24329 <param name="adv_opts_selector" value="advanced"/>
24330 <param name="force" value="false"/>
24331 <param name="test" value="true"/>
24332 </conditional>
24333 <param name="in" value="RTModel_1_input.idXML"/>
24334 <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/>
24335 <param name="svm_type" value="NU_SVR"/>
24336 <param name="nu" value="0.5"/>
24337 <param name="p" value="0.1"/>
24338 <param name="c" value="0.1"/>
24339 <param name="kernel_type" value="POLY"/>
24340 <param name="degree" value="1"/>
24341 <param name="border_length" value="22"/>
24342 <param name="max_std" value="10.0"/>
24343 <param name="k_mer_length" value="1"/>
24344 <param name="sigma" value="5.0"/>
24345 <param name="total_gradient_time" value="3000.0"/>
24346 <param name="first_dim_rt" value="false"/>
24347 <param name="additive_cv" value="false"/>
24348 <section name="cv">
24349 <param name="skip_cv" value="true"/>
24350 <param name="number_of_runs" value="10"/>
24351 <param name="number_of_partitions" value="10"/>
24352 <param name="degree_start" value="1"/>
24353 <param name="degree_step_size" value="2"/>
24354 <param name="degree_stop" value="4"/>
24355 <param name="p_start" value="1.0"/>
24356 <param name="p_step_size" value="10.0"/>
24357 <param name="p_stop" value="1000.0"/>
24358 <param name="c_start" value="1.0"/>
24359 <param name="c_step_size" value="10.0"/>
24360 <param name="c_stop" value="1000.0"/>
24361 <param name="nu_start" value="0.3"/>
24362 <param name="nu_step_size" value="1.2"/>
24363 <param name="nu_stop" value="0.7"/>
24364 <param name="sigma_start" value="1.0"/>
24365 <param name="sigma_step_size" value="1.3"/>
24366 <param name="sigma_stop" value="15.0"/>
24367 </section>
24368 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24369 <output name="ctd_out" ftype="xml">
24370 <assert_contents>
24371 <is_valid_xml/>
24372 </assert_contents>
24373 </output>
24374 </test>
24375 <test expect_num_outputs="2">
24376 <conditional name="adv_opts_cond">
24377 <param name="adv_opts_selector" value="advanced"/>
24378 <param name="force" value="false"/>
24379 <param name="test" value="true"/>
24380 </conditional>
24381 <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
24382 <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
24383 <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
24384 <param name="svm_type" value="NU_SVR"/>
24385 <param name="nu" value="0.5"/>
24386 <param name="p" value="0.1"/>
24387 <param name="c" value="0.5"/>
24388 <param name="kernel_type" value="OLIGO"/>
24389 <param name="degree" value="1"/>
24390 <param name="border_length" value="22"/>
24391 <param name="max_std" value="10.0"/>
24392 <param name="k_mer_length" value="1"/>
24393 <param name="sigma" value="5.0"/>
24394 <param name="total_gradient_time" value="1.0"/>
24395 <param name="first_dim_rt" value="false"/>
24396 <param name="additive_cv" value="false"/>
24397 <section name="cv">
24398 <param name="skip_cv" value="true"/>
24399 <param name="number_of_runs" value="10"/>
24400 <param name="number_of_partitions" value="10"/>
24401 <param name="degree_start" value="1"/>
24402 <param name="degree_step_size" value="2"/>
24403 <param name="degree_stop" value="4"/>
24404 <param name="p_start" value="1.0"/>
24405 <param name="p_step_size" value="10.0"/>
24406 <param name="p_stop" value="1000.0"/>
24407 <param name="c_start" value="1.0"/>
24408 <param name="c_step_size" value="10.0"/>
24409 <param name="c_stop" value="1000.0"/>
24410 <param name="nu_start" value="0.3"/>
24411 <param name="nu_step_size" value="1.2"/>
24412 <param name="nu_stop" value="0.7"/>
24413 <param name="sigma_start" value="1.0"/>
24414 <param name="sigma_step_size" value="1.3"/>
24415 <param name="sigma_stop" value="15.0"/>
24416 </section>
24417 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24418 <output name="ctd_out" ftype="xml">
24419 <assert_contents>
24420 <is_valid_xml/>
24421 </assert_contents>
24422 </output>
24423 </test>
24424 <test expect_num_outputs="2">
24425 <conditional name="adv_opts_cond">
24426 <param name="adv_opts_selector" value="advanced"/>
24427 <param name="force" value="false"/>
24428 <param name="test" value="true"/>
24429 </conditional>
24430 <param name="in" value="RTModel_3_input.idXML"/>
24431 <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
24432 <param name="svm_type" value="NU_SVR"/>
24433 <param name="nu" value="0.5"/>
24434 <param name="p" value="0.1"/>
24435 <param name="c" value="0.001953125"/>
24436 <param name="kernel_type" value="OLIGO"/>
24437 <param name="degree" value="1"/>
24438 <param name="border_length" value="22"/>
24439 <param name="max_std" value="10.0"/>
24440 <param name="k_mer_length" value="1"/>
24441 <param name="sigma" value="1.0"/>
24442 <param name="total_gradient_time" value="1.0"/>
24443 <param name="first_dim_rt" value="false"/>
24444 <param name="additive_cv" value="false"/>
24445 <section name="cv">
24446 <param name="skip_cv" value="false"/>
24447 <param name="number_of_runs" value="1"/>
24448 <param name="number_of_partitions" value="5"/>
24449 <param name="degree_start" value="1"/>
24450 <param name="degree_step_size" value="2"/>
24451 <param name="degree_stop" value="4"/>
24452 <param name="p_start" value="1.0"/>
24453 <param name="p_step_size" value="10.0"/>
24454 <param name="p_stop" value="1000.0"/>
24455 <param name="c_start" value="0.001953125"/>
24456 <param name="c_step_size" value="2.0"/>
24457 <param name="c_stop" value="0.001953125"/>
24458 <param name="nu_start" value="0.4"/>
24459 <param name="nu_step_size" value="1.2"/>
24460 <param name="nu_stop" value="0.4"/>
24461 <param name="sigma_start" value="5.0"/>
24462 <param name="sigma_step_size" value="1.221055"/>
24463 <param name="sigma_stop" value="5.0"/>
24464 </section>
24465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24466 <output name="ctd_out" ftype="xml">
24467 <assert_contents>
24468 <is_valid_xml/>
24469 </assert_contents>
24470 </output>
24471 </test>
24472 <test expect_num_outputs="2">
24473 <conditional name="adv_opts_cond">
24474 <param name="adv_opts_selector" value="advanced"/>
24475 <param name="force" value="false"/>
24476 <param name="test" value="true"/>
24477 </conditional>
24478 <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
24479 <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
24480 <param name="svm_type" value="NU_SVR"/>
24481 <param name="nu" value="0.5"/>
24482 <param name="p" value="0.1"/>
24483 <param name="c" value="0.001953125"/>
24484 <param name="kernel_type" value="OLIGO"/>
24485 <param name="degree" value="1"/>
24486 <param name="border_length" value="22"/>
24487 <param name="max_std" value="10.0"/>
24488 <param name="k_mer_length" value="1"/>
24489 <param name="sigma" value="1.0"/>
24490 <param name="total_gradient_time" value="1.0"/>
24491 <param name="first_dim_rt" value="false"/>
24492 <param name="additive_cv" value="false"/>
24493 <section name="cv">
24494 <param name="skip_cv" value="false"/>
24495 <param name="number_of_runs" value="1"/>
24496 <param name="number_of_partitions" value="5"/>
24497 <param name="degree_start" value="1"/>
24498 <param name="degree_step_size" value="2"/>
24499 <param name="degree_stop" value="4"/>
24500 <param name="p_start" value="1.0"/>
24501 <param name="p_step_size" value="10.0"/>
24502 <param name="p_stop" value="1000.0"/>
24503 <param name="c_start" value="0.001953125"/>
24504 <param name="c_step_size" value="2.0"/>
24505 <param name="c_stop" value="0.001953125"/>
24506 <param name="nu_start" value="0.4"/>
24507 <param name="nu_step_size" value="1.2"/>
24508 <param name="nu_stop" value="0.4"/>
24509 <param name="sigma_start" value="5.0"/>
24510 <param name="sigma_step_size" value="1.221055"/>
24511 <param name="sigma_stop" value="5.0"/>
24512 </section>
24513 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24514 <output name="ctd_out" ftype="xml">
24515 <assert_contents>
24516 <is_valid_xml/>
24517 </assert_contents>
24518 </output>
24519 </test>
24520 </xml>
24521 <xml name="autotest_SeedListGenerator">
24522 <test expect_num_outputs="2">
24523 <conditional name="adv_opts_cond">
24524 <param name="adv_opts_selector" value="advanced"/>
24525 <param name="force" value="false"/>
24526 <param name="test" value="true"/>
24527 </conditional>
24528 <param name="in" value="PepXMLFile_test.mzML"/>
24529 <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
24530 <param name="use_peptide_mass" value="false"/>
24531 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24532 <output name="ctd_out" ftype="xml">
24533 <assert_contents>
24534 <is_valid_xml/>
24535 </assert_contents>
24536 </output>
24537 </test>
24538 <test expect_num_outputs="2">
24539 <conditional name="adv_opts_cond">
24540 <param name="adv_opts_selector" value="advanced"/>
24541 <param name="force" value="false"/>
24542 <param name="test" value="true"/>
24543 </conditional>
24544 <param name="in" value="IDMapper_1_output.featureXML"/>
24545 <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
24546 <param name="use_peptide_mass" value="false"/>
24547 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24548 <output name="ctd_out" ftype="xml">
24549 <assert_contents>
24550 <is_valid_xml/>
24551 </assert_contents>
24552 </output>
24553 </test>
24554 </xml>
24555 <xml name="autotest_SemanticValidator">
24556 </xml>
24557 <xml name="autotest_SequenceCoverageCalculator">
24558 </xml>
24559 <xml name="autotest_SimpleSearchEngine">
24560 <test expect_num_outputs="2">
24561 <conditional name="adv_opts_cond">
24562 <param name="adv_opts_selector" value="advanced"/>
24563 <param name="force" value="false"/>
24564 <param name="test" value="true"/>
24565 </conditional>
24566 <param name="in" value="SimpleSearchEngine_1.mzML"/>
24567 <param name="database" value="SimpleSearchEngine_1.fasta"/>
24568 <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
24569 <section name="Search">
24570 <param name="enzyme" value="Trypsin"/>
24571 <section name="precursor">
24572 <param name="mass_tolerance" value="5.0"/>
24573 <param name="mass_tolerance_unit" value="ppm"/>
24574 <param name="min_charge" value="2"/>
24575 <param name="max_charge" value="5"/>
24576 <param name="isotopes" value="0 1"/>
24577 </section>
24578 <section name="fragment">
24579 <param name="mass_tolerance" value="0.3"/>
24580 <param name="mass_tolerance_unit" value="Da"/>
24581 </section>
24582 <section name="modifications">
24583 <param name="fixed" value=""/>
24584 <param name="variable" value="Oxidation (M)"/>
24585 <param name="variable_max_per_peptide" value="2"/>
24586 </section>
24587 <section name="peptide">
24588 <param name="min_size" value="7"/>
24589 <param name="max_size" value="40"/>
24590 <param name="missed_cleavages" value="1"/>
24591 <param name="motif" value=""/>
24592 </section>
24593 <section name="report">
24594 <param name="top_hits" value="1"/>
24595 </section>
24596 </section>
24597 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24598 <output name="ctd_out" ftype="xml">
24599 <assert_contents>
24600 <is_valid_xml/>
24601 </assert_contents>
24602 </output>
24603 </test>
24604 </xml>
24605 <xml name="autotest_SiriusAdapter">
24606 <test expect_num_outputs="2">
24607 <conditional name="adv_opts_cond">
24608 <param name="adv_opts_selector" value="advanced"/>
24609 <param name="converter_mode" value="false"/>
24610 <param name="force" value="false"/>
24611 <param name="test" value="true"/>
24612 </conditional>
24613 <param name="in" value="SiriusAdapter_1_input.mzML"/>
24614 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24615 <param name="out_workspace_directory" value=""/>
24616 <section name="preprocessing">
24617 <param name="filter_by_num_masstraces" value="1"/>
24618 <param name="precursor_mz_tolerance" value="0.005"/>
24619 <param name="precursor_mz_tolerance_unit" value="Da"/>
24620 <param name="precursor_rt_tolerance" value="5"/>
24621 <param name="isotope_pattern_iterations" value="3"/>
24622 <param name="feature_only" value="false"/>
24623 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24624 </section>
24625 <section name="sirius">
24626 <param name="profile" value="qtof"/>
24627 <param name="candidates" value="5"/>
24628 <param name="database" value="all"/>
24629 <param name="noise" value="0"/>
24630 <param name="ppm_max" value="10"/>
24631 <param name="isotope" value="both"/>
24632 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24633 <param name="compound_timeout" value="10"/>
24634 <param name="tree_timeout" value="0"/>
24635 <param name="top_n_hits" value="10"/>
24636 <param name="cores" value="1"/>
24637 <param name="auto_charge" value="true"/>
24638 <param name="ion_tree" value="false"/>
24639 <param name="no_recalibration" value="false"/>
24640 <param name="most_intense_ms2" value="false"/>
24641 </section>
24642 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
24643 <output name="ctd_out" ftype="xml">
24644 <assert_contents>
24645 <is_valid_xml/>
24646 </assert_contents>
24647 </output>
24648 </test>
24649 <test expect_num_outputs="2">
24650 <conditional name="adv_opts_cond">
24651 <param name="adv_opts_selector" value="advanced"/>
24652 <param name="converter_mode" value="false"/>
24653 <param name="force" value="false"/>
24654 <param name="test" value="true"/>
24655 </conditional>
24656 <param name="in" value="SiriusAdapter_2_input.mzML"/>
24657 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
24658 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24659 <param name="out_workspace_directory" value=""/>
24660 <section name="preprocessing">
24661 <param name="filter_by_num_masstraces" value="3"/>
24662 <param name="precursor_mz_tolerance" value="0.005"/>
24663 <param name="precursor_mz_tolerance_unit" value="Da"/>
24664 <param name="precursor_rt_tolerance" value="5"/>
24665 <param name="isotope_pattern_iterations" value="3"/>
24666 <param name="feature_only" value="true"/>
24667 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24668 </section>
24669 <section name="sirius">
24670 <param name="profile" value="qtof"/>
24671 <param name="candidates" value="5"/>
24672 <param name="database" value="all"/>
24673 <param name="noise" value="0"/>
24674 <param name="ppm_max" value="10"/>
24675 <param name="isotope" value="both"/>
24676 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24677 <param name="compound_timeout" value="10"/>
24678 <param name="tree_timeout" value="0"/>
24679 <param name="top_n_hits" value="10"/>
24680 <param name="cores" value="1"/>
24681 <param name="auto_charge" value="true"/>
24682 <param name="ion_tree" value="false"/>
24683 <param name="no_recalibration" value="false"/>
24684 <param name="most_intense_ms2" value="false"/>
24685 </section>
24686 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
24687 <output name="ctd_out" ftype="xml">
24688 <assert_contents>
24689 <is_valid_xml/>
24690 </assert_contents>
24691 </output>
24692 </test>
24693 <test expect_num_outputs="2">
24694 <conditional name="adv_opts_cond">
24695 <param name="adv_opts_selector" value="advanced"/>
24696 <param name="converter_mode" value="false"/>
24697 <param name="force" value="false"/>
24698 <param name="test" value="true"/>
24699 </conditional>
24700 <param name="in" value="SiriusAdapter_3_input.mzML"/>
24701 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
24702 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24703 <param name="out_workspace_directory" value=""/>
24704 <section name="preprocessing">
24705 <param name="filter_by_num_masstraces" value="3"/>
24706 <param name="precursor_mz_tolerance" value="0.005"/>
24707 <param name="precursor_mz_tolerance_unit" value="Da"/>
24708 <param name="precursor_rt_tolerance" value="5"/>
24709 <param name="isotope_pattern_iterations" value="3"/>
24710 <param name="feature_only" value="false"/>
24711 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24712 </section>
24713 <section name="sirius">
24714 <param name="profile" value="qtof"/>
24715 <param name="candidates" value="5"/>
24716 <param name="database" value="all"/>
24717 <param name="noise" value="0"/>
24718 <param name="ppm_max" value="10"/>
24719 <param name="isotope" value="both"/>
24720 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24721 <param name="compound_timeout" value="10"/>
24722 <param name="tree_timeout" value="0"/>
24723 <param name="top_n_hits" value="10"/>
24724 <param name="cores" value="1"/>
24725 <param name="auto_charge" value="true"/>
24726 <param name="ion_tree" value="false"/>
24727 <param name="no_recalibration" value="false"/>
24728 <param name="most_intense_ms2" value="false"/>
24729 </section>
24730 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
24731 <output name="ctd_out" ftype="xml">
24732 <assert_contents>
24733 <is_valid_xml/>
24734 </assert_contents>
24735 </output>
24736 </test>
24737 <test expect_num_outputs="2">
24738 <conditional name="adv_opts_cond">
24739 <param name="adv_opts_selector" value="advanced"/>
24740 <param name="converter_mode" value="true"/>
24741 <param name="force" value="false"/>
24742 <param name="test" value="true"/>
24743 </conditional>
24744 <param name="in" value="SiriusAdapter_3_input.mzML"/>
24745 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
24746 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
24747 <param name="out_workspace_directory" value=""/>
24748 <section name="preprocessing">
24749 <param name="filter_by_num_masstraces" value="1"/>
24750 <param name="precursor_mz_tolerance" value="0.005"/>
24751 <param name="precursor_mz_tolerance_unit" value="Da"/>
24752 <param name="precursor_rt_tolerance" value="5"/>
24753 <param name="isotope_pattern_iterations" value="3"/>
24754 <param name="feature_only" value="false"/>
24755 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24756 </section>
24757 <section name="sirius">
24758 <param name="profile" value="qtof"/>
24759 <param name="candidates" value="5"/>
24760 <param name="database" value="all"/>
24761 <param name="noise" value="0"/>
24762 <param name="ppm_max" value="10"/>
24763 <param name="isotope" value="both"/>
24764 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24765 <param name="compound_timeout" value="10"/>
24766 <param name="tree_timeout" value="0"/>
24767 <param name="top_n_hits" value="10"/>
24768 <param name="cores" value="1"/>
24769 <param name="auto_charge" value="false"/>
24770 <param name="ion_tree" value="false"/>
24771 <param name="no_recalibration" value="false"/>
24772 <param name="most_intense_ms2" value="false"/>
24773 </section>
24774 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
24775 <output name="ctd_out" ftype="xml">
24776 <assert_contents>
24777 <is_valid_xml/>
24778 </assert_contents>
24779 </output>
24780 </test>
24781 <test expect_num_outputs="2">
24782 <conditional name="adv_opts_cond">
24783 <param name="adv_opts_selector" value="advanced"/>
24784 <param name="converter_mode" value="true"/>
24785 <param name="force" value="false"/>
24786 <param name="test" value="true"/>
24787 </conditional>
24788 <param name="in" value="SiriusAdapter_4_input.mzML"/>
24789 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
24790 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
24791 <param name="out_workspace_directory" value=""/>
24792 <section name="preprocessing">
24793 <param name="filter_by_num_masstraces" value="1"/>
24794 <param name="precursor_mz_tolerance" value="0.005"/>
24795 <param name="precursor_mz_tolerance_unit" value="Da"/>
24796 <param name="precursor_rt_tolerance" value="5"/>
24797 <param name="isotope_pattern_iterations" value="3"/>
24798 <param name="feature_only" value="false"/>
24799 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24800 </section>
24801 <section name="sirius">
24802 <param name="profile" value="qtof"/>
24803 <param name="candidates" value="5"/>
24804 <param name="database" value="all"/>
24805 <param name="noise" value="0"/>
24806 <param name="ppm_max" value="10"/>
24807 <param name="isotope" value="both"/>
24808 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24809 <param name="compound_timeout" value="10"/>
24810 <param name="tree_timeout" value="0"/>
24811 <param name="top_n_hits" value="10"/>
24812 <param name="cores" value="1"/>
24813 <param name="auto_charge" value="false"/>
24814 <param name="ion_tree" value="false"/>
24815 <param name="no_recalibration" value="false"/>
24816 <param name="most_intense_ms2" value="false"/>
24817 </section>
24818 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
24819 <output name="ctd_out" ftype="xml">
24820 <assert_contents>
24821 <is_valid_xml/>
24822 </assert_contents>
24823 </output>
24824 </test>
24825 <test expect_num_outputs="2">
24826 <conditional name="adv_opts_cond">
24827 <param name="adv_opts_selector" value="advanced"/>
24828 <param name="converter_mode" value="false"/>
24829 <param name="force" value="false"/>
24830 <param name="test" value="true"/>
24831 </conditional>
24832 <param name="in" value="SiriusAdapter_4_input.mzML"/>
24833 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
24834 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24835 <param name="out_workspace_directory" value=""/>
24836 <section name="preprocessing">
24837 <param name="filter_by_num_masstraces" value="1"/>
24838 <param name="precursor_mz_tolerance" value="0.005"/>
24839 <param name="precursor_mz_tolerance_unit" value="Da"/>
24840 <param name="precursor_rt_tolerance" value="5"/>
24841 <param name="isotope_pattern_iterations" value="3"/>
24842 <param name="feature_only" value="true"/>
24843 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24844 </section>
24845 <section name="sirius">
24846 <param name="profile" value="qtof"/>
24847 <param name="candidates" value="5"/>
24848 <param name="database" value="all"/>
24849 <param name="noise" value="0"/>
24850 <param name="ppm_max" value="10"/>
24851 <param name="isotope" value="both"/>
24852 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24853 <param name="compound_timeout" value="10"/>
24854 <param name="tree_timeout" value="0"/>
24855 <param name="top_n_hits" value="10"/>
24856 <param name="cores" value="1"/>
24857 <param name="auto_charge" value="false"/>
24858 <param name="ion_tree" value="false"/>
24859 <param name="no_recalibration" value="false"/>
24860 <param name="most_intense_ms2" value="false"/>
24861 </section>
24862 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
24863 <output name="ctd_out" ftype="xml">
24864 <assert_contents>
24865 <is_valid_xml/>
24866 </assert_contents>
24867 </output>
24868 </test>
24869 <test expect_num_outputs="3">
24870 <conditional name="adv_opts_cond">
24871 <param name="adv_opts_selector" value="advanced"/>
24872 <param name="converter_mode" value="false"/>
24873 <param name="force" value="false"/>
24874 <param name="test" value="true"/>
24875 </conditional>
24876 <param name="in" value="SiriusAdapter_2_input.mzML"/>
24877 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
24878 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>
24879 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
24880 <param name="out_workspace_directory" value=""/>
24881 <section name="preprocessing">
24882 <param name="filter_by_num_masstraces" value="1"/>
24883 <param name="precursor_mz_tolerance" value="0.005"/>
24884 <param name="precursor_mz_tolerance_unit" value="Da"/>
24885 <param name="precursor_rt_tolerance" value="5"/>
24886 <param name="isotope_pattern_iterations" value="3"/>
24887 <param name="feature_only" value="false"/>
24888 <param name="no_masstrace_info_isotope_pattern" value="false"/>
24889 </section>
24890 <section name="sirius">
24891 <param name="profile" value="qtof"/>
24892 <param name="candidates" value="5"/>
24893 <param name="database" value="all"/>
24894 <param name="noise" value="0"/>
24895 <param name="ppm_max" value="10"/>
24896 <param name="isotope" value="both"/>
24897 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
24898 <param name="compound_timeout" value="10"/>
24899 <param name="tree_timeout" value="0"/>
24900 <param name="top_n_hits" value="10"/>
24901 <param name="cores" value="1"/>
24902 <param name="auto_charge" value="true"/>
24903 <param name="ion_tree" value="false"/>
24904 <param name="no_recalibration" value="false"/>
24905 <param name="most_intense_ms2" value="false"/>
24906 </section>
24907 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
24908 <output name="ctd_out" ftype="xml">
24909 <assert_contents>
24910 <is_valid_xml/>
24911 </assert_contents>
24912 </output>
24913 </test>
24914 </xml>
24915 <xml name="autotest_SpecLibCreator">
24916 </xml>
24917 <xml name="autotest_SpecLibSearcher">
24918 <test expect_num_outputs="2">
24919 <conditional name="adv_opts_cond">
24920 <param name="adv_opts_selector" value="advanced"/>
24921 <param name="force" value="false"/>
24922 <param name="test" value="true"/>
24923 </conditional>
24924 <param name="in" value="SpecLibSearcher_1.mzML"/>
24925 <param name="lib" value="SpecLibSearcher_1.MSP"/>
24926 <output_collection name="out" count="1"/>
24927 <param name="compare_function" value="ZhangSimilarityScore"/>
24928 <section name="precursor">
24929 <param name="mass_tolerance" value="3.0"/>
24930 <param name="mass_tolerance_unit" value="Da"/>
24931 <param name="min_charge" value="1"/>
24932 <param name="max_charge" value="5"/>
24933 <param name="isotopes" value="0 1"/>
24934 </section>
24935 <section name="fragment">
24936 <param name="mass_tolerance" value="10.0"/>
24937 </section>
24938 <section name="report">
24939 <param name="top_hits" value="10"/>
24940 </section>
24941 <section name="filter">
24942 <param name="remove_peaks_below_threshold" value="2.01"/>
24943 <param name="min_peaks" value="5"/>
24944 <param name="max_peaks" value="150"/>
24945 <param name="cut_peaks_below" value="1000"/>
24946 </section>
24947 <section name="modifications">
24948 <param name="fixed" value=""/>
24949 <param name="variable" value=""/>
24950 <param name="variable_max_per_peptide" value="2"/>
24951 </section>
24952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24953 <output name="ctd_out" ftype="xml">
24954 <assert_contents>
24955 <is_valid_xml/>
24956 </assert_contents>
24957 </output>
24958 </test>
24959 </xml>
24960 <xml name="autotest_SpectraFilterBernNorm">
24961 </xml>
24962 <xml name="autotest_SpectraFilterMarkerMower">
24963 </xml>
24964 <xml name="autotest_SpectraFilterNLargest">
24965 </xml>
24966 <xml name="autotest_SpectraFilterNormalizer">
24967 </xml>
24968 <xml name="autotest_SpectraFilterParentPeakMower">
24969 </xml>
24970 <xml name="autotest_SpectraFilterScaler">
24971 </xml>
24972 <xml name="autotest_SpectraFilterSqrtMower">
24973 <test expect_num_outputs="2">
24974 <conditional name="adv_opts_cond">
24975 <param name="adv_opts_selector" value="advanced"/>
24976 <param name="force" value="false"/>
24977 <param name="test" value="true"/>
24978 </conditional>
24979 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
24980 <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
24981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
24982 <output name="ctd_out" ftype="xml">
24983 <assert_contents>
24984 <is_valid_xml/>
24985 </assert_contents>
24986 </output>
24987 </test>
24988 </xml>
24989 <xml name="autotest_SpectraFilterThresholdMower">
24990 </xml>
24991 <xml name="autotest_SpectraFilterWindowMower">
24992 <test expect_num_outputs="2">
24993 <conditional name="adv_opts_cond">
24994 <param name="adv_opts_selector" value="advanced"/>
24995 <param name="force" value="false"/>
24996 <param name="test" value="true"/>
24997 </conditional>
24998 <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
24999 <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25000 <section name="algorithm">
25001 <param name="windowsize" value="50.0"/>
25002 <param name="peakcount" value="2"/>
25003 <param name="movetype" value="slide"/>
25004 </section>
25005 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25006 <output name="ctd_out" ftype="xml">
25007 <assert_contents>
25008 <is_valid_xml/>
25009 </assert_contents>
25010 </output>
25011 </test>
25012 <test expect_num_outputs="2">
25013 <conditional name="adv_opts_cond">
25014 <param name="adv_opts_selector" value="advanced"/>
25015 <param name="force" value="false"/>
25016 <param name="test" value="true"/>
25017 </conditional>
25018 <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
25019 <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25020 <section name="algorithm">
25021 <param name="windowsize" value="20.0"/>
25022 <param name="peakcount" value="4"/>
25023 <param name="movetype" value="slide"/>
25024 </section>
25025 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25026 <output name="ctd_out" ftype="xml">
25027 <assert_contents>
25028 <is_valid_xml/>
25029 </assert_contents>
25030 </output>
25031 </test>
25032 </xml>
25033 <xml name="autotest_SpectraMerger">
25034 </xml>
25035 <xml name="autotest_SpectraSTSearchAdapter"/>
25036 <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
25037 </xml>
25038 <xml name="autotest_TargetedFileConverter">
25039 <test expect_num_outputs="2">
25040 <conditional name="adv_opts_cond">
25041 <param name="adv_opts_selector" value="advanced"/>
25042 <param name="legacy_traml_id" value="false"/>
25043 <param name="force" value="false"/>
25044 <param name="test" value="true"/>
25045 </conditional>
25046 <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
25047 <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25048 <param name="out_type" value="TraML"/>
25049 <section name="algorithm">
25050 <param name="retentionTimeInterpretation" value="iRT"/>
25051 <param name="override_group_label_check" value="false"/>
25052 <param name="force_invalid_mods" value="false"/>
25053 </section>
25054 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25055 <output name="ctd_out" ftype="xml">
25056 <assert_contents>
25057 <is_valid_xml/>
25058 </assert_contents>
25059 </output>
25060 </test>
25061 <test expect_num_outputs="2">
25062 <conditional name="adv_opts_cond">
25063 <param name="adv_opts_selector" value="advanced"/>
25064 <param name="legacy_traml_id" value="false"/>
25065 <param name="force" value="false"/>
25066 <param name="test" value="true"/>
25067 </conditional>
25068 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
25069 <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25070 <param name="out_type" value="TraML"/>
25071 <section name="algorithm">
25072 <param name="retentionTimeInterpretation" value="minutes"/>
25073 <param name="override_group_label_check" value="false"/>
25074 <param name="force_invalid_mods" value="false"/>
25075 </section>
25076 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25077 <output name="ctd_out" ftype="xml">
25078 <assert_contents>
25079 <is_valid_xml/>
25080 </assert_contents>
25081 </output>
25082 </test>
25083 <test expect_num_outputs="2">
25084 <conditional name="adv_opts_cond">
25085 <param name="adv_opts_selector" value="advanced"/>
25086 <param name="legacy_traml_id" value="false"/>
25087 <param name="force" value="false"/>
25088 <param name="test" value="true"/>
25089 </conditional>
25090 <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
25091 <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25092 <param name="out_type" value="TraML"/>
25093 <section name="algorithm">
25094 <param name="retentionTimeInterpretation" value="seconds"/>
25095 <param name="override_group_label_check" value="false"/>
25096 <param name="force_invalid_mods" value="false"/>
25097 </section>
25098 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25099 <output name="ctd_out" ftype="xml">
25100 <assert_contents>
25101 <is_valid_xml/>
25102 </assert_contents>
25103 </output>
25104 </test>
25105 <test expect_num_outputs="2">
25106 <conditional name="adv_opts_cond">
25107 <param name="adv_opts_selector" value="advanced"/>
25108 <param name="legacy_traml_id" value="false"/>
25109 <param name="force" value="false"/>
25110 <param name="test" value="true"/>
25111 </conditional>
25112 <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
25113 <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25114 <param name="out_type" value="TraML"/>
25115 <section name="algorithm">
25116 <param name="retentionTimeInterpretation" value="iRT"/>
25117 <param name="override_group_label_check" value="false"/>
25118 <param name="force_invalid_mods" value="false"/>
25119 </section>
25120 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25121 <output name="ctd_out" ftype="xml">
25122 <assert_contents>
25123 <is_valid_xml/>
25124 </assert_contents>
25125 </output>
25126 </test>
25127 <test expect_num_outputs="2">
25128 <conditional name="adv_opts_cond">
25129 <param name="adv_opts_selector" value="advanced"/>
25130 <param name="legacy_traml_id" value="false"/>
25131 <param name="force" value="false"/>
25132 <param name="test" value="true"/>
25133 </conditional>
25134 <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
25135 <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25136 <param name="out_type" value="TraML"/>
25137 <section name="algorithm">
25138 <param name="retentionTimeInterpretation" value="iRT"/>
25139 <param name="override_group_label_check" value="false"/>
25140 <param name="force_invalid_mods" value="false"/>
25141 </section>
25142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25143 <output name="ctd_out" ftype="xml">
25144 <assert_contents>
25145 <is_valid_xml/>
25146 </assert_contents>
25147 </output>
25148 </test>
25149 <test expect_num_outputs="2">
25150 <conditional name="adv_opts_cond">
25151 <param name="adv_opts_selector" value="advanced"/>
25152 <param name="legacy_traml_id" value="false"/>
25153 <param name="force" value="false"/>
25154 <param name="test" value="true"/>
25155 </conditional>
25156 <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
25157 <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25158 <param name="out_type" value="TraML"/>
25159 <section name="algorithm">
25160 <param name="retentionTimeInterpretation" value="iRT"/>
25161 <param name="override_group_label_check" value="false"/>
25162 <param name="force_invalid_mods" value="false"/>
25163 </section>
25164 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25165 <output name="ctd_out" ftype="xml">
25166 <assert_contents>
25167 <is_valid_xml/>
25168 </assert_contents>
25169 </output>
25170 </test>
25171 <test expect_num_outputs="2">
25172 <conditional name="adv_opts_cond">
25173 <param name="adv_opts_selector" value="advanced"/>
25174 <param name="legacy_traml_id" value="false"/>
25175 <param name="force" value="false"/>
25176 <param name="test" value="true"/>
25177 </conditional>
25178 <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
25179 <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25180 <param name="out_type" value="TraML"/>
25181 <section name="algorithm">
25182 <param name="retentionTimeInterpretation" value="iRT"/>
25183 <param name="override_group_label_check" value="false"/>
25184 <param name="force_invalid_mods" value="false"/>
25185 </section>
25186 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25187 <output name="ctd_out" ftype="xml">
25188 <assert_contents>
25189 <is_valid_xml/>
25190 </assert_contents>
25191 </output>
25192 </test>
25193 <test expect_num_outputs="2">
25194 <conditional name="adv_opts_cond">
25195 <param name="adv_opts_selector" value="advanced"/>
25196 <param name="legacy_traml_id" value="false"/>
25197 <param name="force" value="false"/>
25198 <param name="test" value="true"/>
25199 </conditional>
25200 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
25201 <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25202 <param name="out_type" value="TraML"/>
25203 <section name="algorithm">
25204 <param name="retentionTimeInterpretation" value="iRT"/>
25205 <param name="override_group_label_check" value="false"/>
25206 <param name="force_invalid_mods" value="false"/>
25207 </section>
25208 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25209 <output name="ctd_out" ftype="xml">
25210 <assert_contents>
25211 <is_valid_xml/>
25212 </assert_contents>
25213 </output>
25214 </test>
25215 <test expect_num_outputs="2">
25216 <conditional name="adv_opts_cond">
25217 <param name="adv_opts_selector" value="advanced"/>
25218 <param name="legacy_traml_id" value="true"/>
25219 <param name="force" value="false"/>
25220 <param name="test" value="true"/>
25221 </conditional>
25222 <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
25223 <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25224 <param name="out_type" value="TraML"/>
25225 <section name="algorithm">
25226 <param name="retentionTimeInterpretation" value="iRT"/>
25227 <param name="override_group_label_check" value="false"/>
25228 <param name="force_invalid_mods" value="false"/>
25229 </section>
25230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25231 <output name="ctd_out" ftype="xml">
25232 <assert_contents>
25233 <is_valid_xml/>
25234 </assert_contents>
25235 </output>
25236 </test>
25237 <test expect_num_outputs="2">
25238 <conditional name="adv_opts_cond">
25239 <param name="adv_opts_selector" value="advanced"/>
25240 <param name="legacy_traml_id" value="false"/>
25241 <param name="force" value="false"/>
25242 <param name="test" value="true"/>
25243 </conditional>
25244 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
25245 <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25246 <param name="out_type" value="TraML"/>
25247 <section name="algorithm">
25248 <param name="retentionTimeInterpretation" value="iRT"/>
25249 <param name="override_group_label_check" value="false"/>
25250 <param name="force_invalid_mods" value="false"/>
25251 </section>
25252 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25253 <output name="ctd_out" ftype="xml">
25254 <assert_contents>
25255 <is_valid_xml/>
25256 </assert_contents>
25257 </output>
25258 </test>
25259 <test expect_num_outputs="2">
25260 <conditional name="adv_opts_cond">
25261 <param name="adv_opts_selector" value="advanced"/>
25262 <param name="legacy_traml_id" value="true"/>
25263 <param name="force" value="false"/>
25264 <param name="test" value="true"/>
25265 </conditional>
25266 <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
25267 <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25268 <param name="out_type" value="TraML"/>
25269 <section name="algorithm">
25270 <param name="retentionTimeInterpretation" value="iRT"/>
25271 <param name="override_group_label_check" value="false"/>
25272 <param name="force_invalid_mods" value="false"/>
25273 </section>
25274 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25275 <output name="ctd_out" ftype="xml">
25276 <assert_contents>
25277 <is_valid_xml/>
25278 </assert_contents>
25279 </output>
25280 </test>
25281 <test expect_num_outputs="2">
25282 <conditional name="adv_opts_cond">
25283 <param name="adv_opts_selector" value="advanced"/>
25284 <param name="legacy_traml_id" value="false"/>
25285 <param name="force" value="false"/>
25286 <param name="test" value="true"/>
25287 </conditional>
25288 <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
25289 <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25290 <param name="out_type" value="tsv"/>
25291 <section name="algorithm">
25292 <param name="retentionTimeInterpretation" value="iRT"/>
25293 <param name="override_group_label_check" value="false"/>
25294 <param name="force_invalid_mods" value="false"/>
25295 </section>
25296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25297 <output name="ctd_out" ftype="xml">
25298 <assert_contents>
25299 <is_valid_xml/>
25300 </assert_contents>
25301 </output>
25302 </test>
25303 <test expect_num_outputs="2">
25304 <conditional name="adv_opts_cond">
25305 <param name="adv_opts_selector" value="advanced"/>
25306 <param name="legacy_traml_id" value="false"/>
25307 <param name="force" value="false"/>
25308 <param name="test" value="true"/>
25309 </conditional>
25310 <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
25311 <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25312 <param name="out_type" value="TraML"/>
25313 <section name="algorithm">
25314 <param name="retentionTimeInterpretation" value="iRT"/>
25315 <param name="override_group_label_check" value="false"/>
25316 <param name="force_invalid_mods" value="false"/>
25317 </section>
25318 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25319 <output name="ctd_out" ftype="xml">
25320 <assert_contents>
25321 <is_valid_xml/>
25322 </assert_contents>
25323 </output>
25324 </test>
25325 <test expect_num_outputs="2">
25326 <conditional name="adv_opts_cond">
25327 <param name="adv_opts_selector" value="advanced"/>
25328 <param name="legacy_traml_id" value="false"/>
25329 <param name="force" value="false"/>
25330 <param name="test" value="true"/>
25331 </conditional>
25332 <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
25333 <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25334 <param name="out_type" value="tsv"/>
25335 <section name="algorithm">
25336 <param name="retentionTimeInterpretation" value="iRT"/>
25337 <param name="override_group_label_check" value="true"/>
25338 <param name="force_invalid_mods" value="false"/>
25339 </section>
25340 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25341 <output name="ctd_out" ftype="xml">
25342 <assert_contents>
25343 <is_valid_xml/>
25344 </assert_contents>
25345 </output>
25346 </test>
25347 <test expect_num_outputs="2">
25348 <conditional name="adv_opts_cond">
25349 <param name="adv_opts_selector" value="advanced"/>
25350 <param name="legacy_traml_id" value="false"/>
25351 <param name="force" value="false"/>
25352 <param name="test" value="true"/>
25353 </conditional>
25354 <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
25355 <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25356 <param name="out_type" value="TraML"/>
25357 <section name="algorithm">
25358 <param name="retentionTimeInterpretation" value="iRT"/>
25359 <param name="override_group_label_check" value="true"/>
25360 <param name="force_invalid_mods" value="false"/>
25361 </section>
25362 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25363 <output name="ctd_out" ftype="xml">
25364 <assert_contents>
25365 <is_valid_xml/>
25366 </assert_contents>
25367 </output>
25368 </test>
25369 <test expect_num_outputs="2">
25370 <conditional name="adv_opts_cond">
25371 <param name="adv_opts_selector" value="advanced"/>
25372 <param name="legacy_traml_id" value="false"/>
25373 <param name="force" value="false"/>
25374 <param name="test" value="true"/>
25375 </conditional>
25376 <param name="in" value="ConvertTSVToTraML_output.TraML"/>
25377 <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25378 <param name="out_type" value="tsv"/>
25379 <section name="algorithm">
25380 <param name="retentionTimeInterpretation" value="iRT"/>
25381 <param name="override_group_label_check" value="false"/>
25382 <param name="force_invalid_mods" value="false"/>
25383 </section>
25384 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25385 <output name="ctd_out" ftype="xml">
25386 <assert_contents>
25387 <is_valid_xml/>
25388 </assert_contents>
25389 </output>
25390 </test>
25391 <test expect_num_outputs="2">
25392 <conditional name="adv_opts_cond">
25393 <param name="adv_opts_selector" value="advanced"/>
25394 <param name="legacy_traml_id" value="false"/>
25395 <param name="force" value="false"/>
25396 <param name="test" value="true"/>
25397 </conditional>
25398 <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
25399 <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25400 <param name="out_type" value="TraML"/>
25401 <section name="algorithm">
25402 <param name="retentionTimeInterpretation" value="iRT"/>
25403 <param name="override_group_label_check" value="true"/>
25404 <param name="force_invalid_mods" value="false"/>
25405 </section>
25406 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25407 <output name="ctd_out" ftype="xml">
25408 <assert_contents>
25409 <is_valid_xml/>
25410 </assert_contents>
25411 </output>
25412 </test>
25413 <test expect_num_outputs="2">
25414 <conditional name="adv_opts_cond">
25415 <param name="adv_opts_selector" value="advanced"/>
25416 <param name="legacy_traml_id" value="false"/>
25417 <param name="force" value="false"/>
25418 <param name="test" value="true"/>
25419 </conditional>
25420 <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
25421 <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25422 <param name="out_type" value="TraML"/>
25423 <section name="algorithm">
25424 <param name="retentionTimeInterpretation" value="iRT"/>
25425 <param name="override_group_label_check" value="false"/>
25426 <param name="force_invalid_mods" value="false"/>
25427 </section>
25428 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25429 <output name="ctd_out" ftype="xml">
25430 <assert_contents>
25431 <is_valid_xml/>
25432 </assert_contents>
25433 </output>
25434 </test>
25435 <test expect_num_outputs="2">
25436 <conditional name="adv_opts_cond">
25437 <param name="adv_opts_selector" value="advanced"/>
25438 <param name="legacy_traml_id" value="false"/>
25439 <param name="force" value="false"/>
25440 <param name="test" value="true"/>
25441 </conditional>
25442 <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
25443 <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
25444 <param name="out_type" value="tsv"/>
25445 <section name="algorithm">
25446 <param name="retentionTimeInterpretation" value="iRT"/>
25447 <param name="override_group_label_check" value="false"/>
25448 <param name="force_invalid_mods" value="false"/>
25449 </section>
25450 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25451 <output name="ctd_out" ftype="xml">
25452 <assert_contents>
25453 <is_valid_xml/>
25454 </assert_contents>
25455 </output>
25456 </test>
25457 <test expect_num_outputs="2">
25458 <conditional name="adv_opts_cond">
25459 <param name="adv_opts_selector" value="advanced"/>
25460 <param name="legacy_traml_id" value="false"/>
25461 <param name="force" value="false"/>
25462 <param name="test" value="true"/>
25463 </conditional>
25464 <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
25465 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/>
25466 <param name="out_type" value="traml"/>
25467 <section name="algorithm">
25468 <param name="retentionTimeInterpretation" value="iRT"/>
25469 <param name="override_group_label_check" value="false"/>
25470 <param name="force_invalid_mods" value="false"/>
25471 </section>
25472 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25473 <output name="ctd_out" ftype="xml">
25474 <assert_contents>
25475 <is_valid_xml/>
25476 </assert_contents>
25477 </output>
25478 </test>
25479 </xml>
25480 <xml name="autotest_TextExporter">
25481 <test expect_num_outputs="2">
25482 <conditional name="adv_opts_cond">
25483 <param name="adv_opts_selector" value="advanced"/>
25484 <param name="force" value="false"/>
25485 <param name="test" value="true"/>
25486 </conditional>
25487 <param name="in" value="TextExporter_1_input.featureXML"/>
25488 <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
25489 <param name="separator" value=""/>
25490 <param name="replacement" value="_"/>
25491 <param name="quoting" value="none"/>
25492 <param name="no_ids" value="false"/>
25493 <section name="feature">
25494 <param name="minimal" value="false"/>
25495 <param name="add_metavalues" value="-1"/>
25496 </section>
25497 <section name="id">
25498 <param name="proteins_only" value="false"/>
25499 <param name="peptides_only" value="false"/>
25500 <param name="protein_groups" value="false"/>
25501 <param name="first_dim_rt" value="false"/>
25502 <param name="add_metavalues" value="-1"/>
25503 <param name="add_hit_metavalues" value="-1"/>
25504 <param name="add_protein_hit_metavalues" value="-1"/>
25505 </section>
25506 <section name="consensus">
25507 <param name="sorting_method" value="none"/>
25508 <param name="sort_by_maps" value="false"/>
25509 <param name="sort_by_size" value="false"/>
25510 </section>
25511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25512 <output name="ctd_out" ftype="xml">
25513 <assert_contents>
25514 <is_valid_xml/>
25515 </assert_contents>
25516 </output>
25517 </test>
25518 <test expect_num_outputs="5">
25519 <conditional name="adv_opts_cond">
25520 <param name="adv_opts_selector" value="advanced"/>
25521 <param name="force" value="false"/>
25522 <param name="test" value="true"/>
25523 </conditional>
25524 <param name="in" value="TextExporter_2_input.consensusXML"/>
25525 <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25526 <param name="separator" value=""/>
25527 <param name="replacement" value="_"/>
25528 <param name="quoting" value="none"/>
25529 <param name="no_ids" value="true"/>
25530 <section name="feature">
25531 <param name="minimal" value="false"/>
25532 <param name="add_metavalues" value="-1"/>
25533 </section>
25534 <section name="id">
25535 <param name="proteins_only" value="false"/>
25536 <param name="peptides_only" value="false"/>
25537 <param name="protein_groups" value="false"/>
25538 <param name="first_dim_rt" value="false"/>
25539 <param name="add_metavalues" value="-1"/>
25540 <param name="add_hit_metavalues" value="-1"/>
25541 <param name="add_protein_hit_metavalues" value="-1"/>
25542 </section>
25543 <section name="consensus">
25544 <param name="sorting_method" value="RT_then_MZ"/>
25545 <param name="sort_by_maps" value="true"/>
25546 <param name="sort_by_size" value="true"/>
25547 </section>
25548 <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25549 <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25550 <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25551 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
25552 <output name="ctd_out" ftype="xml">
25553 <assert_contents>
25554 <is_valid_xml/>
25555 </assert_contents>
25556 </output>
25557 </test>
25558 <test expect_num_outputs="2">
25559 <conditional name="adv_opts_cond">
25560 <param name="adv_opts_selector" value="advanced"/>
25561 <param name="force" value="false"/>
25562 <param name="test" value="true"/>
25563 </conditional>
25564 <param name="in" value="TextExporter_3_input.idXML"/>
25565 <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
25566 <param name="separator" value=""/>
25567 <param name="replacement" value="_"/>
25568 <param name="quoting" value="none"/>
25569 <param name="no_ids" value="false"/>
25570 <section name="feature">
25571 <param name="minimal" value="false"/>
25572 <param name="add_metavalues" value="-1"/>
25573 </section>
25574 <section name="id">
25575 <param name="proteins_only" value="false"/>
25576 <param name="peptides_only" value="false"/>
25577 <param name="protein_groups" value="false"/>
25578 <param name="first_dim_rt" value="false"/>
25579 <param name="add_metavalues" value="-1"/>
25580 <param name="add_hit_metavalues" value="-1"/>
25581 <param name="add_protein_hit_metavalues" value="-1"/>
25582 </section>
25583 <section name="consensus">
25584 <param name="sorting_method" value="none"/>
25585 <param name="sort_by_maps" value="false"/>
25586 <param name="sort_by_size" value="false"/>
25587 </section>
25588 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25589 <output name="ctd_out" ftype="xml">
25590 <assert_contents>
25591 <is_valid_xml/>
25592 </assert_contents>
25593 </output>
25594 </test>
25595 <test expect_num_outputs="2">
25596 <conditional name="adv_opts_cond">
25597 <param name="adv_opts_selector" value="advanced"/>
25598 <param name="force" value="false"/>
25599 <param name="test" value="true"/>
25600 </conditional>
25601 <param name="in" value="TextExporter_3_input.idXML"/>
25602 <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="csv"/>
25603 <param name="separator" value=""/>
25604 <param name="replacement" value="_"/>
25605 <param name="quoting" value="none"/>
25606 <param name="no_ids" value="false"/>
25607 <section name="feature">
25608 <param name="minimal" value="false"/>
25609 <param name="add_metavalues" value="-1"/>
25610 </section>
25611 <section name="id">
25612 <param name="proteins_only" value="true"/>
25613 <param name="peptides_only" value="false"/>
25614 <param name="protein_groups" value="false"/>
25615 <param name="first_dim_rt" value="false"/>
25616 <param name="add_metavalues" value="-1"/>
25617 <param name="add_hit_metavalues" value="-1"/>
25618 <param name="add_protein_hit_metavalues" value="-1"/>
25619 </section>
25620 <section name="consensus">
25621 <param name="sorting_method" value="none"/>
25622 <param name="sort_by_maps" value="false"/>
25623 <param name="sort_by_size" value="false"/>
25624 </section>
25625 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25626 <output name="ctd_out" ftype="xml">
25627 <assert_contents>
25628 <is_valid_xml/>
25629 </assert_contents>
25630 </output>
25631 </test>
25632 <test expect_num_outputs="2">
25633 <conditional name="adv_opts_cond">
25634 <param name="adv_opts_selector" value="advanced"/>
25635 <param name="force" value="false"/>
25636 <param name="test" value="true"/>
25637 </conditional>
25638 <param name="in" value="TextExporter_5_input.idXML"/>
25639 <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="csv"/>
25640 <param name="separator" value=""/>
25641 <param name="replacement" value="_"/>
25642 <param name="quoting" value="none"/>
25643 <param name="no_ids" value="false"/>
25644 <section name="feature">
25645 <param name="minimal" value="false"/>
25646 <param name="add_metavalues" value="-1"/>
25647 </section>
25648 <section name="id">
25649 <param name="proteins_only" value="false"/>
25650 <param name="peptides_only" value="true"/>
25651 <param name="protein_groups" value="false"/>
25652 <param name="first_dim_rt" value="true"/>
25653 <param name="add_metavalues" value="-1"/>
25654 <param name="add_hit_metavalues" value="-1"/>
25655 <param name="add_protein_hit_metavalues" value="-1"/>
25656 </section>
25657 <section name="consensus">
25658 <param name="sorting_method" value="none"/>
25659 <param name="sort_by_maps" value="false"/>
25660 <param name="sort_by_size" value="false"/>
25661 </section>
25662 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25663 <output name="ctd_out" ftype="xml">
25664 <assert_contents>
25665 <is_valid_xml/>
25666 </assert_contents>
25667 </output>
25668 </test>
25669 <test expect_num_outputs="2">
25670 <conditional name="adv_opts_cond">
25671 <param name="adv_opts_selector" value="advanced"/>
25672 <param name="force" value="false"/>
25673 <param name="test" value="true"/>
25674 </conditional>
25675 <param name="in" value="TextExporter_6_input.featureXML"/>
25676 <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
25677 <param name="separator" value=""/>
25678 <param name="replacement" value="_"/>
25679 <param name="quoting" value="none"/>
25680 <param name="no_ids" value="true"/>
25681 <section name="feature">
25682 <param name="minimal" value="false"/>
25683 <param name="add_metavalues" value="-1"/>
25684 </section>
25685 <section name="id">
25686 <param name="proteins_only" value="false"/>
25687 <param name="peptides_only" value="false"/>
25688 <param name="protein_groups" value="false"/>
25689 <param name="first_dim_rt" value="false"/>
25690 <param name="add_metavalues" value="-1"/>
25691 <param name="add_hit_metavalues" value="-1"/>
25692 <param name="add_protein_hit_metavalues" value="-1"/>
25693 </section>
25694 <section name="consensus">
25695 <param name="sorting_method" value="none"/>
25696 <param name="sort_by_maps" value="false"/>
25697 <param name="sort_by_size" value="false"/>
25698 </section>
25699 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25700 <output name="ctd_out" ftype="xml">
25701 <assert_contents>
25702 <is_valid_xml/>
25703 </assert_contents>
25704 </output>
25705 </test>
25706 <test expect_num_outputs="2">
25707 <conditional name="adv_opts_cond">
25708 <param name="adv_opts_selector" value="advanced"/>
25709 <param name="force" value="false"/>
25710 <param name="test" value="true"/>
25711 </conditional>
25712 <param name="in" value="TextExporter_7_input.consensusXML"/>
25713 <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="csv"/>
25714 <param name="separator" value=""/>
25715 <param name="replacement" value="_"/>
25716 <param name="quoting" value="none"/>
25717 <param name="no_ids" value="false"/>
25718 <section name="feature">
25719 <param name="minimal" value="false"/>
25720 <param name="add_metavalues" value="-1"/>
25721 </section>
25722 <section name="id">
25723 <param name="proteins_only" value="false"/>
25724 <param name="peptides_only" value="false"/>
25725 <param name="protein_groups" value="false"/>
25726 <param name="first_dim_rt" value="false"/>
25727 <param name="add_metavalues" value="-1"/>
25728 <param name="add_hit_metavalues" value="-1"/>
25729 <param name="add_protein_hit_metavalues" value="-1"/>
25730 </section>
25731 <section name="consensus">
25732 <param name="sorting_method" value="RT_then_MZ"/>
25733 <param name="sort_by_maps" value="true"/>
25734 <param name="sort_by_size" value="true"/>
25735 </section>
25736 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25737 <output name="ctd_out" ftype="xml">
25738 <assert_contents>
25739 <is_valid_xml/>
25740 </assert_contents>
25741 </output>
25742 </test>
25743 <test expect_num_outputs="2">
25744 <conditional name="adv_opts_cond">
25745 <param name="adv_opts_selector" value="advanced"/>
25746 <param name="force" value="false"/>
25747 <param name="test" value="true"/>
25748 </conditional>
25749 <param name="in" value="TextExporter_1_input.featureXML"/>
25750 <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
25751 <param name="separator" value=""/>
25752 <param name="replacement" value="_"/>
25753 <param name="quoting" value="none"/>
25754 <param name="no_ids" value="true"/>
25755 <section name="feature">
25756 <param name="minimal" value="false"/>
25757 <param name="add_metavalues" value="-1"/>
25758 </section>
25759 <section name="id">
25760 <param name="proteins_only" value="false"/>
25761 <param name="peptides_only" value="false"/>
25762 <param name="protein_groups" value="false"/>
25763 <param name="first_dim_rt" value="false"/>
25764 <param name="add_metavalues" value="-1"/>
25765 <param name="add_hit_metavalues" value="-1"/>
25766 <param name="add_protein_hit_metavalues" value="-1"/>
25767 </section>
25768 <section name="consensus">
25769 <param name="sorting_method" value="none"/>
25770 <param name="sort_by_maps" value="false"/>
25771 <param name="sort_by_size" value="false"/>
25772 </section>
25773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25774 <output name="ctd_out" ftype="xml">
25775 <assert_contents>
25776 <is_valid_xml/>
25777 </assert_contents>
25778 </output>
25779 </test>
25780 <test expect_num_outputs="2">
25781 <conditional name="adv_opts_cond">
25782 <param name="adv_opts_selector" value="advanced"/>
25783 <param name="force" value="false"/>
25784 <param name="test" value="true"/>
25785 </conditional>
25786 <param name="in" value="TextExporter_9_input.idXML"/>
25787 <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
25788 <param name="separator" value=""/>
25789 <param name="replacement" value="_"/>
25790 <param name="quoting" value="none"/>
25791 <param name="no_ids" value="false"/>
25792 <section name="feature">
25793 <param name="minimal" value="false"/>
25794 <param name="add_metavalues" value="-1"/>
25795 </section>
25796 <section name="id">
25797 <param name="proteins_only" value="false"/>
25798 <param name="peptides_only" value="false"/>
25799 <param name="protein_groups" value="false"/>
25800 <param name="first_dim_rt" value="false"/>
25801 <param name="add_metavalues" value="0"/>
25802 <param name="add_hit_metavalues" value="0"/>
25803 <param name="add_protein_hit_metavalues" value="-1"/>
25804 </section>
25805 <section name="consensus">
25806 <param name="sorting_method" value="none"/>
25807 <param name="sort_by_maps" value="false"/>
25808 <param name="sort_by_size" value="false"/>
25809 </section>
25810 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
25811 <output name="ctd_out" ftype="xml">
25812 <assert_contents>
25813 <is_valid_xml/>
25814 </assert_contents>
25815 </output>
25816 </test>
25817 </xml>
25818 <xml name="autotest_TICCalculator">
25819 <test expect_num_outputs="1">
25820 <conditional name="adv_opts_cond">
25821 <param name="adv_opts_selector" value="advanced"/>
25822 <param name="force" value="false"/>
25823 <param name="test" value="true"/>
25824 </conditional>
25825 <param name="in" value="MapNormalizer_output.mzML"/>
25826 <param name="read_method" value="regular"/>
25827 <param name="loadData" value="true"/>
25828 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25829 <output name="ctd_out" ftype="xml">
25830 <assert_contents>
25831 <is_valid_xml/>
25832 </assert_contents>
25833 </output>
25834 </test>
25835 <test expect_num_outputs="1">
25836 <conditional name="adv_opts_cond">
25837 <param name="adv_opts_selector" value="advanced"/>
25838 <param name="force" value="false"/>
25839 <param name="test" value="true"/>
25840 </conditional>
25841 <param name="in" value="MapNormalizer_output.mzML"/>
25842 <param name="read_method" value="streaming"/>
25843 <param name="loadData" value="true"/>
25844 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25845 <output name="ctd_out" ftype="xml">
25846 <assert_contents>
25847 <is_valid_xml/>
25848 </assert_contents>
25849 </output>
25850 </test>
25851 <test expect_num_outputs="1">
25852 <conditional name="adv_opts_cond">
25853 <param name="adv_opts_selector" value="advanced"/>
25854 <param name="force" value="false"/>
25855 <param name="test" value="true"/>
25856 </conditional>
25857 <param name="in" value="MapNormalizer_output.mzML"/>
25858 <param name="read_method" value="streaming"/>
25859 <param name="loadData" value="false"/>
25860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25861 <output name="ctd_out" ftype="xml">
25862 <assert_contents>
25863 <is_valid_xml/>
25864 </assert_contents>
25865 </output>
25866 </test>
25867 <test expect_num_outputs="1">
25868 <conditional name="adv_opts_cond">
25869 <param name="adv_opts_selector" value="advanced"/>
25870 <param name="force" value="false"/>
25871 <param name="test" value="true"/>
25872 </conditional>
25873 <param name="in" value="MapNormalizer_output.mzML"/>
25874 <param name="read_method" value="indexed"/>
25875 <param name="loadData" value="true"/>
25876 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25877 <output name="ctd_out" ftype="xml">
25878 <assert_contents>
25879 <is_valid_xml/>
25880 </assert_contents>
25881 </output>
25882 </test>
25883 <test expect_num_outputs="1">
25884 <conditional name="adv_opts_cond">
25885 <param name="adv_opts_selector" value="advanced"/>
25886 <param name="force" value="false"/>
25887 <param name="test" value="true"/>
25888 </conditional>
25889 <param name="in" value="MapNormalizer_output.mzML"/>
25890 <param name="read_method" value="indexed_parallel"/>
25891 <param name="loadData" value="true"/>
25892 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25893 <output name="ctd_out" ftype="xml">
25894 <assert_contents>
25895 <is_valid_xml/>
25896 </assert_contents>
25897 </output>
25898 </test>
25899 </xml>
25900 <xml name="autotest_TOFCalibration">
25901 <test expect_num_outputs="2">
25902 <conditional name="adv_opts_cond">
25903 <param name="adv_opts_selector" value="advanced"/>
25904 <param name="force" value="false"/>
25905 <param name="test" value="true"/>
25906 </conditional>
25907 <param name="in" value="TOFCalibration_1_input.mzML"/>
25908 <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25909 <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
25910 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
25911 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
25912 <param name="peak_data" value="false"/>
25913 <section name="algorithm">
25914 <section name="PeakPicker">
25915 <param name="signal_to_noise" value="3.0"/>
25916 <param name="centroid_percentage" value="0.6"/>
25917 <param name="peak_width" value="0.15"/>
25918 <param name="estimate_peak_width" value="false"/>
25919 <param name="fwhm_lower_bound_factor" value="0.7"/>
25920 <param name="fwhm_upper_bound_factor" value="20.0"/>
25921 <section name="optimization">
25922 <param name="iterations" value="400"/>
25923 <section name="penalties">
25924 <param name="position" value="0.0"/>
25925 <param name="left_width" value="1.0"/>
25926 <param name="right_width" value="1.0"/>
25927 <param name="height" value="1.0"/>
25928 </section>
25929 <section name="2d">
25930 <param name="tolerance_mz" value="2.2"/>
25931 <param name="max_peak_distance" value="1.2"/>
25932 </section>
25933 </section>
25934 <section name="thresholds">
25935 <param name="peak_bound" value="400.0"/>
25936 <param name="peak_bound_ms2_level" value="10.0"/>
25937 <param name="correlation" value="0.0"/>
25938 <param name="noise_level" value="0.1"/>
25939 <param name="search_radius" value="3"/>
25940 </section>
25941 <section name="wavelet_transform">
25942 <param name="spacing" value="0.001"/>
25943 </section>
25944 <section name="deconvolution">
25945 <param name="deconvolution" value="false"/>
25946 <param name="asym_threshold" value="0.3"/>
25947 <param name="left_width" value="2.0"/>
25948 <param name="right_width" value="2.0"/>
25949 <param name="scaling" value="0.12"/>
25950 <section name="fitting">
25951 <param name="fwhm_threshold" value="0.7"/>
25952 <param name="eps_abs" value="9.999999747378752e-06"/>
25953 <param name="eps_rel" value="9.999999747378752e-06"/>
25954 <param name="max_iteration" value="10"/>
25955 <section name="penalties">
25956 <param name="position" value="0.0"/>
25957 <param name="height" value="1.0"/>
25958 <param name="left_width" value="0.0"/>
25959 <param name="right_width" value="0.0"/>
25960 </section>
25961 </section>
25962 </section>
25963 <section name="SignalToNoiseEstimationParameter">
25964 <param name="max_intensity" value="-1"/>
25965 <param name="auto_max_stdev_factor" value="3.0"/>
25966 <param name="auto_max_percentile" value="95"/>
25967 <param name="auto_mode" value="0"/>
25968 <param name="win_len" value="200.0"/>
25969 <param name="bin_count" value="30"/>
25970 <param name="stdev_mp" value="3.0"/>
25971 <param name="min_required_elements" value="10"/>
25972 <param name="noise_for_empty_window" value="1e+20"/>
25973 </section>
25974 </section>
25975 </section>
25976 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
25977 <output name="ctd_out" ftype="xml">
25978 <assert_contents>
25979 <is_valid_xml/>
25980 </assert_contents>
25981 </output>
25982 </test>
25983 <test expect_num_outputs="2">
25984 <conditional name="adv_opts_cond">
25985 <param name="adv_opts_selector" value="advanced"/>
25986 <param name="force" value="false"/>
25987 <param name="test" value="true"/>
25988 </conditional>
25989 <param name="in" value="TOFCalibration_2_input.mzML"/>
25990 <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
25991 <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
25992 <param name="ref_masses" value="TOFCalibration_ref_masses.txt" ftype="txt"/>
25993 <param name="tof_const" value="TOFCalibration_const.csv" ftype="csv"/>
25994 <param name="peak_data" value="true"/>
25995 <section name="algorithm">
25996 <section name="PeakPicker">
25997 <param name="signal_to_noise" value="3.0"/>
25998 <param name="centroid_percentage" value="0.6"/>
25999 <param name="peak_width" value="0.15"/>
26000 <param name="estimate_peak_width" value="false"/>
26001 <param name="fwhm_lower_bound_factor" value="0.7"/>
26002 <param name="fwhm_upper_bound_factor" value="20.0"/>
26003 <section name="optimization">
26004 <param name="iterations" value="400"/>
26005 <section name="penalties">
26006 <param name="position" value="0.0"/>
26007 <param name="left_width" value="1.0"/>
26008 <param name="right_width" value="1.0"/>
26009 <param name="height" value="1.0"/>
26010 </section>
26011 <section name="2d">
26012 <param name="tolerance_mz" value="2.2"/>
26013 <param name="max_peak_distance" value="1.2"/>
26014 </section>
26015 </section>
26016 <section name="thresholds">
26017 <param name="peak_bound" value="400.0"/>
26018 <param name="peak_bound_ms2_level" value="10.0"/>
26019 <param name="correlation" value="0.0"/>
26020 <param name="noise_level" value="0.1"/>
26021 <param name="search_radius" value="3"/>
26022 </section>
26023 <section name="wavelet_transform">
26024 <param name="spacing" value="0.001"/>
26025 </section>
26026 <section name="deconvolution">
26027 <param name="deconvolution" value="false"/>
26028 <param name="asym_threshold" value="0.3"/>
26029 <param name="left_width" value="2.0"/>
26030 <param name="right_width" value="2.0"/>
26031 <param name="scaling" value="0.12"/>
26032 <section name="fitting">
26033 <param name="fwhm_threshold" value="0.7"/>
26034 <param name="eps_abs" value="9.999999747378752e-06"/>
26035 <param name="eps_rel" value="9.999999747378752e-06"/>
26036 <param name="max_iteration" value="10"/>
26037 <section name="penalties">
26038 <param name="position" value="0.0"/>
26039 <param name="height" value="1.0"/>
26040 <param name="left_width" value="0.0"/>
26041 <param name="right_width" value="0.0"/>
26042 </section>
26043 </section>
26044 </section>
26045 <section name="SignalToNoiseEstimationParameter">
26046 <param name="max_intensity" value="-1"/>
26047 <param name="auto_max_stdev_factor" value="3.0"/>
26048 <param name="auto_max_percentile" value="95"/>
26049 <param name="auto_mode" value="0"/>
26050 <param name="win_len" value="200.0"/>
26051 <param name="bin_count" value="30"/>
26052 <param name="stdev_mp" value="3.0"/>
26053 <param name="min_required_elements" value="10"/>
26054 <param name="noise_for_empty_window" value="1e+20"/>
26055 </section>
26056 </section>
26057 </section>
26058 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
26059 <output name="ctd_out" ftype="xml">
26060 <assert_contents>
26061 <is_valid_xml/>
26062 </assert_contents>
26063 </output>
26064 </test>
26065 </xml>
26066 <xml name="autotest_TransformationEvaluation">
26067 </xml>
26068 <xml name="autotest_XFDR">
26069 <test expect_num_outputs="4">
26070 <conditional name="adv_opts_cond">
26071 <param name="adv_opts_selector" value="advanced"/>
26072 <param name="force" value="false"/>
26073 <param name="test" value="true"/>
26074 </conditional>
26075 <param name="in" value="XFDR_test_in1.idXML"/>
26076 <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26077 <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26078 <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26079 <param name="decoy_string" value="DECOY_"/>
26080 <param name="minborder" value="-50.0"/>
26081 <param name="maxborder" value="50.0"/>
26082 <param name="mindeltas" value="0.0"/>
26083 <param name="minionsmatched" value="0"/>
26084 <param name="uniquexl" value="false"/>
26085 <param name="no_qvalues" value="false"/>
26086 <param name="minscore" value="-10.0"/>
26087 <param name="binsize" value="0.1"/>
26088 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26089 <output name="ctd_out" ftype="xml">
26090 <assert_contents>
26091 <is_valid_xml/>
26092 </assert_contents>
26093 </output>
26094 </test>
26095 <test expect_num_outputs="4">
26096 <conditional name="adv_opts_cond">
26097 <param name="adv_opts_selector" value="advanced"/>
26098 <param name="force" value="false"/>
26099 <param name="test" value="true"/>
26100 </conditional>
26101 <param name="in" value="XFDR_test_in1.idXML"/>
26102 <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26103 <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26104 <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26105 <param name="decoy_string" value="DECOY_"/>
26106 <param name="minborder" value="-50.0"/>
26107 <param name="maxborder" value="50.0"/>
26108 <param name="mindeltas" value="0.0"/>
26109 <param name="minionsmatched" value="0"/>
26110 <param name="uniquexl" value="true"/>
26111 <param name="no_qvalues" value="true"/>
26112 <param name="minscore" value="-10.0"/>
26113 <param name="binsize" value="0.1"/>
26114 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26115 <output name="ctd_out" ftype="xml">
26116 <assert_contents>
26117 <is_valid_xml/>
26118 </assert_contents>
26119 </output>
26120 </test>
26121 <test expect_num_outputs="4">
26122 <conditional name="adv_opts_cond">
26123 <param name="adv_opts_selector" value="advanced"/>
26124 <param name="force" value="false"/>
26125 <param name="test" value="true"/>
26126 </conditional>
26127 <param name="in" value="XFDR_test_in2.xquest.xml"/>
26128 <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26129 <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26130 <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26131 <param name="decoy_string" value="DECOY_"/>
26132 <param name="minborder" value="-50.0"/>
26133 <param name="maxborder" value="50.0"/>
26134 <param name="mindeltas" value="0.0"/>
26135 <param name="minionsmatched" value="0"/>
26136 <param name="uniquexl" value="false"/>
26137 <param name="no_qvalues" value="false"/>
26138 <param name="minscore" value="0.0"/>
26139 <param name="binsize" value="0.1"/>
26140 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26141 <output name="ctd_out" ftype="xml">
26142 <assert_contents>
26143 <is_valid_xml/>
26144 </assert_contents>
26145 </output>
26146 </test>
26147 <test expect_num_outputs="4">
26148 <conditional name="adv_opts_cond">
26149 <param name="adv_opts_selector" value="advanced"/>
26150 <param name="force" value="false"/>
26151 <param name="test" value="true"/>
26152 </conditional>
26153 <param name="in" value="XFDR_test_in2.xquest.xml"/>
26154 <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26155 <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26156 <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26157 <param name="decoy_string" value="DECOY_"/>
26158 <param name="minborder" value="-3.0"/>
26159 <param name="maxborder" value="3.0"/>
26160 <param name="mindeltas" value="0.0"/>
26161 <param name="minionsmatched" value="0"/>
26162 <param name="uniquexl" value="false"/>
26163 <param name="no_qvalues" value="false"/>
26164 <param name="minscore" value="-10.0"/>
26165 <param name="binsize" value="0.1"/>
26166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26167 <output name="ctd_out" ftype="xml">
26168 <assert_contents>
26169 <is_valid_xml/>
26170 </assert_contents>
26171 </output>
26172 </test>
26173 <test expect_num_outputs="4">
26174 <conditional name="adv_opts_cond">
26175 <param name="adv_opts_selector" value="advanced"/>
26176 <param name="force" value="false"/>
26177 <param name="test" value="true"/>
26178 </conditional>
26179 <param name="in" value="XFDR_test_in3.xquest.xml"/>
26180 <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26181 <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26182 <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26183 <param name="decoy_string" value="DECOY_"/>
26184 <param name="minborder" value="-3.0"/>
26185 <param name="maxborder" value="3.0"/>
26186 <param name="mindeltas" value="0.0"/>
26187 <param name="minionsmatched" value="0"/>
26188 <param name="uniquexl" value="false"/>
26189 <param name="no_qvalues" value="false"/>
26190 <param name="minscore" value="-10.0"/>
26191 <param name="binsize" value="0.1"/>
26192 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26193 <output name="ctd_out" ftype="xml">
26194 <assert_contents>
26195 <is_valid_xml/>
26196 </assert_contents>
26197 </output>
26198 </test>
26199 <test expect_num_outputs="2">
26200 <conditional name="adv_opts_cond">
26201 <param name="adv_opts_selector" value="advanced"/>
26202 <param name="force" value="false"/>
26203 <param name="test" value="true"/>
26204 </conditional>
26205 <param name="in" value="XFDR_test_in4.idXML"/>
26206 <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26207 <param name="decoy_string" value="DECOY_"/>
26208 <param name="minborder" value="-50.0"/>
26209 <param name="maxborder" value="50.0"/>
26210 <param name="mindeltas" value="0.0"/>
26211 <param name="minionsmatched" value="0"/>
26212 <param name="uniquexl" value="false"/>
26213 <param name="no_qvalues" value="false"/>
26214 <param name="minscore" value="-10.0"/>
26215 <param name="binsize" value="0.1"/>
26216 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
26217 <output name="ctd_out" ftype="xml">
26218 <assert_contents>
26219 <is_valid_xml/>
26220 </assert_contents>
26221 </output>
26222 </test>
26223 <test expect_num_outputs="4">
26224 <conditional name="adv_opts_cond">
26225 <param name="adv_opts_selector" value="advanced"/>
26226 <param name="force" value="false"/>
26227 <param name="test" value="true"/>
26228 </conditional>
26229 <param name="in" value="XFDR_test_in2.xquest.xml"/>
26230 <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26231 <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
26232 <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
26233 <param name="decoy_string" value="DECOY_"/>
26234 <param name="minborder" value="-50.0"/>
26235 <param name="maxborder" value="50.0"/>
26236 <param name="mindeltas" value="0.0"/>
26237 <param name="minionsmatched" value="0"/>
26238 <param name="uniquexl" value="true"/>
26239 <param name="no_qvalues" value="false"/>
26240 <param name="minscore" value="0.0"/>
26241 <param name="binsize" value="0.1"/>
26242 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
26243 <output name="ctd_out" ftype="xml">
26244 <assert_contents>
26245 <is_valid_xml/>
26246 </assert_contents>
26247 </output>
26248 </test>
26249 </xml>
26250 <xml name="autotest_XMLValidator">
26251 </xml>
26252 <xml name="autotest_XTandemAdapter">
26253 <test expect_num_outputs="2">
26254 <conditional name="adv_opts_cond">
26255 <param name="adv_opts_selector" value="advanced"/>
26256 <param name="force" value="false"/>
26257 <param name="test" value="true"/>
26258 </conditional>
26259 <param name="in" value="spectra.mzML"/>
26260 <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26261 <param name="database" value="proteins.fasta"/>
26262 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
26263 <param name="ignore_adapter_param" value="false"/>
26264 <param name="precursor_mass_tolerance" value="5.0"/>
26265 <param name="fragment_mass_tolerance" value="0.3"/>
26266 <param name="precursor_error_units" value="ppm"/>
26267 <param name="fragment_error_units" value="Da"/>
26268 <param name="max_precursor_charge" value="0"/>
26269 <param name="no_isotope_error" value="false"/>
26270 <param name="fixed_modifications" value=""/>
26271 <param name="variable_modifications" value="Oxidation (M)"/>
26272 <param name="minimum_fragment_mz" value="150.0"/>
26273 <param name="enzyme" value="Trypsin"/>
26274 <param name="missed_cleavages" value="1"/>
26275 <param name="semi_cleavage" value="false"/>
26276 <param name="output_results" value="all"/>
26277 <param name="max_valid_expect" value="0.1"/>
26278 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
26279 <output name="ctd_out" ftype="xml">
26280 <assert_contents>
26281 <is_valid_xml/>
26282 </assert_contents>
26283 </output>
26284 </test>
26285 <test expect_num_outputs="2">
26286 <conditional name="adv_opts_cond">
26287 <param name="adv_opts_selector" value="advanced"/>
26288 <param name="force" value="false"/>
26289 <param name="test" value="true"/>
26290 </conditional>
26291 <param name="in" value="spectra.mzML"/>
26292 <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
26293 <param name="database" value="proteins.fasta"/>
26294 <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
26295 <param name="ignore_adapter_param" value="false"/>
26296 <param name="precursor_mass_tolerance" value="5.0"/>
26297 <param name="fragment_mass_tolerance" value="0.3"/>
26298 <param name="precursor_error_units" value="ppm"/>
26299 <param name="fragment_error_units" value="Da"/>
26300 <param name="max_precursor_charge" value="0"/>
26301 <param name="no_isotope_error" value="false"/>
26302 <param name="fixed_modifications" value=""/>
26303 <param name="variable_modifications" value="Oxidation (M)"/>
26304 <param name="minimum_fragment_mz" value="150.0"/>
26305 <param name="enzyme" value="Trypsin"/>
26306 <param name="missed_cleavages" value="1"/>
26307 <param name="semi_cleavage" value="false"/>
26308 <param name="output_results" value="valid"/>
26309 <param name="max_valid_expect" value="1e-14"/>
26310 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
26311 <output name="ctd_out" ftype="xml">
26312 <assert_contents>
26313 <is_valid_xml/>
26314 </assert_contents>
26315 </output>
26316 </test>
26317 </xml>
26318 <xml name="autotest_IDDecoyProbability"/><xml name="autotest_PTPredict"/><xml name="autotest_OpenSwathDIAPreScoring"/><xml name="autotest_Digestor"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_InspectAdapter"/><xml name="autotest_DigestorMotif"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/></macros>