comparison macros_autotest.xml @ 12:4d189842ebfc draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:03:12 +0000
parents 76adea1e0fde
children
comparison
equal deleted inserted replaced
11:76adea1e0fde 12:4d189842ebfc
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="auto_charge" value="false"/>
162 <param name="ion_tree" value="false"/>
163 <param name="no_recalibration" value="false"/>
164 <param name="most_intense_ms2" value="false"/>
165 </section>
166 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
167 <output name="ctd_out" ftype="xml">
168 <assert_contents>
169 <is_valid_xml/>
170 </assert_contents>
171 </output>
172 </test>
173 <test expect_num_outputs="2">
174 <conditional name="adv_opts_cond">
175 <param name="adv_opts_selector" value="advanced"/>
176 <param name="precursor_recalibration_window" value="0.1"/>
177 <param name="precursor_recalibration_window_unit" value="Da"/>
178 <param name="min_fragment_mz" value="0.0"/>
179 <param name="max_fragment_mz" value="2000.0"/>
180 <param name="force" value="false"/>
181 <param name="test" value="true"/>
182 </conditional>
183 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
184 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
185 <param name="out_type" value="tsv"/>
186 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
187 <param name="fragment_annotation" value="none"/>
188 <param name="method" value="highest_intensity"/>
189 <param name="use_exact_mass" value="false"/>
190 <param name="exclude_ms2_precursor" value="false"/>
191 <param name="precursor_mz_distance" value="0.0001"/>
192 <param name="precursor_rt_tolerance" value="5.0"/>
193 <param name="use_known_unknowns" value="false"/>
194 <param name="min_transitions" value="1"/>
195 <param name="max_transitions" value="3"/>
196 <param name="cosine_similarity_threshold" value="0.98"/>
197 <param name="transition_threshold" value="5.0"/>
198 <param name="out_workspace_directory" value=""/>
199 <section name="deisotoping">
200 <param name="use_deisotoper" value="false"/>
201 <param name="fragment_tolerance" value="1.0"/>
202 <param name="fragment_unit" value="ppm"/>
203 <param name="min_charge" value="1"/>
204 <param name="max_charge" value="1"/>
205 <param name="min_isopeaks" value="2"/>
206 <param name="max_isopeaks" value="3"/>
207 <param name="keep_only_deisotoped" value="false"/>
208 <param name="annotate_charge" value="false"/>
209 </section>
210 <section name="preprocessing">
211 <param name="filter_by_num_masstraces" value="1"/>
212 <param name="precursor_mz_tolerance" value="0.005"/>
213 <param name="precursor_mz_tolerance_unit" value="Da"/>
214 <param name="precursor_rt_tolerance" value="5"/>
215 <param name="isotope_pattern_iterations" value="3"/>
216 <param name="feature_only" value="false"/>
217 <param name="no_masstrace_info_isotope_pattern" value="false"/>
218 </section>
219 <section name="sirius">
220 <param name="profile" value="qtof"/>
221 <param name="candidates" value="5"/>
222 <param name="database" value="all"/>
223 <param name="noise" value="0"/>
224 <param name="ppm_max" value="10"/>
225 <param name="isotope" value="both"/>
226 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
227 <param name="compound_timeout" value="10"/>
228 <param name="tree_timeout" value="0"/>
229 <param name="top_n_hits" value="10"/>
230 <param name="auto_charge" value="false"/>
231 <param name="ion_tree" value="false"/>
232 <param name="no_recalibration" value="false"/>
233 <param name="most_intense_ms2" value="false"/>
234 </section>
235 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
236 <output name="ctd_out" ftype="xml">
237 <assert_contents>
238 <is_valid_xml/>
239 </assert_contents>
240 </output>
241 </test>
242 <test expect_num_outputs="2">
243 <conditional name="adv_opts_cond">
244 <param name="adv_opts_selector" value="advanced"/>
245 <param name="precursor_recalibration_window" value="0.1"/>
246 <param name="precursor_recalibration_window_unit" value="Da"/>
247 <param name="min_fragment_mz" value="0.0"/>
248 <param name="max_fragment_mz" value="2000.0"/>
249 <param name="force" value="false"/>
250 <param name="test" value="true"/>
251 </conditional>
252 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
253 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
254 <param name="out_type" value="tsv"/>
255 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
256 <param name="fragment_annotation" value="none"/>
257 <param name="method" value="consensus_spectrum"/>
258 <param name="use_exact_mass" value="false"/>
259 <param name="exclude_ms2_precursor" value="false"/>
260 <param name="precursor_mz_distance" value="0.0001"/>
261 <param name="precursor_rt_tolerance" value="5.0"/>
262 <param name="use_known_unknowns" value="false"/>
263 <param name="min_transitions" value="1"/>
264 <param name="max_transitions" value="3"/>
265 <param name="cosine_similarity_threshold" value="0.98"/>
266 <param name="transition_threshold" value="5.0"/>
267 <param name="out_workspace_directory" value=""/>
268 <section name="deisotoping">
269 <param name="use_deisotoper" value="false"/>
270 <param name="fragment_tolerance" value="1.0"/>
271 <param name="fragment_unit" value="ppm"/>
272 <param name="min_charge" value="1"/>
273 <param name="max_charge" value="1"/>
274 <param name="min_isopeaks" value="2"/>
275 <param name="max_isopeaks" value="3"/>
276 <param name="keep_only_deisotoped" value="false"/>
277 <param name="annotate_charge" value="false"/>
278 </section>
279 <section name="preprocessing">
280 <param name="filter_by_num_masstraces" value="1"/>
281 <param name="precursor_mz_tolerance" value="0.005"/>
282 <param name="precursor_mz_tolerance_unit" value="Da"/>
283 <param name="precursor_rt_tolerance" value="5"/>
284 <param name="isotope_pattern_iterations" value="3"/>
285 <param name="feature_only" value="false"/>
286 <param name="no_masstrace_info_isotope_pattern" value="false"/>
287 </section>
288 <section name="sirius">
289 <param name="profile" value="qtof"/>
290 <param name="candidates" value="5"/>
291 <param name="database" value="all"/>
292 <param name="noise" value="0"/>
293 <param name="ppm_max" value="10"/>
294 <param name="isotope" value="both"/>
295 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
296 <param name="compound_timeout" value="10"/>
297 <param name="tree_timeout" value="0"/>
298 <param name="top_n_hits" value="10"/>
299 <param name="auto_charge" value="false"/>
300 <param name="ion_tree" value="false"/>
301 <param name="no_recalibration" value="false"/>
302 <param name="most_intense_ms2" value="false"/>
303 </section>
304 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
305 <output name="ctd_out" ftype="xml">
306 <assert_contents>
307 <is_valid_xml/>
308 </assert_contents>
309 </output>
310 </test>
311 <test expect_num_outputs="2">
312 <conditional name="adv_opts_cond">
313 <param name="adv_opts_selector" value="advanced"/>
314 <param name="precursor_recalibration_window" value="0.1"/>
315 <param name="precursor_recalibration_window_unit" value="Da"/>
316 <param name="min_fragment_mz" value="0.0"/>
317 <param name="max_fragment_mz" value="2000.0"/>
318 <param name="force" value="false"/>
319 <param name="test" value="true"/>
320 </conditional>
321 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
322 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
323 <param name="out_type" value="tsv"/>
324 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
325 <param name="fragment_annotation" value="none"/>
326 <param name="method" value="consensus_spectrum"/>
327 <param name="use_exact_mass" value="false"/>
328 <param name="exclude_ms2_precursor" value="false"/>
329 <param name="precursor_mz_distance" value="0.0001"/>
330 <param name="precursor_rt_tolerance" value="5.0"/>
331 <param name="use_known_unknowns" value="false"/>
332 <param name="min_transitions" value="1"/>
333 <param name="max_transitions" value="3"/>
334 <param name="cosine_similarity_threshold" value="0.98"/>
335 <param name="transition_threshold" value="5.0"/>
336 <param name="out_workspace_directory" value=""/>
337 <section name="deisotoping">
338 <param name="use_deisotoper" value="false"/>
339 <param name="fragment_tolerance" value="1.0"/>
340 <param name="fragment_unit" value="ppm"/>
341 <param name="min_charge" value="1"/>
342 <param name="max_charge" value="1"/>
343 <param name="min_isopeaks" value="2"/>
344 <param name="max_isopeaks" value="3"/>
345 <param name="keep_only_deisotoped" value="false"/>
346 <param name="annotate_charge" value="false"/>
347 </section>
348 <section name="preprocessing">
349 <param name="filter_by_num_masstraces" value="1"/>
350 <param name="precursor_mz_tolerance" value="0.005"/>
351 <param name="precursor_mz_tolerance_unit" value="Da"/>
352 <param name="precursor_rt_tolerance" value="5"/>
353 <param name="isotope_pattern_iterations" value="3"/>
354 <param name="feature_only" value="false"/>
355 <param name="no_masstrace_info_isotope_pattern" value="false"/>
356 </section>
357 <section name="sirius">
358 <param name="profile" value="qtof"/>
359 <param name="candidates" value="5"/>
360 <param name="database" value="all"/>
361 <param name="noise" value="0"/>
362 <param name="ppm_max" value="10"/>
363 <param name="isotope" value="both"/>
364 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
365 <param name="compound_timeout" value="10"/>
366 <param name="tree_timeout" value="0"/>
367 <param name="top_n_hits" value="10"/>
368 <param name="auto_charge" value="false"/>
369 <param name="ion_tree" value="false"/>
370 <param name="no_recalibration" value="false"/>
371 <param name="most_intense_ms2" value="false"/>
372 </section>
373 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
374 <output name="ctd_out" ftype="xml">
375 <assert_contents>
376 <is_valid_xml/>
377 </assert_contents>
378 </output>
379 </test>
380 <test expect_num_outputs="2">
381 <conditional name="adv_opts_cond">
382 <param name="adv_opts_selector" value="advanced"/>
383 <param name="precursor_recalibration_window" value="0.1"/>
384 <param name="precursor_recalibration_window_unit" value="Da"/>
385 <param name="min_fragment_mz" value="0.0"/>
386 <param name="max_fragment_mz" value="2000.0"/>
387 <param name="force" value="false"/>
388 <param name="test" value="true"/>
389 </conditional>
390 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
391 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
392 <param name="out_type" value="tsv"/>
393 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
394 <param name="fragment_annotation" value="none"/>
395 <param name="method" value="consensus_spectrum"/>
396 <param name="use_exact_mass" value="false"/>
397 <param name="exclude_ms2_precursor" value="false"/>
398 <param name="precursor_mz_distance" value="0.0001"/>
399 <param name="precursor_rt_tolerance" value="5.0"/>
400 <param name="use_known_unknowns" value="true"/>
401 <param name="min_transitions" value="1"/>
402 <param name="max_transitions" value="3"/>
403 <param name="cosine_similarity_threshold" value="0.98"/>
404 <param name="transition_threshold" value="5.0"/>
405 <param name="out_workspace_directory" value=""/>
406 <section name="deisotoping">
407 <param name="use_deisotoper" value="false"/>
408 <param name="fragment_tolerance" value="1.0"/>
409 <param name="fragment_unit" value="ppm"/>
410 <param name="min_charge" value="1"/>
411 <param name="max_charge" value="1"/>
412 <param name="min_isopeaks" value="2"/>
413 <param name="max_isopeaks" value="3"/>
414 <param name="keep_only_deisotoped" value="false"/>
415 <param name="annotate_charge" value="false"/>
416 </section>
417 <section name="preprocessing">
418 <param name="filter_by_num_masstraces" value="1"/>
419 <param name="precursor_mz_tolerance" value="0.005"/>
420 <param name="precursor_mz_tolerance_unit" value="Da"/>
421 <param name="precursor_rt_tolerance" value="5"/>
422 <param name="isotope_pattern_iterations" value="3"/>
423 <param name="feature_only" value="false"/>
424 <param name="no_masstrace_info_isotope_pattern" value="false"/>
425 </section>
426 <section name="sirius">
427 <param name="profile" value="qtof"/>
428 <param name="candidates" value="5"/>
429 <param name="database" value="all"/>
430 <param name="noise" value="0"/>
431 <param name="ppm_max" value="10"/>
432 <param name="isotope" value="both"/>
433 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
434 <param name="compound_timeout" value="10"/>
435 <param name="tree_timeout" value="0"/>
436 <param name="top_n_hits" value="10"/>
437 <param name="auto_charge" value="false"/>
438 <param name="ion_tree" value="false"/>
439 <param name="no_recalibration" value="false"/>
440 <param name="most_intense_ms2" value="false"/>
441 </section>
442 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
443 <output name="ctd_out" ftype="xml">
444 <assert_contents>
445 <is_valid_xml/>
446 </assert_contents>
447 </output>
448 </test>
449 <test expect_num_outputs="2">
450 <conditional name="adv_opts_cond">
451 <param name="adv_opts_selector" value="advanced"/>
452 <param name="precursor_recalibration_window" value="0.1"/>
453 <param name="precursor_recalibration_window_unit" value="Da"/>
454 <param name="min_fragment_mz" value="0.0"/>
455 <param name="max_fragment_mz" value="2000.0"/>
456 <param name="force" value="false"/>
457 <param name="test" value="true"/>
458 </conditional>
459 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
460 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
461 <param name="out_type" value="tsv"/>
462 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
463 <param name="fragment_annotation" value="sirius"/>
464 <param name="method" value="highest_intensity"/>
465 <param name="use_exact_mass" value="true"/>
466 <param name="exclude_ms2_precursor" value="false"/>
467 <param name="precursor_mz_distance" value="0.0001"/>
468 <param name="precursor_rt_tolerance" value="5.0"/>
469 <param name="use_known_unknowns" value="false"/>
470 <param name="min_transitions" value="2"/>
471 <param name="max_transitions" value="3"/>
472 <param name="cosine_similarity_threshold" value="0.98"/>
473 <param name="transition_threshold" value="3.0"/>
474 <param name="out_workspace_directory" value=""/>
475 <section name="deisotoping">
476 <param name="use_deisotoper" value="false"/>
477 <param name="fragment_tolerance" value="1.0"/>
478 <param name="fragment_unit" value="ppm"/>
479 <param name="min_charge" value="1"/>
480 <param name="max_charge" value="1"/>
481 <param name="min_isopeaks" value="2"/>
482 <param name="max_isopeaks" value="3"/>
483 <param name="keep_only_deisotoped" value="false"/>
484 <param name="annotate_charge" value="false"/>
485 </section>
486 <section name="preprocessing">
487 <param name="filter_by_num_masstraces" value="1"/>
488 <param name="precursor_mz_tolerance" value="10.0"/>
489 <param name="precursor_mz_tolerance_unit" value="ppm"/>
490 <param name="precursor_rt_tolerance" value="5"/>
491 <param name="isotope_pattern_iterations" value="3"/>
492 <param name="feature_only" value="true"/>
493 <param name="no_masstrace_info_isotope_pattern" value="false"/>
494 </section>
495 <section name="sirius">
496 <param name="profile" value="qtof"/>
497 <param name="candidates" value="5"/>
498 <param name="database" value="all"/>
499 <param name="noise" value="0"/>
500 <param name="ppm_max" value="10"/>
501 <param name="isotope" value="both"/>
502 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
503 <param name="compound_timeout" value="100"/>
504 <param name="tree_timeout" value="0"/>
505 <param name="top_n_hits" value="10"/>
506 <param name="auto_charge" value="false"/>
507 <param name="ion_tree" value="false"/>
508 <param name="no_recalibration" value="false"/>
509 <param name="most_intense_ms2" value="false"/>
510 </section>
511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
512 <output name="ctd_out" ftype="xml">
513 <assert_contents>
514 <is_valid_xml/>
515 </assert_contents>
516 </output>
517 </test>
518 <test expect_num_outputs="2">
519 <conditional name="adv_opts_cond">
520 <param name="adv_opts_selector" value="advanced"/>
521 <param name="precursor_recalibration_window" value="0.1"/>
522 <param name="precursor_recalibration_window_unit" value="Da"/>
523 <param name="min_fragment_mz" value="0.0"/>
524 <param name="max_fragment_mz" value="2000.0"/>
525 <param name="force" value="false"/>
526 <param name="test" value="true"/>
527 </conditional>
528 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
529 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
530 <param name="out_type" value="tsv"/>
531 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
532 <param name="fragment_annotation" value="sirius"/>
533 <param name="method" value="highest_intensity"/>
534 <param name="use_exact_mass" value="true"/>
535 <param name="exclude_ms2_precursor" value="false"/>
536 <param name="precursor_mz_distance" value="0.0001"/>
537 <param name="precursor_rt_tolerance" value="5.0"/>
538 <param name="use_known_unknowns" value="true"/>
539 <param name="min_transitions" value="2"/>
540 <param name="max_transitions" value="3"/>
541 <param name="cosine_similarity_threshold" value="0.98"/>
542 <param name="transition_threshold" value="3.0"/>
543 <param name="out_workspace_directory" value=""/>
544 <section name="deisotoping">
545 <param name="use_deisotoper" value="false"/>
546 <param name="fragment_tolerance" value="1.0"/>
547 <param name="fragment_unit" value="ppm"/>
548 <param name="min_charge" value="1"/>
549 <param name="max_charge" value="1"/>
550 <param name="min_isopeaks" value="2"/>
551 <param name="max_isopeaks" value="3"/>
552 <param name="keep_only_deisotoped" value="false"/>
553 <param name="annotate_charge" value="false"/>
554 </section>
555 <section name="preprocessing">
556 <param name="filter_by_num_masstraces" value="1"/>
557 <param name="precursor_mz_tolerance" value="10.0"/>
558 <param name="precursor_mz_tolerance_unit" value="ppm"/>
559 <param name="precursor_rt_tolerance" value="5"/>
560 <param name="isotope_pattern_iterations" value="3"/>
561 <param name="feature_only" value="true"/>
562 <param name="no_masstrace_info_isotope_pattern" value="false"/>
563 </section>
564 <section name="sirius">
565 <param name="profile" value="qtof"/>
566 <param name="candidates" value="5"/>
567 <param name="database" value="all"/>
568 <param name="noise" value="0"/>
569 <param name="ppm_max" value="10"/>
570 <param name="isotope" value="both"/>
571 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
572 <param name="compound_timeout" value="100"/>
573 <param name="tree_timeout" value="0"/>
574 <param name="top_n_hits" value="10"/>
575 <param name="auto_charge" value="false"/>
576 <param name="ion_tree" value="false"/>
577 <param name="no_recalibration" value="false"/>
578 <param name="most_intense_ms2" value="false"/>
579 </section>
580 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
581 <output name="ctd_out" ftype="xml">
582 <assert_contents>
583 <is_valid_xml/>
584 </assert_contents>
585 </output>
586 </test>
587 <test expect_num_outputs="2">
588 <conditional name="adv_opts_cond">
589 <param name="adv_opts_selector" value="advanced"/>
590 <param name="precursor_recalibration_window" value="0.1"/>
591 <param name="precursor_recalibration_window_unit" value="Da"/>
592 <param name="min_fragment_mz" value="0.0"/>
593 <param name="max_fragment_mz" value="2000.0"/>
594 <param name="force" value="false"/>
595 <param name="test" value="true"/>
596 </conditional>
597 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
598 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
599 <param name="out_type" value="tsv"/>
600 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
601 <param name="fragment_annotation" value="sirius"/>
602 <param name="method" value="highest_intensity"/>
603 <param name="use_exact_mass" value="true"/>
604 <param name="exclude_ms2_precursor" value="false"/>
605 <param name="precursor_mz_distance" value="0.0001"/>
606 <param name="precursor_rt_tolerance" value="5.0"/>
607 <param name="use_known_unknowns" value="false"/>
608 <param name="min_transitions" value="2"/>
609 <param name="max_transitions" value="3"/>
610 <param name="cosine_similarity_threshold" value="0.98"/>
611 <param name="transition_threshold" value="3.0"/>
612 <param name="out_workspace_directory" value=""/>
613 <section name="deisotoping">
614 <param name="use_deisotoper" value="false"/>
615 <param name="fragment_tolerance" value="1.0"/>
616 <param name="fragment_unit" value="ppm"/>
617 <param name="min_charge" value="1"/>
618 <param name="max_charge" value="1"/>
619 <param name="min_isopeaks" value="2"/>
620 <param name="max_isopeaks" value="3"/>
621 <param name="keep_only_deisotoped" value="false"/>
622 <param name="annotate_charge" value="false"/>
623 </section>
624 <section name="preprocessing">
625 <param name="filter_by_num_masstraces" value="1"/>
626 <param name="precursor_mz_tolerance" value="10.0"/>
627 <param name="precursor_mz_tolerance_unit" value="ppm"/>
628 <param name="precursor_rt_tolerance" value="5"/>
629 <param name="isotope_pattern_iterations" value="3"/>
630 <param name="feature_only" value="true"/>
631 <param name="no_masstrace_info_isotope_pattern" value="false"/>
632 </section>
633 <section name="sirius">
634 <param name="profile" value="qtof"/>
635 <param name="candidates" value="5"/>
636 <param name="database" value="all"/>
637 <param name="noise" value="0"/>
638 <param name="ppm_max" value="10"/>
639 <param name="isotope" value="both"/>
640 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
641 <param name="compound_timeout" value="100"/>
642 <param name="tree_timeout" value="0"/>
643 <param name="top_n_hits" value="10"/>
644 <param name="auto_charge" value="false"/>
645 <param name="ion_tree" value="false"/>
646 <param name="no_recalibration" value="false"/>
647 <param name="most_intense_ms2" value="false"/>
648 </section>
649 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
650 <output name="ctd_out" ftype="xml">
651 <assert_contents>
652 <is_valid_xml/>
653 </assert_contents>
654 </output>
655 </test>
656 <test expect_num_outputs="2">
657 <conditional name="adv_opts_cond">
658 <param name="adv_opts_selector" value="advanced"/>
659 <param name="precursor_recalibration_window" value="0.1"/>
660 <param name="precursor_recalibration_window_unit" value="Da"/>
661 <param name="min_fragment_mz" value="100.0"/>
662 <param name="max_fragment_mz" value="900.0"/>
663 <param name="force" value="false"/>
664 <param name="test" value="true"/>
665 </conditional>
666 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
667 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
668 <param name="out_type" value="tsv"/>
669 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
670 <param name="fragment_annotation" value="sirius"/>
671 <param name="method" value="highest_intensity"/>
672 <param name="use_exact_mass" value="true"/>
673 <param name="exclude_ms2_precursor" value="false"/>
674 <param name="precursor_mz_distance" value="0.0001"/>
675 <param name="precursor_rt_tolerance" value="5.0"/>
676 <param name="use_known_unknowns" value="false"/>
677 <param name="min_transitions" value="2"/>
678 <param name="max_transitions" value="3"/>
679 <param name="cosine_similarity_threshold" value="0.98"/>
680 <param name="transition_threshold" value="3.0"/>
681 <param name="out_workspace_directory" value=""/>
682 <section name="deisotoping">
683 <param name="use_deisotoper" value="false"/>
684 <param name="fragment_tolerance" value="1.0"/>
685 <param name="fragment_unit" value="ppm"/>
686 <param name="min_charge" value="1"/>
687 <param name="max_charge" value="1"/>
688 <param name="min_isopeaks" value="2"/>
689 <param name="max_isopeaks" value="3"/>
690 <param name="keep_only_deisotoped" value="false"/>
691 <param name="annotate_charge" value="false"/>
692 </section>
693 <section name="preprocessing">
694 <param name="filter_by_num_masstraces" value="1"/>
695 <param name="precursor_mz_tolerance" value="10.0"/>
696 <param name="precursor_mz_tolerance_unit" value="ppm"/>
697 <param name="precursor_rt_tolerance" value="5"/>
698 <param name="isotope_pattern_iterations" value="3"/>
699 <param name="feature_only" value="true"/>
700 <param name="no_masstrace_info_isotope_pattern" value="false"/>
701 </section>
702 <section name="sirius">
703 <param name="profile" value="qtof"/>
704 <param name="candidates" value="5"/>
705 <param name="database" value="all"/>
706 <param name="noise" value="0"/>
707 <param name="ppm_max" value="10"/>
708 <param name="isotope" value="both"/>
709 <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
710 <param name="compound_timeout" value="100"/>
711 <param name="tree_timeout" value="0"/>
712 <param name="top_n_hits" value="10"/>
713 <param name="auto_charge" value="false"/>
714 <param name="ion_tree" value="false"/>
715 <param name="no_recalibration" value="false"/>
716 <param name="most_intense_ms2" value="false"/>
717 </section>
718 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
719 <output name="ctd_out" ftype="xml">
720 <assert_contents>
721 <is_valid_xml/>
722 </assert_contents>
723 </output>
724 </test>
725 </xml>
726 <xml name="autotest_BaselineFilter">
727 <test expect_num_outputs="2">
728 <conditional name="adv_opts_cond">
729 <param name="adv_opts_selector" value="advanced"/>
730 <param name="force" value="false"/>
731 <param name="test" value="true"/>
732 </conditional>
733 <param name="in" value="BaselineFilter_input.mzML"/>
734 <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
735 <param name="struc_elem_length" value="1.5"/>
736 <param name="struc_elem_unit" value="Thomson"/>
737 <param name="method" value="tophat"/>
738 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
739 <output name="ctd_out" ftype="xml">
740 <assert_contents>
741 <is_valid_xml/>
742 </assert_contents>
743 </output>
744 </test>
745 </xml>
746 <xml name="autotest_ClusterMassTracesByPrecursor">
747 </xml>
748 <xml name="autotest_ClusterMassTraces">
749 </xml>
750 <xml name="autotest_CometAdapter">
751 <test expect_num_outputs="3">
752 <conditional name="adv_opts_cond">
753 <param name="adv_opts_selector" value="advanced"/>
754 <param name="use_A_ions" value="false"/>
755 <param name="use_B_ions" value="true"/>
756 <param name="use_C_ions" value="false"/>
757 <param name="use_X_ions" value="false"/>
758 <param name="use_Y_ions" value="true"/>
759 <param name="use_Z_ions" value="false"/>
760 <param name="use_NL_ions" value="false"/>
761 <param name="second_enzyme" value=""/>
762 <param name="digest_mass_range" value="600:5000"/>
763 <param name="max_precursor_charge" value="5"/>
764 <param name="spectrum_batch_size" value="1000"/>
765 <param name="mass_offsets" value="0.0"/>
766 <param name="minimum_peaks" value="10"/>
767 <param name="minimum_intensity" value="0.0"/>
768 <param name="remove_precursor_peak" value="no"/>
769 <param name="remove_precursor_tolerance" value="1.5"/>
770 <param name="clear_mz_range" value="0:0"/>
771 <param name="max_variable_mods_in_peptide" value="5"/>
772 <param name="require_variable_mod" value="false"/>
773 <param name="force" value="true"/>
774 <param name="test" value="true"/>
775 </conditional>
776 <param name="in" value="spectra_comet.mzML"/>
777 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
778 <param name="database" value="proteins.fasta"/>
779 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
780 <param name="precursor_mass_tolerance" value="3.0"/>
781 <param name="precursor_error_units" value="ppm"/>
782 <param name="isotope_error" value="off"/>
783 <param name="fragment_mass_tolerance" value="0.50025"/>
784 <param name="fragment_error_units" value="Da"/>
785 <param name="fragment_bin_offset" value="0.25"/>
786 <param name="instrument" value="high_res"/>
787 <param name="enzyme" value="Trypsin"/>
788 <param name="num_enzyme_termini" value="fully"/>
789 <param name="missed_cleavages" value="1"/>
790 <param name="min_peptide_length" value="5"/>
791 <param name="max_peptide_length" value="63"/>
792 <param name="num_hits" value="5"/>
793 <param name="precursor_charge" value="0:0"/>
794 <param name="override_charge" value="keep any known"/>
795 <param name="ms_level" value="2"/>
796 <param name="activation_method" value="ALL"/>
797 <param name="max_fragment_charge" value="3"/>
798 <param name="clip_nterm_methionine" value="false"/>
799 <param name="fixed_modifications" value=""/>
800 <param name="variable_modifications" value=""/>
801 <param name="binary_modifications" value=""/>
802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
803 <output name="ctd_out" ftype="xml">
804 <assert_contents>
805 <is_valid_xml/>
806 </assert_contents>
807 </output>
808 </test>
809 <test expect_num_outputs="3">
810 <conditional name="adv_opts_cond">
811 <param name="adv_opts_selector" value="advanced"/>
812 <param name="use_A_ions" value="false"/>
813 <param name="use_B_ions" value="true"/>
814 <param name="use_C_ions" value="false"/>
815 <param name="use_X_ions" value="false"/>
816 <param name="use_Y_ions" value="true"/>
817 <param name="use_Z_ions" value="false"/>
818 <param name="use_NL_ions" value="false"/>
819 <param name="second_enzyme" value=""/>
820 <param name="digest_mass_range" value="600:5000"/>
821 <param name="max_precursor_charge" value="5"/>
822 <param name="spectrum_batch_size" value="1000"/>
823 <param name="mass_offsets" value="0.0"/>
824 <param name="minimum_peaks" value="10"/>
825 <param name="minimum_intensity" value="0.0"/>
826 <param name="remove_precursor_peak" value="no"/>
827 <param name="remove_precursor_tolerance" value="1.5"/>
828 <param name="clear_mz_range" value="0:0"/>
829 <param name="max_variable_mods_in_peptide" value="5"/>
830 <param name="require_variable_mod" value="false"/>
831 <param name="force" value="true"/>
832 <param name="test" value="true"/>
833 </conditional>
834 <param name="in" value="CometAdapter_2_prepared.mzML"/>
835 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
836 <param name="database" value="CometAdapter_2_in.fasta"/>
837 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
838 <param name="precursor_mass_tolerance" value="3.0"/>
839 <param name="precursor_error_units" value="Da"/>
840 <param name="isotope_error" value="off"/>
841 <param name="fragment_mass_tolerance" value="0.50025"/>
842 <param name="fragment_error_units" value="Da"/>
843 <param name="fragment_bin_offset" value="0.25"/>
844 <param name="instrument" value="high_res"/>
845 <param name="enzyme" value="Trypsin"/>
846 <param name="num_enzyme_termini" value="fully"/>
847 <param name="missed_cleavages" value="1"/>
848 <param name="min_peptide_length" value="5"/>
849 <param name="max_peptide_length" value="63"/>
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="binary_modifications" value=""/>
860 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
861 <output name="ctd_out" ftype="xml">
862 <assert_contents>
863 <is_valid_xml/>
864 </assert_contents>
865 </output>
866 </test>
867 <test expect_num_outputs="3">
868 <conditional name="adv_opts_cond">
869 <param name="adv_opts_selector" value="advanced"/>
870 <param name="use_A_ions" value="false"/>
871 <param name="use_B_ions" value="true"/>
872 <param name="use_C_ions" value="false"/>
873 <param name="use_X_ions" value="false"/>
874 <param name="use_Y_ions" value="true"/>
875 <param name="use_Z_ions" value="false"/>
876 <param name="use_NL_ions" value="false"/>
877 <param name="second_enzyme" value=""/>
878 <param name="digest_mass_range" value="600:5000"/>
879 <param name="max_precursor_charge" value="5"/>
880 <param name="spectrum_batch_size" value="20000"/>
881 <param name="mass_offsets" value="0.0"/>
882 <param name="minimum_peaks" value="10"/>
883 <param name="minimum_intensity" value="0.0"/>
884 <param name="remove_precursor_peak" value="no"/>
885 <param name="remove_precursor_tolerance" value="1.5"/>
886 <param name="clear_mz_range" value="0:0"/>
887 <param name="max_variable_mods_in_peptide" value="3"/>
888 <param name="require_variable_mod" value="false"/>
889 <param name="force" value="false"/>
890 <param name="test" value="true"/>
891 </conditional>
892 <param name="in" value="CometAdapter_3.mzML"/>
893 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
894 <param name="database" value="CometAdapter_3.fasta"/>
895 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
896 <param name="precursor_mass_tolerance" value="5.0"/>
897 <param name="precursor_error_units" value="ppm"/>
898 <param name="isotope_error" value="off"/>
899 <param name="fragment_mass_tolerance" value="0.01"/>
900 <param name="fragment_error_units" value="Da"/>
901 <param name="fragment_bin_offset" value="0.0"/>
902 <param name="instrument" value="high_res"/>
903 <param name="enzyme" value="Trypsin"/>
904 <param name="num_enzyme_termini" value="fully"/>
905 <param name="missed_cleavages" value="3"/>
906 <param name="min_peptide_length" value="5"/>
907 <param name="max_peptide_length" value="63"/>
908 <param name="num_hits" value="5"/>
909 <param name="precursor_charge" value="0:0"/>
910 <param name="override_charge" value="keep known search unknown"/>
911 <param name="ms_level" value="2"/>
912 <param name="activation_method" value="ALL"/>
913 <param name="max_fragment_charge" value="3"/>
914 <param name="clip_nterm_methionine" value="false"/>
915 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
916 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
917 <param name="binary_modifications" value=""/>
918 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
919 <output name="ctd_out" ftype="xml">
920 <assert_contents>
921 <is_valid_xml/>
922 </assert_contents>
923 </output>
924 </test>
925 <test expect_num_outputs="2">
926 <conditional name="adv_opts_cond">
927 <param name="adv_opts_selector" value="advanced"/>
928 <param name="use_A_ions" value="false"/>
929 <param name="use_B_ions" value="true"/>
930 <param name="use_C_ions" value="false"/>
931 <param name="use_X_ions" value="false"/>
932 <param name="use_Y_ions" value="true"/>
933 <param name="use_Z_ions" value="false"/>
934 <param name="use_NL_ions" value="false"/>
935 <param name="second_enzyme" value=""/>
936 <param name="digest_mass_range" value="600:1200"/>
937 <param name="max_precursor_charge" value="5"/>
938 <param name="spectrum_batch_size" value="20000"/>
939 <param name="mass_offsets" value="0.0"/>
940 <param name="minimum_peaks" value="10"/>
941 <param name="minimum_intensity" value="0.0"/>
942 <param name="remove_precursor_peak" value="no"/>
943 <param name="remove_precursor_tolerance" value="1.5"/>
944 <param name="clear_mz_range" value="0:0"/>
945 <param name="max_variable_mods_in_peptide" value="3"/>
946 <param name="require_variable_mod" value="false"/>
947 <param name="force" value="false"/>
948 <param name="test" value="true"/>
949 </conditional>
950 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
951 <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
952 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
953 <param name="precursor_mass_tolerance" value="5.0"/>
954 <param name="precursor_error_units" value="ppm"/>
955 <param name="isotope_error" value="off"/>
956 <param name="fragment_mass_tolerance" value="0.01"/>
957 <param name="fragment_error_units" value="Da"/>
958 <param name="fragment_bin_offset" value="0.0"/>
959 <param name="instrument" value="high_res"/>
960 <param name="enzyme" value="Trypsin"/>
961 <param name="num_enzyme_termini" value="fully"/>
962 <param name="missed_cleavages" value="3"/>
963 <param name="min_peptide_length" value="5"/>
964 <param name="max_peptide_length" value="63"/>
965 <param name="num_hits" value="5"/>
966 <param name="precursor_charge" value="0:0"/>
967 <param name="override_charge" value="keep known search unknown"/>
968 <param name="ms_level" value="2"/>
969 <param name="activation_method" value="ALL"/>
970 <param name="max_fragment_charge" value="3"/>
971 <param name="clip_nterm_methionine" value="false"/>
972 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
973 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
974 <param name="binary_modifications" value=""/>
975 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
976 <output name="ctd_out" ftype="xml">
977 <assert_contents>
978 <is_valid_xml/>
979 </assert_contents>
980 </output>
981 </test>
982 </xml>
983 <xml name="autotest_CompNovoCID">
984 <test expect_num_outputs="2">
985 <conditional name="adv_opts_cond">
986 <param name="adv_opts_selector" value="advanced"/>
987 <param name="force" value="false"/>
988 <param name="test" value="true"/>
989 </conditional>
990 <param name="in" value="CompNovoCID_1_input.mzML"/>
991 <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
992 <section name="algorithm">
993 <param name="max_number_aa_per_decomp" value="4"/>
994 <param name="tryptic_only" value="true"/>
995 <param name="precursor_mass_tolerance" value="0.3"/>
996 <param name="fragment_mass_tolerance" value="0.3"/>
997 <param name="max_number_pivot" value="9"/>
998 <param name="max_subscore_number" value="40"/>
999 <param name="decomp_weights_precision" value="0.01"/>
1000 <param name="double_charged_iso_threshold" value="0.6"/>
1001 <param name="max_mz" value="2000.0"/>
1002 <param name="min_mz" value="200.0"/>
1003 <param name="max_isotope_to_score" value="3"/>
1004 <param name="max_decomp_weight" value="450.0"/>
1005 <param name="max_isotope" value="3"/>
1006 <param name="missed_cleavages" value="1"/>
1007 <param name="number_of_hits" value="1"/>
1008 <param name="estimate_precursor_mz" value="true"/>
1009 <param name="number_of_prescoring_hits" value="250"/>
1010 <param name="fixed_modifications" value=""/>
1011 <param name="variable_modifications" value=""/>
1012 <param name="residue_set" value="Natural19WithoutI"/>
1013 </section>
1014 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1015 <output name="ctd_out" ftype="xml">
1016 <assert_contents>
1017 <is_valid_xml/>
1018 </assert_contents>
1019 </output>
1020 </test>
1021 </xml>
1022 <xml name="autotest_CompNovo">
1023 <test expect_num_outputs="2">
1024 <conditional name="adv_opts_cond">
1025 <param name="adv_opts_selector" value="advanced"/>
1026 <param name="force" value="false"/>
1027 <param name="test" value="true"/>
1028 </conditional>
1029 <param name="in" value="CompNovo_1_input.mzML"/>
1030 <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1031 <section name="algorithm">
1032 <param name="max_number_aa_per_decomp" value="4"/>
1033 <param name="tryptic_only" value="true"/>
1034 <param name="precursor_mass_tolerance" value="0.3"/>
1035 <param name="fragment_mass_tolerance" value="0.3"/>
1036 <param name="max_number_pivot" value="9"/>
1037 <param name="max_subscore_number" value="40"/>
1038 <param name="decomp_weights_precision" value="0.01"/>
1039 <param name="double_charged_iso_threshold" value="0.6"/>
1040 <param name="max_mz" value="2000.0"/>
1041 <param name="min_mz" value="200.0"/>
1042 <param name="max_isotope_to_score" value="3"/>
1043 <param name="max_decomp_weight" value="450.0"/>
1044 <param name="max_isotope" value="3"/>
1045 <param name="missed_cleavages" value="1"/>
1046 <param name="number_of_hits" value="1"/>
1047 <param name="estimate_precursor_mz" value="true"/>
1048 <param name="number_of_prescoring_hits" value="250"/>
1049 <param name="fixed_modifications" value=""/>
1050 <param name="variable_modifications" value=""/>
1051 <param name="residue_set" value="Natural19WithoutI"/>
1052 </section>
1053 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1054 <output name="ctd_out" ftype="xml">
1055 <assert_contents>
1056 <is_valid_xml/>
1057 </assert_contents>
1058 </output>
1059 </test>
1060 </xml>
1061 <xml name="autotest_ConsensusID">
1062 <test expect_num_outputs="2">
1063 <conditional name="adv_opts_cond">
1064 <param name="adv_opts_selector" value="advanced"/>
1065 <param name="force" value="false"/>
1066 <param name="test" value="true"/>
1067 </conditional>
1068 <param name="in" value="ConsensusID_1_input.idXML"/>
1069 <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1070 <param name="rt_delta" value="0.1"/>
1071 <param name="mz_delta" value="0.1"/>
1072 <param name="per_spectrum" value="false"/>
1073 <param name="algorithm" value="PEPMatrix"/>
1074 <section name="filter">
1075 <param name="considered_hits" value="0"/>
1076 <param name="min_support" value="0.0"/>
1077 <param name="count_empty" value="false"/>
1078 <param name="keep_old_scores" value="false"/>
1079 </section>
1080 <section name="PEPIons">
1081 <param name="mass_tolerance" value="0.5"/>
1082 <param name="min_shared" value="2"/>
1083 </section>
1084 <section name="PEPMatrix">
1085 <param name="matrix" value="PAM30MS"/>
1086 <param name="penalty" value="5"/>
1087 </section>
1088 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1089 <output name="ctd_out" ftype="xml">
1090 <assert_contents>
1091 <is_valid_xml/>
1092 </assert_contents>
1093 </output>
1094 </test>
1095 <test expect_num_outputs="2">
1096 <conditional name="adv_opts_cond">
1097 <param name="adv_opts_selector" value="advanced"/>
1098 <param name="force" value="false"/>
1099 <param name="test" value="true"/>
1100 </conditional>
1101 <param name="in" value="ConsensusID_2_input.featureXML"/>
1102 <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
1103 <param name="rt_delta" value="0.1"/>
1104 <param name="mz_delta" value="0.1"/>
1105 <param name="per_spectrum" value="false"/>
1106 <param name="algorithm" value="average"/>
1107 <section name="filter">
1108 <param name="considered_hits" value="0"/>
1109 <param name="min_support" value="0.0"/>
1110 <param name="count_empty" value="false"/>
1111 <param name="keep_old_scores" value="false"/>
1112 </section>
1113 <section name="PEPIons">
1114 <param name="mass_tolerance" value="0.5"/>
1115 <param name="min_shared" value="2"/>
1116 </section>
1117 <section name="PEPMatrix">
1118 <param name="matrix" value="identity"/>
1119 <param name="penalty" value="5"/>
1120 </section>
1121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1122 <output name="ctd_out" ftype="xml">
1123 <assert_contents>
1124 <is_valid_xml/>
1125 </assert_contents>
1126 </output>
1127 </test>
1128 <test expect_num_outputs="2">
1129 <conditional name="adv_opts_cond">
1130 <param name="adv_opts_selector" value="advanced"/>
1131 <param name="force" value="false"/>
1132 <param name="test" value="true"/>
1133 </conditional>
1134 <param name="in" value="ConsensusID_3_input.consensusXML"/>
1135 <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1136 <param name="rt_delta" value="0.1"/>
1137 <param name="mz_delta" value="0.1"/>
1138 <param name="per_spectrum" value="false"/>
1139 <param name="algorithm" value="best"/>
1140 <section name="filter">
1141 <param name="considered_hits" value="0"/>
1142 <param name="min_support" value="0.0"/>
1143 <param name="count_empty" value="false"/>
1144 <param name="keep_old_scores" value="false"/>
1145 </section>
1146 <section name="PEPIons">
1147 <param name="mass_tolerance" value="0.5"/>
1148 <param name="min_shared" value="2"/>
1149 </section>
1150 <section name="PEPMatrix">
1151 <param name="matrix" value="identity"/>
1152 <param name="penalty" value="5"/>
1153 </section>
1154 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1155 <output name="ctd_out" ftype="xml">
1156 <assert_contents>
1157 <is_valid_xml/>
1158 </assert_contents>
1159 </output>
1160 </test>
1161 <test expect_num_outputs="2">
1162 <conditional name="adv_opts_cond">
1163 <param name="adv_opts_selector" value="advanced"/>
1164 <param name="force" value="false"/>
1165 <param name="test" value="true"/>
1166 </conditional>
1167 <param name="in" value="ConsensusID_1_input.idXML"/>
1168 <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1169 <param name="rt_delta" value="0.1"/>
1170 <param name="mz_delta" value="0.1"/>
1171 <param name="per_spectrum" value="false"/>
1172 <param name="algorithm" value="PEPMatrix"/>
1173 <section name="filter">
1174 <param name="considered_hits" value="6"/>
1175 <param name="min_support" value="0.0"/>
1176 <param name="count_empty" value="false"/>
1177 <param name="keep_old_scores" value="false"/>
1178 </section>
1179 <section name="PEPIons">
1180 <param name="mass_tolerance" value="0.5"/>
1181 <param name="min_shared" value="2"/>
1182 </section>
1183 <section name="PEPMatrix">
1184 <param name="matrix" value="identity"/>
1185 <param name="penalty" value="5"/>
1186 </section>
1187 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1188 <output name="ctd_out" ftype="xml">
1189 <assert_contents>
1190 <is_valid_xml/>
1191 </assert_contents>
1192 </output>
1193 </test>
1194 <test expect_num_outputs="2">
1195 <conditional name="adv_opts_cond">
1196 <param name="adv_opts_selector" value="advanced"/>
1197 <param name="force" value="false"/>
1198 <param name="test" value="true"/>
1199 </conditional>
1200 <param name="in" value="ConsensusID_1_input.idXML"/>
1201 <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1202 <param name="rt_delta" value="0.1"/>
1203 <param name="mz_delta" value="0.1"/>
1204 <param name="per_spectrum" value="false"/>
1205 <param name="algorithm" value="PEPIons"/>
1206 <section name="filter">
1207 <param name="considered_hits" value="0"/>
1208 <param name="min_support" value="0.0"/>
1209 <param name="count_empty" value="false"/>
1210 <param name="keep_old_scores" value="false"/>
1211 </section>
1212 <section name="PEPIons">
1213 <param name="mass_tolerance" value="0.5"/>
1214 <param name="min_shared" value="2"/>
1215 </section>
1216 <section name="PEPMatrix">
1217 <param name="matrix" value="identity"/>
1218 <param name="penalty" value="5"/>
1219 </section>
1220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1221 <output name="ctd_out" ftype="xml">
1222 <assert_contents>
1223 <is_valid_xml/>
1224 </assert_contents>
1225 </output>
1226 </test>
1227 <test expect_num_outputs="2">
1228 <conditional name="adv_opts_cond">
1229 <param name="adv_opts_selector" value="advanced"/>
1230 <param name="force" value="false"/>
1231 <param name="test" value="true"/>
1232 </conditional>
1233 <param name="in" value="ConsensusID_1_input.idXML"/>
1234 <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1235 <param name="rt_delta" value="0.1"/>
1236 <param name="mz_delta" value="0.1"/>
1237 <param name="per_spectrum" value="false"/>
1238 <param name="algorithm" value="best"/>
1239 <section name="filter">
1240 <param name="considered_hits" value="0"/>
1241 <param name="min_support" value="0.5"/>
1242 <param name="count_empty" value="false"/>
1243 <param name="keep_old_scores" value="false"/>
1244 </section>
1245 <section name="PEPIons">
1246 <param name="mass_tolerance" value="0.5"/>
1247 <param name="min_shared" value="2"/>
1248 </section>
1249 <section name="PEPMatrix">
1250 <param name="matrix" value="identity"/>
1251 <param name="penalty" value="5"/>
1252 </section>
1253 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1254 <output name="ctd_out" ftype="xml">
1255 <assert_contents>
1256 <is_valid_xml/>
1257 </assert_contents>
1258 </output>
1259 </test>
1260 <test expect_num_outputs="2">
1261 <conditional name="adv_opts_cond">
1262 <param name="adv_opts_selector" value="advanced"/>
1263 <param name="force" value="false"/>
1264 <param name="test" value="true"/>
1265 </conditional>
1266 <param name="in" value="ConsensusID_6_input.idXML"/>
1267 <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1268 <param name="rt_delta" value="0.1"/>
1269 <param name="mz_delta" value="0.1"/>
1270 <param name="per_spectrum" value="true"/>
1271 <param name="algorithm" value="best"/>
1272 <section name="filter">
1273 <param name="considered_hits" value="0"/>
1274 <param name="min_support" value="0.0"/>
1275 <param name="count_empty" value="false"/>
1276 <param name="keep_old_scores" value="true"/>
1277 </section>
1278 <section name="PEPIons">
1279 <param name="mass_tolerance" value="0.5"/>
1280 <param name="min_shared" value="2"/>
1281 </section>
1282 <section name="PEPMatrix">
1283 <param name="matrix" value="identity"/>
1284 <param name="penalty" value="5"/>
1285 </section>
1286 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1287 <output name="ctd_out" ftype="xml">
1288 <assert_contents>
1289 <is_valid_xml/>
1290 </assert_contents>
1291 </output>
1292 </test>
1293 <test expect_num_outputs="2">
1294 <conditional name="adv_opts_cond">
1295 <param name="adv_opts_selector" value="advanced"/>
1296 <param name="force" value="false"/>
1297 <param name="test" value="true"/>
1298 </conditional>
1299 <param name="in" value="ConsensusID_8_input.idXML"/>
1300 <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1301 <param name="rt_delta" value="0.1"/>
1302 <param name="mz_delta" value="0.1"/>
1303 <param name="per_spectrum" value="true"/>
1304 <param name="algorithm" value="best"/>
1305 <section name="filter">
1306 <param name="considered_hits" value="0"/>
1307 <param name="min_support" value="0.0"/>
1308 <param name="count_empty" value="false"/>
1309 <param name="keep_old_scores" value="true"/>
1310 </section>
1311 <section name="PEPIons">
1312 <param name="mass_tolerance" value="0.5"/>
1313 <param name="min_shared" value="2"/>
1314 </section>
1315 <section name="PEPMatrix">
1316 <param name="matrix" value="identity"/>
1317 <param name="penalty" value="5"/>
1318 </section>
1319 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1320 <output name="ctd_out" ftype="xml">
1321 <assert_contents>
1322 <is_valid_xml/>
1323 </assert_contents>
1324 </output>
1325 </test>
1326 </xml>
1327 <xml name="autotest_ConsensusMapNormalizer">
1328 <test expect_num_outputs="2">
1329 <conditional name="adv_opts_cond">
1330 <param name="adv_opts_selector" value="advanced"/>
1331 <param name="accession_filter" value=""/>
1332 <param name="description_filter" value=""/>
1333 <param name="force" value="false"/>
1334 <param name="test" value="true"/>
1335 </conditional>
1336 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
1337 <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1338 <param name="algorithm_type" value="robust_regression"/>
1339 <param name="ratio_threshold" value="0.67"/>
1340 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1341 <output name="ctd_out" ftype="xml">
1342 <assert_contents>
1343 <is_valid_xml/>
1344 </assert_contents>
1345 </output>
1346 </test>
1347 </xml>
1348 <xml name="autotest_CruxAdapter">
1349 <test expect_num_outputs="2">
1350 <conditional name="adv_opts_cond">
1351 <param name="adv_opts_selector" value="advanced"/>
1352 <param name="custom_enzyme" value=""/>
1353 <param name="decoy_prefix" value="decoy_"/>
1354 <param name="deisotope" value="false"/>
1355 <param name="report_decoys" value="false"/>
1356 <param name="force" value="false"/>
1357 <param name="test" value="true"/>
1358 </conditional>
1359 <param name="in" value="spectra_comet.mzML"/>
1360 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1361 <param name="database" value="proteins.fasta"/>
1362 <param name="extra_index_args" value=""/>
1363 <param name="extra_search_args" value=""/>
1364 <param name="extra_percolator_args" value=""/>
1365 <param name="precursor_mass_tolerance" value="10.0"/>
1366 <param name="precursor_mass_units" value="ppm"/>
1367 <param name="fragment_bin_offset" value="0.0"/>
1368 <param name="fragment_bin_width" value="0.02"/>
1369 <param name="isotope_error" value=""/>
1370 <param name="run_percolator" value="false"/>
1371 <param name="enzyme" value="trypsin"/>
1372 <param name="digestion" value="full-digest"/>
1373 <param name="allowed_missed_cleavages" value="0"/>
1374 <param name="decoy_format" value="peptide-reverse"/>
1375 <param name="keep_terminal_aminos" value="NC"/>
1376 <param name="cterm_modifications" value=""/>
1377 <param name="nterm_modifications" value=""/>
1378 <param name="modifications" value=""/>
1379 <param name="test_fdr" value="0.01"/>
1380 <param name="train_fdr" value="0.01"/>
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 </xml>
1389 <xml name="autotest_CVInspector">
1390 </xml>
1391 <xml name="autotest_DatabaseFilter">
1392 <test expect_num_outputs="2">
1393 <conditional name="adv_opts_cond">
1394 <param name="adv_opts_selector" value="advanced"/>
1395 <param name="force" value="false"/>
1396 <param name="test" value="true"/>
1397 </conditional>
1398 <param name="in" value="DatabaseFilter_1.fasta"/>
1399 <param name="id" value="DatabaseFilter_1.idXML"/>
1400 <param name="method" value="whitelist"/>
1401 <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1402 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1403 <output name="ctd_out" ftype="xml">
1404 <assert_contents>
1405 <is_valid_xml/>
1406 </assert_contents>
1407 </output>
1408 </test>
1409 <test expect_num_outputs="2">
1410 <conditional name="adv_opts_cond">
1411 <param name="adv_opts_selector" value="advanced"/>
1412 <param name="force" value="false"/>
1413 <param name="test" value="true"/>
1414 </conditional>
1415 <param name="in" value="DatabaseFilter_1.fasta"/>
1416 <param name="id" value="DatabaseFilter_1.idXML"/>
1417 <param name="method" value="blacklist"/>
1418 <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1419 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1420 <output name="ctd_out" ftype="xml">
1421 <assert_contents>
1422 <is_valid_xml/>
1423 </assert_contents>
1424 </output>
1425 </test>
1426 <test expect_num_outputs="2">
1427 <conditional name="adv_opts_cond">
1428 <param name="adv_opts_selector" value="advanced"/>
1429 <param name="force" value="false"/>
1430 <param name="test" value="true"/>
1431 </conditional>
1432 <param name="in" value="DatabaseFilter_3.fasta"/>
1433 <param name="id" value="DatabaseFilter_3.mzid"/>
1434 <param name="method" value="whitelist"/>
1435 <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1436 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1437 <output name="ctd_out" ftype="xml">
1438 <assert_contents>
1439 <is_valid_xml/>
1440 </assert_contents>
1441 </output>
1442 </test>
1443 <test expect_num_outputs="2">
1444 <conditional name="adv_opts_cond">
1445 <param name="adv_opts_selector" value="advanced"/>
1446 <param name="force" value="false"/>
1447 <param name="test" value="true"/>
1448 </conditional>
1449 <param name="in" value="DatabaseFilter_3.fasta"/>
1450 <param name="id" value="DatabaseFilter_3.mzid"/>
1451 <param name="method" value="blacklist"/>
1452 <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1453 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1454 <output name="ctd_out" ftype="xml">
1455 <assert_contents>
1456 <is_valid_xml/>
1457 </assert_contents>
1458 </output>
1459 </test>
1460 </xml>
1461 <xml name="autotest_DatabaseSuitability">
1462 <test expect_num_outputs="2">
1463 <conditional name="adv_opts_cond">
1464 <param name="adv_opts_selector" value="advanced"/>
1465 <param name="force" value="false"/>
1466 <param name="test" value="true"/>
1467 </conditional>
1468 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1469 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1470 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1471 <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1472 <section name="algorithm">
1473 <param name="no_rerank" value="false"/>
1474 <param name="reranking_cutoff_percentile" value="0.01"/>
1475 <param name="FDR" value="0.8"/>
1476 </section>
1477 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1478 <output name="ctd_out" ftype="xml">
1479 <assert_contents>
1480 <is_valid_xml/>
1481 </assert_contents>
1482 </output>
1483 </test>
1484 <test expect_num_outputs="2">
1485 <conditional name="adv_opts_cond">
1486 <param name="adv_opts_selector" value="advanced"/>
1487 <param name="force" value="false"/>
1488 <param name="test" value="true"/>
1489 </conditional>
1490 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1491 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1492 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1493 <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1494 <section name="algorithm">
1495 <param name="no_rerank" value="false"/>
1496 <param name="reranking_cutoff_percentile" value="0.9"/>
1497 <param name="FDR" value="1.0"/>
1498 </section>
1499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1500 <output name="ctd_out" ftype="xml">
1501 <assert_contents>
1502 <is_valid_xml/>
1503 </assert_contents>
1504 </output>
1505 </test>
1506 <test expect_num_outputs="2">
1507 <conditional name="adv_opts_cond">
1508 <param name="adv_opts_selector" value="advanced"/>
1509 <param name="force" value="false"/>
1510 <param name="test" value="true"/>
1511 </conditional>
1512 <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
1513 <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
1514 <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
1515 <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
1516 <section name="algorithm">
1517 <param name="no_rerank" value="true"/>
1518 <param name="reranking_cutoff_percentile" value="0.01"/>
1519 <param name="FDR" value="0.9"/>
1520 </section>
1521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
1522 <output name="ctd_out" ftype="xml">
1523 <assert_contents>
1524 <is_valid_xml/>
1525 </assert_contents>
1526 </output>
1527 </test>
1528 </xml>
1529 <xml name="autotest_Decharger">
1530 <test expect_num_outputs="4">
1531 <conditional name="adv_opts_cond">
1532 <param name="adv_opts_selector" value="advanced"/>
1533 <param name="force" value="false"/>
1534 <param name="test" value="true"/>
1535 </conditional>
1536 <param name="in" value="Decharger_input.featureXML"/>
1537 <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1538 <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
1539 <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
1540 <section name="algorithm">
1541 <section name="FeatureDeconvolution">
1542 <param name="charge_min" value="1"/>
1543 <param name="charge_max" value="10"/>
1544 <param name="charge_span_max" value="4"/>
1545 <param name="q_try" value="feature"/>
1546 <param name="retention_max_diff" value="1.0"/>
1547 <param name="retention_max_diff_local" value="1.0"/>
1548 <param name="mass_max_diff" value="0.1"/>
1549 <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;"/>
1550 <param name="max_neutrals" value="0"/>
1551 <param name="max_minority_bound" value="2"/>
1552 <param name="min_rt_overlap" value="0.66"/>
1553 <param name="intensity_filter" value="false"/>
1554 <param name="negative_mode" value="false"/>
1555 <param name="default_map_label" value="decharged features"/>
1556 <param name="verbose_level" value="0"/>
1557 </section>
1558 </section>
1559 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
1560 <output name="ctd_out" ftype="xml">
1561 <assert_contents>
1562 <is_valid_xml/>
1563 </assert_contents>
1564 </output>
1565 </test>
1566 </xml>
1567 <xml name="autotest_DecoyDatabase">
1568 <test expect_num_outputs="2">
1569 <conditional name="adv_opts_cond">
1570 <param name="adv_opts_selector" value="advanced"/>
1571 <param name="shuffle_max_attempts" value="30"/>
1572 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1573 <param name="seed" value="1"/>
1574 <param name="force" value="false"/>
1575 <param name="test" value="true"/>
1576 </conditional>
1577 <param name="in" value="DecoyDatabase_1.fasta"/>
1578 <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1579 <param name="decoy_string" value="DECOY_"/>
1580 <param name="decoy_string_position" value="prefix"/>
1581 <param name="only_decoy" value="true"/>
1582 <param name="type" value="protein"/>
1583 <param name="method" value="reverse"/>
1584 <param name="enzyme" value="Trypsin"/>
1585 <section name="Decoy">
1586 <param name="non_shuffle_pattern" value=""/>
1587 <param name="keepPeptideNTerm" value="true"/>
1588 <param name="keepPeptideCTerm" value="true"/>
1589 </section>
1590 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1591 <output name="ctd_out" ftype="xml">
1592 <assert_contents>
1593 <is_valid_xml/>
1594 </assert_contents>
1595 </output>
1596 </test>
1597 <test expect_num_outputs="2">
1598 <conditional name="adv_opts_cond">
1599 <param name="adv_opts_selector" value="advanced"/>
1600 <param name="shuffle_max_attempts" value="30"/>
1601 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1602 <param name="seed" value="42"/>
1603 <param name="force" value="false"/>
1604 <param name="test" value="true"/>
1605 </conditional>
1606 <param name="in" value="DecoyDatabase_1.fasta"/>
1607 <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1608 <param name="decoy_string" value="blabla"/>
1609 <param name="decoy_string_position" value="prefix"/>
1610 <param name="only_decoy" value="false"/>
1611 <param name="type" value="protein"/>
1612 <param name="method" value="shuffle"/>
1613 <param name="enzyme" value="Trypsin"/>
1614 <section name="Decoy">
1615 <param name="non_shuffle_pattern" value="KRP"/>
1616 <param name="keepPeptideNTerm" value="true"/>
1617 <param name="keepPeptideCTerm" value="true"/>
1618 </section>
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 <test expect_num_outputs="2">
1627 <conditional name="adv_opts_cond">
1628 <param name="adv_opts_selector" value="advanced"/>
1629 <param name="shuffle_max_attempts" value="30"/>
1630 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1631 <param name="seed" value="42"/>
1632 <param name="force" value="false"/>
1633 <param name="test" value="true"/>
1634 </conditional>
1635 <param name="in" value="DecoyDatabase_1.fasta"/>
1636 <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1637 <param name="decoy_string" value="blabla"/>
1638 <param name="decoy_string_position" value="prefix"/>
1639 <param name="only_decoy" value="false"/>
1640 <param name="type" value="protein"/>
1641 <param name="method" value="shuffle"/>
1642 <param name="enzyme" value="Chymotrypsin"/>
1643 <section name="Decoy">
1644 <param name="non_shuffle_pattern" value="KR"/>
1645 <param name="keepPeptideNTerm" value="true"/>
1646 <param name="keepPeptideCTerm" value="true"/>
1647 </section>
1648 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1649 <output name="ctd_out" ftype="xml">
1650 <assert_contents>
1651 <is_valid_xml/>
1652 </assert_contents>
1653 </output>
1654 </test>
1655 <test expect_num_outputs="2">
1656 <conditional name="adv_opts_cond">
1657 <param name="adv_opts_selector" value="advanced"/>
1658 <param name="shuffle_max_attempts" value="30"/>
1659 <param name="shuffle_sequence_identity_threshold" value="0.5"/>
1660 <param name="seed" value="42"/>
1661 <param name="force" value="false"/>
1662 <param name="test" value="true"/>
1663 </conditional>
1664 <param name="in" value="DecoyDatabase_4.fasta"/>
1665 <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
1666 <param name="decoy_string" value="blabla"/>
1667 <param name="decoy_string_position" value="prefix"/>
1668 <param name="only_decoy" value="false"/>
1669 <param name="type" value="RNA"/>
1670 <param name="method" value="reverse"/>
1671 <param name="enzyme" value="Trypsin"/>
1672 <section name="Decoy">
1673 <param name="non_shuffle_pattern" value=""/>
1674 <param name="keepPeptideNTerm" value="true"/>
1675 <param name="keepPeptideCTerm" value="true"/>
1676 </section>
1677 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1678 <output name="ctd_out" ftype="xml">
1679 <assert_contents>
1680 <is_valid_xml/>
1681 </assert_contents>
1682 </output>
1683 </test>
1684 </xml>
1685 <xml name="autotest_DeMeanderize">
1686 </xml>
1687 <xml name="autotest_DigestorMotif">
1688 </xml>
1689 <xml name="autotest_Digestor">
1690 </xml>
1691 <xml name="autotest_DTAExtractor">
1692 <test expect_num_outputs="1">
1693 <conditional name="adv_opts_cond">
1694 <param name="adv_opts_selector" value="advanced"/>
1695 <param name="force" value="false"/>
1696 <param name="test" value="true"/>
1697 </conditional>
1698 <param name="in" value="DTAExtractor_1_input.mzML"/>
1699 <param name="out" value="DTAExtractor"/>
1700 <param name="mz" value=":"/>
1701 <param name="rt" value=":61"/>
1702 <param name="level" value="1,2,3"/>
1703 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1704 <output name="ctd_out" ftype="xml">
1705 <assert_contents>
1706 <is_valid_xml/>
1707 </assert_contents>
1708 </output>
1709 </test>
1710 <test expect_num_outputs="1">
1711 <conditional name="adv_opts_cond">
1712 <param name="adv_opts_selector" value="advanced"/>
1713 <param name="force" value="false"/>
1714 <param name="test" value="true"/>
1715 </conditional>
1716 <param name="in" value="DTAExtractor_1_input.mzML"/>
1717 <param name="out" value="DTAExtractor"/>
1718 <param name="mz" value=":"/>
1719 <param name="rt" value=":"/>
1720 <param name="level" value="1"/>
1721 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1722 <output name="ctd_out" ftype="xml">
1723 <assert_contents>
1724 <is_valid_xml/>
1725 </assert_contents>
1726 </output>
1727 </test>
1728 <test expect_num_outputs="1">
1729 <conditional name="adv_opts_cond">
1730 <param name="adv_opts_selector" value="advanced"/>
1731 <param name="force" value="false"/>
1732 <param name="test" value="true"/>
1733 </conditional>
1734 <param name="in" value="DTAExtractor_1_input.mzML"/>
1735 <param name="out" value="DTAExtractor"/>
1736 <param name="mz" value=":1000"/>
1737 <param name="rt" value=":"/>
1738 <param name="level" value="2"/>
1739 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1740 <output name="ctd_out" ftype="xml">
1741 <assert_contents>
1742 <is_valid_xml/>
1743 </assert_contents>
1744 </output>
1745 </test>
1746 </xml>
1747 <xml name="autotest_EICExtractor">
1748 </xml>
1749 <xml name="autotest_Epifany">
1750 <test expect_num_outputs="2">
1751 <conditional name="adv_opts_cond">
1752 <param name="adv_opts_selector" value="advanced"/>
1753 <param name="conservative_fdr" value="true"/>
1754 <param name="min_psms_extreme_probability" value="0.0"/>
1755 <param name="force" value="false"/>
1756 <param name="test" value="true"/>
1757 </conditional>
1758 <param name="in" value="FidoAdapter_1_input.idXML"/>
1759 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1760 <param name="out_type" value="idxml"/>
1761 <param name="protein_fdr" value="false"/>
1762 <param name="greedy_group_resolution" value="none"/>
1763 <param name="max_psms_extreme_probability" value="1.0"/>
1764 <section name="algorithm">
1765 <param name="psm_probability_cutoff" value="0.001"/>
1766 <param name="top_PSMs" value="1"/>
1767 <param name="keep_best_PSM_only" value="true"/>
1768 <param name="update_PSM_probabilities" value="true"/>
1769 <param name="user_defined_priors" value="false"/>
1770 <param name="annotate_group_probabilities" value="true"/>
1771 <param name="use_ids_outside_features" value="false"/>
1772 <section name="model_parameters">
1773 <param name="prot_prior" value="0.7"/>
1774 <param name="pep_emission" value="0.1"/>
1775 <param name="pep_spurious_emission" value="0.001"/>
1776 <param name="pep_prior" value="0.1"/>
1777 <param name="regularize" value="false"/>
1778 <param name="extended_model" value="false"/>
1779 </section>
1780 <section name="loopy_belief_propagation">
1781 <param name="scheduling_type" value="priority"/>
1782 <param name="convergence_threshold" value="1e-05"/>
1783 <param name="dampening_lambda" value="0.001"/>
1784 <param name="max_nr_iterations" value="2147483647"/>
1785 <param name="p_norm_inference" value="1.0"/>
1786 </section>
1787 <section name="param_optimize">
1788 <param name="aucweight" value="0.3"/>
1789 <param name="conservative_fdr" value="true"/>
1790 <param name="regularized_fdr" value="true"/>
1791 </section>
1792 </section>
1793 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1794 <output name="ctd_out" ftype="xml">
1795 <assert_contents>
1796 <is_valid_xml/>
1797 </assert_contents>
1798 </output>
1799 </test>
1800 <test expect_num_outputs="2">
1801 <conditional name="adv_opts_cond">
1802 <param name="adv_opts_selector" value="advanced"/>
1803 <param name="conservative_fdr" value="true"/>
1804 <param name="min_psms_extreme_probability" value="0.0"/>
1805 <param name="force" value="false"/>
1806 <param name="test" value="true"/>
1807 </conditional>
1808 <param name="in" value="Epifany_2_input.consensusXML"/>
1809 <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1810 <param name="out_type" value="consensusXML"/>
1811 <param name="protein_fdr" value="false"/>
1812 <param name="greedy_group_resolution" value="none"/>
1813 <param name="max_psms_extreme_probability" value="1.0"/>
1814 <section name="algorithm">
1815 <param name="psm_probability_cutoff" value="0.001"/>
1816 <param name="top_PSMs" value="1"/>
1817 <param name="keep_best_PSM_only" value="true"/>
1818 <param name="update_PSM_probabilities" value="true"/>
1819 <param name="user_defined_priors" value="false"/>
1820 <param name="annotate_group_probabilities" value="true"/>
1821 <param name="use_ids_outside_features" value="false"/>
1822 <section name="model_parameters">
1823 <param name="prot_prior" value="0.7"/>
1824 <param name="pep_emission" value="0.1"/>
1825 <param name="pep_spurious_emission" value="0.001"/>
1826 <param name="pep_prior" value="0.1"/>
1827 <param name="regularize" value="false"/>
1828 <param name="extended_model" value="false"/>
1829 </section>
1830 <section name="loopy_belief_propagation">
1831 <param name="scheduling_type" value="priority"/>
1832 <param name="convergence_threshold" value="1e-05"/>
1833 <param name="dampening_lambda" value="0.001"/>
1834 <param name="max_nr_iterations" value="2147483647"/>
1835 <param name="p_norm_inference" value="1.0"/>
1836 </section>
1837 <section name="param_optimize">
1838 <param name="aucweight" value="0.3"/>
1839 <param name="conservative_fdr" value="true"/>
1840 <param name="regularized_fdr" value="true"/>
1841 </section>
1842 </section>
1843 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1844 <output name="ctd_out" ftype="xml">
1845 <assert_contents>
1846 <is_valid_xml/>
1847 </assert_contents>
1848 </output>
1849 </test>
1850 <test expect_num_outputs="2">
1851 <conditional name="adv_opts_cond">
1852 <param name="adv_opts_selector" value="advanced"/>
1853 <param name="conservative_fdr" value="true"/>
1854 <param name="min_psms_extreme_probability" value="0.0"/>
1855 <param name="force" value="false"/>
1856 <param name="test" value="true"/>
1857 </conditional>
1858 <param name="in" value="Epifany_2_input.consensusXML"/>
1859 <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
1860 <param name="out_type" value="consensusXML"/>
1861 <param name="protein_fdr" value="false"/>
1862 <param name="greedy_group_resolution" value="none"/>
1863 <param name="max_psms_extreme_probability" value="1.0"/>
1864 <section name="algorithm">
1865 <param name="psm_probability_cutoff" value="0.001"/>
1866 <param name="top_PSMs" value="1"/>
1867 <param name="keep_best_PSM_only" value="false"/>
1868 <param name="update_PSM_probabilities" value="true"/>
1869 <param name="user_defined_priors" value="false"/>
1870 <param name="annotate_group_probabilities" value="true"/>
1871 <param name="use_ids_outside_features" value="false"/>
1872 <section name="model_parameters">
1873 <param name="prot_prior" value="0.7"/>
1874 <param name="pep_emission" value="0.1"/>
1875 <param name="pep_spurious_emission" value="0.001"/>
1876 <param name="pep_prior" value="0.1"/>
1877 <param name="regularize" value="false"/>
1878 <param name="extended_model" value="false"/>
1879 </section>
1880 <section name="loopy_belief_propagation">
1881 <param name="scheduling_type" value="priority"/>
1882 <param name="convergence_threshold" value="1e-05"/>
1883 <param name="dampening_lambda" value="0.001"/>
1884 <param name="max_nr_iterations" value="2147483647"/>
1885 <param name="p_norm_inference" value="1.0"/>
1886 </section>
1887 <section name="param_optimize">
1888 <param name="aucweight" value="0.3"/>
1889 <param name="conservative_fdr" value="true"/>
1890 <param name="regularized_fdr" value="true"/>
1891 </section>
1892 </section>
1893 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1894 <output name="ctd_out" ftype="xml">
1895 <assert_contents>
1896 <is_valid_xml/>
1897 </assert_contents>
1898 </output>
1899 </test>
1900 </xml>
1901 <xml name="autotest_ERPairFinder">
1902 </xml>
1903 <xml name="autotest_ExternalCalibration">
1904 <test expect_num_outputs="2">
1905 <conditional name="adv_opts_cond">
1906 <param name="adv_opts_selector" value="advanced"/>
1907 <param name="force" value="false"/>
1908 <param name="test" value="true"/>
1909 </conditional>
1910 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1911 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1912 <param name="offset" value="-5.5"/>
1913 <param name="slope" value="0.0001"/>
1914 <param name="power" value="0.0"/>
1915 <param name="ms_level" value="1"/>
1916 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1917 <output name="ctd_out" ftype="xml">
1918 <assert_contents>
1919 <is_valid_xml/>
1920 </assert_contents>
1921 </output>
1922 </test>
1923 <test expect_num_outputs="2">
1924 <conditional name="adv_opts_cond">
1925 <param name="adv_opts_selector" value="advanced"/>
1926 <param name="force" value="false"/>
1927 <param name="test" value="true"/>
1928 </conditional>
1929 <param name="in" value="ExternalCalibration_1_input.mzML"/>
1930 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
1931 <param name="offset" value="-5.5"/>
1932 <param name="slope" value="0.0001"/>
1933 <param name="power" value="0.0"/>
1934 <param name="ms_level" value="2"/>
1935 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1936 <output name="ctd_out" ftype="xml">
1937 <assert_contents>
1938 <is_valid_xml/>
1939 </assert_contents>
1940 </output>
1941 </test>
1942 </xml>
1943 <xml name="autotest_FalseDiscoveryRate">
1944 <test expect_num_outputs="2">
1945 <conditional name="adv_opts_cond">
1946 <param name="adv_opts_selector" value="advanced"/>
1947 <param name="force" value="false"/>
1948 <param name="test" value="true"/>
1949 </conditional>
1950 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1951 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1952 <param name="PSM" value="true"/>
1953 <param name="protein" value="false"/>
1954 <section name="FDR">
1955 <param name="PSM" value="1.0"/>
1956 <param name="protein" value="1.0"/>
1957 <section name="cleanup">
1958 <param name="remove_proteins_without_psms" value="true"/>
1959 <param name="remove_psms_without_proteins" value="true"/>
1960 <param name="remove_spectra_without_psms" value="true"/>
1961 </section>
1962 </section>
1963 <section name="algorithm">
1964 <param name="no_qvalues" value="false"/>
1965 <param name="use_all_hits" value="false"/>
1966 <param name="split_charge_variants" value="false"/>
1967 <param name="treat_runs_separately" value="false"/>
1968 <param name="add_decoy_peptides" value="false"/>
1969 <param name="add_decoy_proteins" value="false"/>
1970 <param name="conservative" value="true"/>
1971 </section>
1972 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
1973 <output name="ctd_out" ftype="xml">
1974 <assert_contents>
1975 <is_valid_xml/>
1976 </assert_contents>
1977 </output>
1978 </test>
1979 <test expect_num_outputs="2">
1980 <conditional name="adv_opts_cond">
1981 <param name="adv_opts_selector" value="advanced"/>
1982 <param name="force" value="false"/>
1983 <param name="test" value="true"/>
1984 </conditional>
1985 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
1986 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
1987 <param name="PSM" value="true"/>
1988 <param name="protein" value="false"/>
1989 <section name="FDR">
1990 <param name="PSM" value="1.0"/>
1991 <param name="protein" value="1.0"/>
1992 <section name="cleanup">
1993 <param name="remove_proteins_without_psms" value="true"/>
1994 <param name="remove_psms_without_proteins" value="true"/>
1995 <param name="remove_spectra_without_psms" value="true"/>
1996 </section>
1997 </section>
1998 <section name="algorithm">
1999 <param name="no_qvalues" value="false"/>
2000 <param name="use_all_hits" value="false"/>
2001 <param name="split_charge_variants" value="false"/>
2002 <param name="treat_runs_separately" value="true"/>
2003 <param name="add_decoy_peptides" value="false"/>
2004 <param name="add_decoy_proteins" value="false"/>
2005 <param name="conservative" value="true"/>
2006 </section>
2007 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2008 <output name="ctd_out" ftype="xml">
2009 <assert_contents>
2010 <is_valid_xml/>
2011 </assert_contents>
2012 </output>
2013 </test>
2014 <test expect_num_outputs="2">
2015 <conditional name="adv_opts_cond">
2016 <param name="adv_opts_selector" value="advanced"/>
2017 <param name="force" value="false"/>
2018 <param name="test" value="true"/>
2019 </conditional>
2020 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
2021 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2022 <param name="PSM" value="true"/>
2023 <param name="protein" value="false"/>
2024 <section name="FDR">
2025 <param name="PSM" value="1.0"/>
2026 <param name="protein" value="1.0"/>
2027 <section name="cleanup">
2028 <param name="remove_proteins_without_psms" value="true"/>
2029 <param name="remove_psms_without_proteins" value="true"/>
2030 <param name="remove_spectra_without_psms" value="true"/>
2031 </section>
2032 </section>
2033 <section name="algorithm">
2034 <param name="no_qvalues" value="false"/>
2035 <param name="use_all_hits" value="false"/>
2036 <param name="split_charge_variants" value="true"/>
2037 <param name="treat_runs_separately" value="false"/>
2038 <param name="add_decoy_peptides" value="false"/>
2039 <param name="add_decoy_proteins" value="false"/>
2040 <param name="conservative" value="true"/>
2041 </section>
2042 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2043 <output name="ctd_out" ftype="xml">
2044 <assert_contents>
2045 <is_valid_xml/>
2046 </assert_contents>
2047 </output>
2048 </test>
2049 <test expect_num_outputs="2">
2050 <conditional name="adv_opts_cond">
2051 <param name="adv_opts_selector" value="advanced"/>
2052 <param name="force" value="false"/>
2053 <param name="test" value="true"/>
2054 </conditional>
2055 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
2056 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2057 <param name="PSM" value="true"/>
2058 <param name="protein" value="false"/>
2059 <section name="FDR">
2060 <param name="PSM" value="1.0"/>
2061 <param name="protein" value="1.0"/>
2062 <section name="cleanup">
2063 <param name="remove_proteins_without_psms" value="true"/>
2064 <param name="remove_psms_without_proteins" value="true"/>
2065 <param name="remove_spectra_without_psms" value="true"/>
2066 </section>
2067 </section>
2068 <section name="algorithm">
2069 <param name="no_qvalues" value="false"/>
2070 <param name="use_all_hits" value="false"/>
2071 <param name="split_charge_variants" value="true"/>
2072 <param name="treat_runs_separately" value="false"/>
2073 <param name="add_decoy_peptides" value="false"/>
2074 <param name="add_decoy_proteins" value="false"/>
2075 <param name="conservative" value="true"/>
2076 </section>
2077 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2078 <output name="ctd_out" ftype="xml">
2079 <assert_contents>
2080 <is_valid_xml/>
2081 </assert_contents>
2082 </output>
2083 </test>
2084 <test expect_num_outputs="2">
2085 <conditional name="adv_opts_cond">
2086 <param name="adv_opts_selector" value="advanced"/>
2087 <param name="force" value="true"/>
2088 <param name="test" value="true"/>
2089 </conditional>
2090 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
2091 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2092 <param name="PSM" value="false"/>
2093 <param name="protein" value="true"/>
2094 <section name="FDR">
2095 <param name="PSM" value="1.0"/>
2096 <param name="protein" value="1.0"/>
2097 <section name="cleanup">
2098 <param name="remove_proteins_without_psms" value="true"/>
2099 <param name="remove_psms_without_proteins" value="true"/>
2100 <param name="remove_spectra_without_psms" value="true"/>
2101 </section>
2102 </section>
2103 <section name="algorithm">
2104 <param name="no_qvalues" value="false"/>
2105 <param name="use_all_hits" value="false"/>
2106 <param name="split_charge_variants" value="false"/>
2107 <param name="treat_runs_separately" value="false"/>
2108 <param name="add_decoy_peptides" value="false"/>
2109 <param name="add_decoy_proteins" value="true"/>
2110 <param name="conservative" value="true"/>
2111 </section>
2112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2113 <output name="ctd_out" ftype="xml">
2114 <assert_contents>
2115 <is_valid_xml/>
2116 </assert_contents>
2117 </output>
2118 </test>
2119 <test expect_num_outputs="2">
2120 <conditional name="adv_opts_cond">
2121 <param name="adv_opts_selector" value="advanced"/>
2122 <param name="force" value="false"/>
2123 <param name="test" value="true"/>
2124 </conditional>
2125 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
2126 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2127 <param name="PSM" value="true"/>
2128 <param name="protein" value="false"/>
2129 <section name="FDR">
2130 <param name="PSM" value="0.05"/>
2131 <param name="protein" value="1.0"/>
2132 <section name="cleanup">
2133 <param name="remove_proteins_without_psms" value="true"/>
2134 <param name="remove_psms_without_proteins" value="true"/>
2135 <param name="remove_spectra_without_psms" value="true"/>
2136 </section>
2137 </section>
2138 <section name="algorithm">
2139 <param name="no_qvalues" value="false"/>
2140 <param name="use_all_hits" value="false"/>
2141 <param name="split_charge_variants" value="false"/>
2142 <param name="treat_runs_separately" value="false"/>
2143 <param name="add_decoy_peptides" value="false"/>
2144 <param name="add_decoy_proteins" value="false"/>
2145 <param name="conservative" value="true"/>
2146 </section>
2147 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2148 <output name="ctd_out" ftype="xml">
2149 <assert_contents>
2150 <is_valid_xml/>
2151 </assert_contents>
2152 </output>
2153 </test>
2154 <test expect_num_outputs="2">
2155 <conditional name="adv_opts_cond">
2156 <param name="adv_opts_selector" value="advanced"/>
2157 <param name="force" value="true"/>
2158 <param name="test" value="true"/>
2159 </conditional>
2160 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
2161 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
2162 <param name="PSM" value="false"/>
2163 <param name="protein" value="true"/>
2164 <section name="FDR">
2165 <param name="PSM" value="1.0"/>
2166 <param name="protein" value="0.3"/>
2167 <section name="cleanup">
2168 <param name="remove_proteins_without_psms" value="true"/>
2169 <param name="remove_psms_without_proteins" value="true"/>
2170 <param name="remove_spectra_without_psms" value="true"/>
2171 </section>
2172 </section>
2173 <section name="algorithm">
2174 <param name="no_qvalues" value="false"/>
2175 <param name="use_all_hits" value="false"/>
2176 <param name="split_charge_variants" value="false"/>
2177 <param name="treat_runs_separately" value="false"/>
2178 <param name="add_decoy_peptides" value="false"/>
2179 <param name="add_decoy_proteins" value="false"/>
2180 <param name="conservative" value="true"/>
2181 </section>
2182 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2183 <output name="ctd_out" ftype="xml">
2184 <assert_contents>
2185 <is_valid_xml/>
2186 </assert_contents>
2187 </output>
2188 </test>
2189 </xml>
2190 <xml name="autotest_FeatureFinderCentroided">
2191 <test expect_num_outputs="2">
2192 <conditional name="adv_opts_cond">
2193 <param name="adv_opts_selector" value="advanced"/>
2194 <param name="force" value="false"/>
2195 <param name="test" value="true"/>
2196 <param name="pseudo_rt_shift" value="500.0"/>
2197 </conditional>
2198 <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
2199 <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2200 <section name="algorithm">
2201 <section name="intensity">
2202 <param name="bins" value="1"/>
2203 </section>
2204 <section name="mass_trace">
2205 <param name="mz_tolerance" value="0.02"/>
2206 <param name="min_spectra" value="14"/>
2207 <param name="max_missing" value="1"/>
2208 <param name="slope_bound" value="0.1"/>
2209 </section>
2210 <section name="isotopic_pattern">
2211 <param name="charge_low" value="2"/>
2212 <param name="charge_high" value="2"/>
2213 <param name="mz_tolerance" value="0.02"/>
2214 <param name="intensity_percentage" value="10.0"/>
2215 <param name="intensity_percentage_optional" value="0.1"/>
2216 <param name="optional_fit_improvement" value="2.0"/>
2217 <param name="mass_window_width" value="100.0"/>
2218 <param name="abundance_12C" value="98.93"/>
2219 <param name="abundance_14N" value="99.632"/>
2220 </section>
2221 <section name="seed">
2222 <param name="min_score" value="0.8"/>
2223 </section>
2224 <section name="fit">
2225 <param name="max_iterations" value="500"/>
2226 </section>
2227 <section name="feature">
2228 <param name="min_score" value="0.7"/>
2229 <param name="min_isotope_fit" value="0.8"/>
2230 <param name="min_trace_score" value="0.5"/>
2231 <param name="min_rt_span" value="0.333"/>
2232 <param name="max_rt_span" value="2.5"/>
2233 <param name="rt_shape" value="symmetric"/>
2234 <param name="max_intersection" value="0.35"/>
2235 <param name="reported_mz" value="monoisotopic"/>
2236 </section>
2237 <section name="user-seed">
2238 <param name="rt_tolerance" value="5.0"/>
2239 <param name="mz_tolerance" value="1.1"/>
2240 <param name="min_score" value="0.5"/>
2241 </section>
2242 </section>
2243 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2244 <output name="ctd_out" ftype="xml">
2245 <assert_contents>
2246 <is_valid_xml/>
2247 </assert_contents>
2248 </output>
2249 </test>
2250 </xml>
2251 <xml name="autotest_FeatureFinderIdentification">
2252 <test expect_num_outputs="2">
2253 <conditional name="adv_opts_cond">
2254 <param name="adv_opts_selector" value="advanced"/>
2255 <param name="force" value="false"/>
2256 <param name="test" value="true"/>
2257 </conditional>
2258 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2259 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2260 <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2261 <section name="extract">
2262 <param name="batch_size" value="1000"/>
2263 <param name="mz_window" value="0.1"/>
2264 <param name="n_isotopes" value="2"/>
2265 <param name="isotope_pmin" value="0.0"/>
2266 <param name="rt_quantile" value="0.95"/>
2267 <param name="rt_window" value="0.0"/>
2268 </section>
2269 <section name="detect">
2270 <param name="peak_width" value="60.0"/>
2271 <param name="min_peak_width" value="0.2"/>
2272 <param name="signal_to_noise" value="0.8"/>
2273 <param name="mapping_tolerance" value="0.0"/>
2274 </section>
2275 <section name="svm">
2276 <param name="samples" value="0"/>
2277 <param name="no_selection" value="false"/>
2278 <param name="kernel" value="RBF"/>
2279 <param name="xval" value="5"/>
2280 <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"/>
2281 <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"/>
2282 <param name="epsilon" value="0.001"/>
2283 <param name="cache_size" value="100.0"/>
2284 <param name="no_shrinking" value="false"/>
2285 <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"/>
2286 <param name="min_prob" value="0.0"/>
2287 </section>
2288 <section name="model">
2289 <param name="type" value="none"/>
2290 <param name="add_zeros" value="0.2"/>
2291 <param name="unweighted_fit" value="false"/>
2292 <param name="no_imputation" value="false"/>
2293 <param name="each_trace" value="false"/>
2294 <section name="check">
2295 <param name="min_area" value="1.0"/>
2296 <param name="boundaries" value="0.5"/>
2297 <param name="width" value="10.0"/>
2298 <param name="asymmetry" value="10.0"/>
2299 </section>
2300 </section>
2301 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2302 <output name="ctd_out" ftype="xml">
2303 <assert_contents>
2304 <is_valid_xml/>
2305 </assert_contents>
2306 </output>
2307 </test>
2308 <test expect_num_outputs="2">
2309 <conditional name="adv_opts_cond">
2310 <param name="adv_opts_selector" value="advanced"/>
2311 <param name="force" value="false"/>
2312 <param name="test" value="true"/>
2313 </conditional>
2314 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
2315 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
2316 <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2317 <section name="extract">
2318 <param name="batch_size" value="1000"/>
2319 <param name="mz_window" value="0.1"/>
2320 <param name="n_isotopes" value="2"/>
2321 <param name="isotope_pmin" value="0.0"/>
2322 <param name="rt_quantile" value="0.95"/>
2323 <param name="rt_window" value="0.0"/>
2324 </section>
2325 <section name="detect">
2326 <param name="peak_width" value="60.0"/>
2327 <param name="min_peak_width" value="0.2"/>
2328 <param name="signal_to_noise" value="0.8"/>
2329 <param name="mapping_tolerance" value="0.0"/>
2330 </section>
2331 <section name="svm">
2332 <param name="samples" value="0"/>
2333 <param name="no_selection" value="false"/>
2334 <param name="kernel" value="RBF"/>
2335 <param name="xval" value="5"/>
2336 <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"/>
2337 <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"/>
2338 <param name="epsilon" value="0.001"/>
2339 <param name="cache_size" value="100.0"/>
2340 <param name="no_shrinking" value="false"/>
2341 <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"/>
2342 <param name="min_prob" value="0.0"/>
2343 </section>
2344 <section name="model">
2345 <param name="type" value="symmetric"/>
2346 <param name="add_zeros" value="0.2"/>
2347 <param name="unweighted_fit" value="false"/>
2348 <param name="no_imputation" value="false"/>
2349 <param name="each_trace" value="false"/>
2350 <section name="check">
2351 <param name="min_area" value="1.0"/>
2352 <param name="boundaries" value="0.5"/>
2353 <param name="width" value="10.0"/>
2354 <param name="asymmetry" value="10.0"/>
2355 </section>
2356 </section>
2357 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2358 <output name="ctd_out" ftype="xml">
2359 <assert_contents>
2360 <is_valid_xml/>
2361 </assert_contents>
2362 </output>
2363 </test>
2364 </xml>
2365 <xml name="autotest_FeatureFinderIsotopeWavelet">
2366 </xml>
2367 <xml name="autotest_FeatureFinderMetaboIdent">
2368 <test expect_num_outputs="2">
2369 <conditional name="adv_opts_cond">
2370 <param name="adv_opts_selector" value="advanced"/>
2371 <param name="force" value="false"/>
2372 <param name="test" value="true"/>
2373 </conditional>
2374 <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
2375 <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
2376 <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2377 <section name="extract">
2378 <param name="mz_window" value="5.0"/>
2379 <param name="n_isotopes" value="2"/>
2380 <param name="isotope_pmin" value="0.0"/>
2381 <param name="rt_window" value="20.0"/>
2382 </section>
2383 <section name="detect">
2384 <param name="peak_width" value="3.0"/>
2385 <param name="min_peak_width" value="0.2"/>
2386 <param name="signal_to_noise" value="0.8"/>
2387 </section>
2388 <section name="model">
2389 <param name="type" value="symmetric"/>
2390 <param name="add_zeros" value="0.2"/>
2391 <param name="unweighted_fit" value="false"/>
2392 <param name="no_imputation" value="false"/>
2393 <param name="each_trace" value="false"/>
2394 <section name="check">
2395 <param name="min_area" value="1.0"/>
2396 <param name="boundaries" value="0.5"/>
2397 <param name="width" value="10.0"/>
2398 <param name="asymmetry" value="10.0"/>
2399 </section>
2400 </section>
2401 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2402 <output name="ctd_out" ftype="xml">
2403 <assert_contents>
2404 <is_valid_xml/>
2405 </assert_contents>
2406 </output>
2407 </test>
2408 </xml>
2409 <xml name="autotest_FeatureFinderMetabo">
2410 <test expect_num_outputs="2">
2411 <conditional name="adv_opts_cond">
2412 <param name="adv_opts_selector" value="advanced"/>
2413 <param name="force" value="false"/>
2414 <param name="test" value="true"/>
2415 </conditional>
2416 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2417 <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2418 <section name="algorithm">
2419 <section name="common">
2420 <param name="noise_threshold_int" value="10.0"/>
2421 <param name="chrom_peak_snr" value="3.0"/>
2422 <param name="chrom_fwhm" value="5.0"/>
2423 </section>
2424 <section name="mtd">
2425 <param name="mass_error_ppm" value="20.0"/>
2426 <param name="reestimate_mt_sd" value="true"/>
2427 <param name="quant_method" value="area"/>
2428 <param name="trace_termination_criterion" value="outlier"/>
2429 <param name="trace_termination_outliers" value="5"/>
2430 <param name="min_sample_rate" value="0.5"/>
2431 <param name="min_trace_length" value="5.0"/>
2432 <param name="max_trace_length" value="300.0"/>
2433 </section>
2434 <section name="epd">
2435 <param name="enabled" value="true"/>
2436 <param name="width_filtering" value="off"/>
2437 <param name="min_fwhm" value="3.0"/>
2438 <param name="max_fwhm" value="60.0"/>
2439 <param name="masstrace_snr_filtering" value="false"/>
2440 </section>
2441 <section name="ffm">
2442 <param name="local_rt_range" value="10.0"/>
2443 <param name="local_mz_range" value="6.5"/>
2444 <param name="charge_lower_bound" value="1"/>
2445 <param name="charge_upper_bound" value="3"/>
2446 <param name="report_summed_ints" value="false"/>
2447 <param name="enable_RT_filtering" value="true"/>
2448 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2449 <param name="mz_scoring_13C" value="true"/>
2450 <param name="use_smoothed_intensities" value="true"/>
2451 <param name="report_convex_hulls" value="false"/>
2452 <param name="remove_single_traces" value="false"/>
2453 <param name="mz_scoring_by_elements" value="false"/>
2454 <param name="elements" value="CHNOPS"/>
2455 </section>
2456 </section>
2457 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2458 <output name="ctd_out" ftype="xml">
2459 <assert_contents>
2460 <is_valid_xml/>
2461 </assert_contents>
2462 </output>
2463 </test>
2464 <test expect_num_outputs="2">
2465 <conditional name="adv_opts_cond">
2466 <param name="adv_opts_selector" value="advanced"/>
2467 <param name="force" value="false"/>
2468 <param name="test" value="true"/>
2469 </conditional>
2470 <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
2471 <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2472 <section name="algorithm">
2473 <section name="common">
2474 <param name="noise_threshold_int" value="100.0"/>
2475 <param name="chrom_peak_snr" value="0.0"/>
2476 <param name="chrom_fwhm" value="100.0"/>
2477 </section>
2478 <section name="mtd">
2479 <param name="mass_error_ppm" value="5.0"/>
2480 <param name="reestimate_mt_sd" value="true"/>
2481 <param name="quant_method" value="median"/>
2482 <param name="trace_termination_criterion" value="sample_rate"/>
2483 <param name="trace_termination_outliers" value="2"/>
2484 <param name="min_sample_rate" value="0.01"/>
2485 <param name="min_trace_length" value="30.0"/>
2486 <param name="max_trace_length" value="3000.0"/>
2487 </section>
2488 <section name="epd">
2489 <param name="enabled" value="false"/>
2490 <param name="width_filtering" value="off"/>
2491 <param name="min_fwhm" value="10.0"/>
2492 <param name="max_fwhm" value="80.0"/>
2493 <param name="masstrace_snr_filtering" value="false"/>
2494 </section>
2495 <section name="ffm">
2496 <param name="local_rt_range" value="10.0"/>
2497 <param name="local_mz_range" value="4.5"/>
2498 <param name="charge_lower_bound" value="1"/>
2499 <param name="charge_upper_bound" value="3"/>
2500 <param name="report_summed_ints" value="false"/>
2501 <param name="enable_RT_filtering" value="false"/>
2502 <param name="isotope_filtering_model" value="none"/>
2503 <param name="mz_scoring_13C" value="false"/>
2504 <param name="use_smoothed_intensities" value="false"/>
2505 <param name="report_convex_hulls" value="true"/>
2506 <param name="remove_single_traces" value="false"/>
2507 <param name="mz_scoring_by_elements" value="false"/>
2508 <param name="elements" value="CHNOPS"/>
2509 </section>
2510 </section>
2511 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2512 <output name="ctd_out" ftype="xml">
2513 <assert_contents>
2514 <is_valid_xml/>
2515 </assert_contents>
2516 </output>
2517 </test>
2518 <test expect_num_outputs="3">
2519 <conditional name="adv_opts_cond">
2520 <param name="adv_opts_selector" value="advanced"/>
2521 <param name="force" value="false"/>
2522 <param name="test" value="true"/>
2523 </conditional>
2524 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2525 <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
2526 <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2527 <section name="algorithm">
2528 <section name="common">
2529 <param name="noise_threshold_int" value="10.0"/>
2530 <param name="chrom_peak_snr" value="3.0"/>
2531 <param name="chrom_fwhm" value="5.0"/>
2532 </section>
2533 <section name="mtd">
2534 <param name="mass_error_ppm" value="5.0"/>
2535 <param name="reestimate_mt_sd" value="true"/>
2536 <param name="quant_method" value="area"/>
2537 <param name="trace_termination_criterion" value="outlier"/>
2538 <param name="trace_termination_outliers" value="5"/>
2539 <param name="min_sample_rate" value="0.5"/>
2540 <param name="min_trace_length" value="5.0"/>
2541 <param name="max_trace_length" value="-1.0"/>
2542 </section>
2543 <section name="epd">
2544 <param name="enabled" value="true"/>
2545 <param name="width_filtering" value="fixed"/>
2546 <param name="min_fwhm" value="3.0"/>
2547 <param name="max_fwhm" value="60.0"/>
2548 <param name="masstrace_snr_filtering" value="false"/>
2549 </section>
2550 <section name="ffm">
2551 <param name="local_rt_range" value="10.0"/>
2552 <param name="local_mz_range" value="6.5"/>
2553 <param name="charge_lower_bound" value="1"/>
2554 <param name="charge_upper_bound" value="3"/>
2555 <param name="report_summed_ints" value="false"/>
2556 <param name="enable_RT_filtering" value="true"/>
2557 <param name="isotope_filtering_model" value="none"/>
2558 <param name="mz_scoring_13C" value="true"/>
2559 <param name="use_smoothed_intensities" value="true"/>
2560 <param name="report_convex_hulls" value="true"/>
2561 <param name="remove_single_traces" value="false"/>
2562 <param name="mz_scoring_by_elements" value="false"/>
2563 <param name="elements" value="CHNOPS"/>
2564 </section>
2565 </section>
2566 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2567 <output name="ctd_out" ftype="xml">
2568 <assert_contents>
2569 <is_valid_xml/>
2570 </assert_contents>
2571 </output>
2572 </test>
2573 <test expect_num_outputs="3">
2574 <conditional name="adv_opts_cond">
2575 <param name="adv_opts_selector" value="advanced"/>
2576 <param name="force" value="false"/>
2577 <param name="test" value="true"/>
2578 </conditional>
2579 <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
2580 <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2581 <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
2582 <section name="algorithm">
2583 <section name="common">
2584 <param name="noise_threshold_int" value="10.0"/>
2585 <param name="chrom_peak_snr" value="3.0"/>
2586 <param name="chrom_fwhm" value="5.0"/>
2587 </section>
2588 <section name="mtd">
2589 <param name="mass_error_ppm" value="5.0"/>
2590 <param name="reestimate_mt_sd" value="true"/>
2591 <param name="quant_method" value="area"/>
2592 <param name="trace_termination_criterion" value="outlier"/>
2593 <param name="trace_termination_outliers" value="5"/>
2594 <param name="min_sample_rate" value="0.5"/>
2595 <param name="min_trace_length" value="5.0"/>
2596 <param name="max_trace_length" value="-1.0"/>
2597 </section>
2598 <section name="epd">
2599 <param name="enabled" value="true"/>
2600 <param name="width_filtering" value="fixed"/>
2601 <param name="min_fwhm" value="3.0"/>
2602 <param name="max_fwhm" value="60.0"/>
2603 <param name="masstrace_snr_filtering" value="false"/>
2604 </section>
2605 <section name="ffm">
2606 <param name="local_rt_range" value="10.0"/>
2607 <param name="local_mz_range" value="6.5"/>
2608 <param name="charge_lower_bound" value="1"/>
2609 <param name="charge_upper_bound" value="3"/>
2610 <param name="report_summed_ints" value="false"/>
2611 <param name="enable_RT_filtering" value="true"/>
2612 <param name="isotope_filtering_model" value="none"/>
2613 <param name="mz_scoring_13C" value="true"/>
2614 <param name="use_smoothed_intensities" value="true"/>
2615 <param name="report_convex_hulls" value="true"/>
2616 <param name="remove_single_traces" value="true"/>
2617 <param name="mz_scoring_by_elements" value="false"/>
2618 <param name="elements" value="CHNOPS"/>
2619 </section>
2620 </section>
2621 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
2622 <output name="ctd_out" ftype="xml">
2623 <assert_contents>
2624 <is_valid_xml/>
2625 </assert_contents>
2626 </output>
2627 </test>
2628 <test expect_num_outputs="2">
2629 <conditional name="adv_opts_cond">
2630 <param name="adv_opts_selector" value="advanced"/>
2631 <param name="force" value="false"/>
2632 <param name="test" value="true"/>
2633 </conditional>
2634 <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
2635 <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2636 <section name="algorithm">
2637 <section name="common">
2638 <param name="noise_threshold_int" value="10.0"/>
2639 <param name="chrom_peak_snr" value="3.0"/>
2640 <param name="chrom_fwhm" value="5.0"/>
2641 </section>
2642 <section name="mtd">
2643 <param name="mass_error_ppm" value="20.0"/>
2644 <param name="reestimate_mt_sd" value="true"/>
2645 <param name="quant_method" value="max_height"/>
2646 <param name="trace_termination_criterion" value="outlier"/>
2647 <param name="trace_termination_outliers" value="5"/>
2648 <param name="min_sample_rate" value="0.5"/>
2649 <param name="min_trace_length" value="5.0"/>
2650 <param name="max_trace_length" value="300.0"/>
2651 </section>
2652 <section name="epd">
2653 <param name="enabled" value="true"/>
2654 <param name="width_filtering" value="off"/>
2655 <param name="min_fwhm" value="3.0"/>
2656 <param name="max_fwhm" value="60.0"/>
2657 <param name="masstrace_snr_filtering" value="false"/>
2658 </section>
2659 <section name="ffm">
2660 <param name="local_rt_range" value="10.0"/>
2661 <param name="local_mz_range" value="6.5"/>
2662 <param name="charge_lower_bound" value="1"/>
2663 <param name="charge_upper_bound" value="3"/>
2664 <param name="report_summed_ints" value="false"/>
2665 <param name="enable_RT_filtering" value="true"/>
2666 <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
2667 <param name="mz_scoring_13C" value="true"/>
2668 <param name="use_smoothed_intensities" value="true"/>
2669 <param name="report_convex_hulls" value="false"/>
2670 <param name="remove_single_traces" value="false"/>
2671 <param name="mz_scoring_by_elements" value="false"/>
2672 <param name="elements" value="CHNOPS"/>
2673 </section>
2674 </section>
2675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2676 <output name="ctd_out" ftype="xml">
2677 <assert_contents>
2678 <is_valid_xml/>
2679 </assert_contents>
2680 </output>
2681 </test>
2682 </xml>
2683 <xml name="autotest_FeatureFinderMRM">
2684 <test expect_num_outputs="2">
2685 <conditional name="adv_opts_cond">
2686 <param name="adv_opts_selector" value="advanced"/>
2687 <param name="force" value="false"/>
2688 <param name="test" value="true"/>
2689 </conditional>
2690 <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
2691 <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2692 <section name="algorithm">
2693 <param name="min_rt_distance" value="10.0"/>
2694 <param name="min_num_peaks_per_feature" value="5"/>
2695 <param name="min_signal_to_noise_ratio" value="2.0"/>
2696 <param name="write_debug_files" value="false"/>
2697 <param name="resample_traces" value="false"/>
2698 <param name="write_debuginfo" value="false"/>
2699 </section>
2700 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2701 <output name="ctd_out" ftype="xml">
2702 <assert_contents>
2703 <is_valid_xml/>
2704 </assert_contents>
2705 </output>
2706 </test>
2707 </xml>
2708 <xml name="autotest_FeatureFinderMultiplex">
2709 <test expect_num_outputs="3">
2710 <conditional name="adv_opts_cond">
2711 <param name="adv_opts_selector" value="advanced"/>
2712 <param name="force" value="false"/>
2713 <param name="test" value="true"/>
2714 </conditional>
2715 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
2716 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2717 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2718 <section name="algorithm">
2719 <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
2720 <param name="charge" value="1:4"/>
2721 <param name="isotopes_per_peptide" value="3:6"/>
2722 <param name="rt_typical" value="90.0"/>
2723 <param name="rt_band" value="10.0"/>
2724 <param name="rt_min" value="5.0"/>
2725 <param name="mz_tolerance" value="40.0"/>
2726 <param name="mz_unit" value="ppm"/>
2727 <param name="intensity_cutoff" value="10.0"/>
2728 <param name="peptide_similarity" value="0.8"/>
2729 <param name="averagine_similarity" value="0.75"/>
2730 <param name="averagine_similarity_scaling" value="0.75"/>
2731 <param name="missed_cleavages" value="1"/>
2732 <param name="spectrum_type" value="automatic"/>
2733 <param name="averagine_type" value="peptide"/>
2734 <param name="knock_out" value="false"/>
2735 </section>
2736 <section name="labels">
2737 <param name="Arg6" value="6.0201290268"/>
2738 <param name="Arg10" value="10.0082686"/>
2739 <param name="Lys4" value="4.0251069836"/>
2740 <param name="Lys6" value="6.0201290268"/>
2741 <param name="Lys8" value="8.0141988132"/>
2742 <param name="Leu3" value="3.01883"/>
2743 <param name="Dimethyl0" value="28.0313"/>
2744 <param name="Dimethyl4" value="32.056407"/>
2745 <param name="Dimethyl6" value="34.063117"/>
2746 <param name="Dimethyl8" value="36.07567"/>
2747 <param name="ICPL0" value="105.021464"/>
2748 <param name="ICPL4" value="109.046571"/>
2749 <param name="ICPL6" value="111.041593"/>
2750 <param name="ICPL10" value="115.0667"/>
2751 </section>
2752 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2753 <output name="ctd_out" ftype="xml">
2754 <assert_contents>
2755 <is_valid_xml/>
2756 </assert_contents>
2757 </output>
2758 </test>
2759 <test expect_num_outputs="3">
2760 <conditional name="adv_opts_cond">
2761 <param name="adv_opts_selector" value="advanced"/>
2762 <param name="force" value="false"/>
2763 <param name="test" value="true"/>
2764 </conditional>
2765 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
2766 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2767 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2768 <section name="algorithm">
2769 <param name="labels" value="[][Lys8,Arg10]"/>
2770 <param name="charge" value="1:4"/>
2771 <param name="isotopes_per_peptide" value="3:6"/>
2772 <param name="rt_typical" value="40.0"/>
2773 <param name="rt_band" value="5.0"/>
2774 <param name="rt_min" value="2.0"/>
2775 <param name="mz_tolerance" value="6.0"/>
2776 <param name="mz_unit" value="ppm"/>
2777 <param name="intensity_cutoff" value="1000.0"/>
2778 <param name="peptide_similarity" value="0.5"/>
2779 <param name="averagine_similarity" value="0.4"/>
2780 <param name="averagine_similarity_scaling" value="0.75"/>
2781 <param name="missed_cleavages" value="0"/>
2782 <param name="spectrum_type" value="automatic"/>
2783 <param name="averagine_type" value="peptide"/>
2784 <param name="knock_out" value="false"/>
2785 </section>
2786 <section name="labels">
2787 <param name="Arg6" value="6.0201290268"/>
2788 <param name="Arg10" value="10.0082686"/>
2789 <param name="Lys4" value="4.0251069836"/>
2790 <param name="Lys6" value="6.0201290268"/>
2791 <param name="Lys8" value="8.0141988132"/>
2792 <param name="Leu3" value="3.01883"/>
2793 <param name="Dimethyl0" value="28.0313"/>
2794 <param name="Dimethyl4" value="32.056407"/>
2795 <param name="Dimethyl6" value="34.063117"/>
2796 <param name="Dimethyl8" value="36.07567"/>
2797 <param name="ICPL0" value="105.021464"/>
2798 <param name="ICPL4" value="109.046571"/>
2799 <param name="ICPL6" value="111.041593"/>
2800 <param name="ICPL10" value="115.0667"/>
2801 </section>
2802 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2803 <output name="ctd_out" ftype="xml">
2804 <assert_contents>
2805 <is_valid_xml/>
2806 </assert_contents>
2807 </output>
2808 </test>
2809 <test expect_num_outputs="3">
2810 <conditional name="adv_opts_cond">
2811 <param name="adv_opts_selector" value="advanced"/>
2812 <param name="force" value="false"/>
2813 <param name="test" value="true"/>
2814 </conditional>
2815 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
2816 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2817 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2818 <section name="algorithm">
2819 <param name="labels" value="[]"/>
2820 <param name="charge" value="5:15"/>
2821 <param name="isotopes_per_peptide" value="5:10"/>
2822 <param name="rt_typical" value="45.0"/>
2823 <param name="rt_band" value="5.0"/>
2824 <param name="rt_min" value="2.0"/>
2825 <param name="mz_tolerance" value="6.0"/>
2826 <param name="mz_unit" value="ppm"/>
2827 <param name="intensity_cutoff" value="200.0"/>
2828 <param name="peptide_similarity" value="0.5"/>
2829 <param name="averagine_similarity" value="0.4"/>
2830 <param name="averagine_similarity_scaling" value="0.75"/>
2831 <param name="missed_cleavages" value="0"/>
2832 <param name="spectrum_type" value="automatic"/>
2833 <param name="averagine_type" value="RNA"/>
2834 <param name="knock_out" value="false"/>
2835 </section>
2836 <section name="labels">
2837 <param name="Arg6" value="6.0201290268"/>
2838 <param name="Arg10" value="10.0082686"/>
2839 <param name="Lys4" value="4.0251069836"/>
2840 <param name="Lys6" value="6.0201290268"/>
2841 <param name="Lys8" value="8.0141988132"/>
2842 <param name="Leu3" value="3.01883"/>
2843 <param name="Dimethyl0" value="28.0313"/>
2844 <param name="Dimethyl4" value="32.056407"/>
2845 <param name="Dimethyl6" value="34.063117"/>
2846 <param name="Dimethyl8" value="36.07567"/>
2847 <param name="ICPL0" value="105.021464"/>
2848 <param name="ICPL4" value="109.046571"/>
2849 <param name="ICPL6" value="111.041593"/>
2850 <param name="ICPL10" value="115.0667"/>
2851 </section>
2852 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2853 <output name="ctd_out" ftype="xml">
2854 <assert_contents>
2855 <is_valid_xml/>
2856 </assert_contents>
2857 </output>
2858 </test>
2859 <test expect_num_outputs="3">
2860 <conditional name="adv_opts_cond">
2861 <param name="adv_opts_selector" value="advanced"/>
2862 <param name="force" value="false"/>
2863 <param name="test" value="true"/>
2864 </conditional>
2865 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
2866 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2867 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2868 <section name="algorithm">
2869 <param name="labels" value="[]"/>
2870 <param name="charge" value="5:15"/>
2871 <param name="isotopes_per_peptide" value="5:10"/>
2872 <param name="rt_typical" value="45.0"/>
2873 <param name="rt_band" value="5.0"/>
2874 <param name="rt_min" value="2.0"/>
2875 <param name="mz_tolerance" value="6.0"/>
2876 <param name="mz_unit" value="ppm"/>
2877 <param name="intensity_cutoff" value="200.0"/>
2878 <param name="peptide_similarity" value="0.5"/>
2879 <param name="averagine_similarity" value="0.4"/>
2880 <param name="averagine_similarity_scaling" value="0.75"/>
2881 <param name="missed_cleavages" value="0"/>
2882 <param name="spectrum_type" value="automatic"/>
2883 <param name="averagine_type" value="DNA"/>
2884 <param name="knock_out" value="false"/>
2885 </section>
2886 <section name="labels">
2887 <param name="Arg6" value="6.0201290268"/>
2888 <param name="Arg10" value="10.0082686"/>
2889 <param name="Lys4" value="4.0251069836"/>
2890 <param name="Lys6" value="6.0201290268"/>
2891 <param name="Lys8" value="8.0141988132"/>
2892 <param name="Leu3" value="3.01883"/>
2893 <param name="Dimethyl0" value="28.0313"/>
2894 <param name="Dimethyl4" value="32.056407"/>
2895 <param name="Dimethyl6" value="34.063117"/>
2896 <param name="Dimethyl8" value="36.07567"/>
2897 <param name="ICPL0" value="105.021464"/>
2898 <param name="ICPL4" value="109.046571"/>
2899 <param name="ICPL6" value="111.041593"/>
2900 <param name="ICPL10" value="115.0667"/>
2901 </section>
2902 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2903 <output name="ctd_out" ftype="xml">
2904 <assert_contents>
2905 <is_valid_xml/>
2906 </assert_contents>
2907 </output>
2908 </test>
2909 <test expect_num_outputs="3">
2910 <conditional name="adv_opts_cond">
2911 <param name="adv_opts_selector" value="advanced"/>
2912 <param name="force" value="false"/>
2913 <param name="test" value="true"/>
2914 </conditional>
2915 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
2916 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2917 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2918 <section name="algorithm">
2919 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2920 <param name="charge" value="1:5"/>
2921 <param name="isotopes_per_peptide" value="3:6"/>
2922 <param name="rt_typical" value="50.0"/>
2923 <param name="rt_band" value="3.0"/>
2924 <param name="rt_min" value="8.0"/>
2925 <param name="mz_tolerance" value="10.0"/>
2926 <param name="mz_unit" value="ppm"/>
2927 <param name="intensity_cutoff" value="10000000.0"/>
2928 <param name="peptide_similarity" value="0.95"/>
2929 <param name="averagine_similarity" value="0.8"/>
2930 <param name="averagine_similarity_scaling" value="0.95"/>
2931 <param name="missed_cleavages" value="3"/>
2932 <param name="spectrum_type" value="profile"/>
2933 <param name="averagine_type" value="peptide"/>
2934 <param name="knock_out" value="false"/>
2935 </section>
2936 <section name="labels">
2937 <param name="Arg6" value="6.0201290268"/>
2938 <param name="Arg10" value="10.0082686"/>
2939 <param name="Lys4" value="4.0251069836"/>
2940 <param name="Lys6" value="6.0201290268"/>
2941 <param name="Lys8" value="8.0141988132"/>
2942 <param name="Leu3" value="3.01883"/>
2943 <param name="Dimethyl0" value="28.0313"/>
2944 <param name="Dimethyl4" value="32.056407"/>
2945 <param name="Dimethyl6" value="34.063117"/>
2946 <param name="Dimethyl8" value="36.07567"/>
2947 <param name="ICPL0" value="105.021464"/>
2948 <param name="ICPL4" value="109.046571"/>
2949 <param name="ICPL6" value="111.041593"/>
2950 <param name="ICPL10" value="115.0667"/>
2951 </section>
2952 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
2953 <output name="ctd_out" ftype="xml">
2954 <assert_contents>
2955 <is_valid_xml/>
2956 </assert_contents>
2957 </output>
2958 </test>
2959 <test expect_num_outputs="3">
2960 <conditional name="adv_opts_cond">
2961 <param name="adv_opts_selector" value="advanced"/>
2962 <param name="force" value="false"/>
2963 <param name="test" value="true"/>
2964 </conditional>
2965 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
2966 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
2967 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
2968 <section name="algorithm">
2969 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
2970 <param name="charge" value="1:5"/>
2971 <param name="isotopes_per_peptide" value="3:6"/>
2972 <param name="rt_typical" value="50.0"/>
2973 <param name="rt_band" value="3.0"/>
2974 <param name="rt_min" value="8.0"/>
2975 <param name="mz_tolerance" value="10.0"/>
2976 <param name="mz_unit" value="ppm"/>
2977 <param name="intensity_cutoff" value="10000000.0"/>
2978 <param name="peptide_similarity" value="0.95"/>
2979 <param name="averagine_similarity" value="0.8"/>
2980 <param name="averagine_similarity_scaling" value="1.0"/>
2981 <param name="missed_cleavages" value="3"/>
2982 <param name="spectrum_type" value="profile"/>
2983 <param name="averagine_type" value="peptide"/>
2984 <param name="knock_out" value="false"/>
2985 </section>
2986 <section name="labels">
2987 <param name="Arg6" value="6.0201290268"/>
2988 <param name="Arg10" value="10.0082686"/>
2989 <param name="Lys4" value="4.0251069836"/>
2990 <param name="Lys6" value="6.0201290268"/>
2991 <param name="Lys8" value="8.0141988132"/>
2992 <param name="Leu3" value="3.01883"/>
2993 <param name="Dimethyl0" value="28.0313"/>
2994 <param name="Dimethyl4" value="32.056407"/>
2995 <param name="Dimethyl6" value="34.063117"/>
2996 <param name="Dimethyl8" value="36.07567"/>
2997 <param name="ICPL0" value="105.021464"/>
2998 <param name="ICPL4" value="109.046571"/>
2999 <param name="ICPL6" value="111.041593"/>
3000 <param name="ICPL10" value="115.0667"/>
3001 </section>
3002 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3003 <output name="ctd_out" ftype="xml">
3004 <assert_contents>
3005 <is_valid_xml/>
3006 </assert_contents>
3007 </output>
3008 </test>
3009 <test expect_num_outputs="3">
3010 <conditional name="adv_opts_cond">
3011 <param name="adv_opts_selector" value="advanced"/>
3012 <param name="force" value="false"/>
3013 <param name="test" value="true"/>
3014 </conditional>
3015 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
3016 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3017 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3018 <section name="algorithm">
3019 <param name="labels" value="[][Dimethyl4]"/>
3020 <param name="charge" value="1:4"/>
3021 <param name="isotopes_per_peptide" value="3:6"/>
3022 <param name="rt_typical" value="40.0"/>
3023 <param name="rt_band" value="5.0"/>
3024 <param name="rt_min" value="2.0"/>
3025 <param name="mz_tolerance" value="6.0"/>
3026 <param name="mz_unit" value="ppm"/>
3027 <param name="intensity_cutoff" value="1000.0"/>
3028 <param name="peptide_similarity" value="0.5"/>
3029 <param name="averagine_similarity" value="0.4"/>
3030 <param name="averagine_similarity_scaling" value="0.75"/>
3031 <param name="missed_cleavages" value="0"/>
3032 <param name="spectrum_type" value="automatic"/>
3033 <param name="averagine_type" value="peptide"/>
3034 <param name="knock_out" value="false"/>
3035 </section>
3036 <section name="labels">
3037 <param name="Arg6" value="6.0201290268"/>
3038 <param name="Arg10" value="10.0082686"/>
3039 <param name="Lys4" value="4.0251069836"/>
3040 <param name="Lys6" value="6.0201290268"/>
3041 <param name="Lys8" value="8.0141988132"/>
3042 <param name="Leu3" value="3.01883"/>
3043 <param name="Dimethyl0" value="28.0313"/>
3044 <param name="Dimethyl4" value="31.0094"/>
3045 <param name="Dimethyl6" value="34.063117"/>
3046 <param name="Dimethyl8" value="36.07567"/>
3047 <param name="ICPL0" value="105.021464"/>
3048 <param name="ICPL4" value="109.046571"/>
3049 <param name="ICPL6" value="111.041593"/>
3050 <param name="ICPL10" value="115.0667"/>
3051 </section>
3052 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3053 <output name="ctd_out" ftype="xml">
3054 <assert_contents>
3055 <is_valid_xml/>
3056 </assert_contents>
3057 </output>
3058 </test>
3059 <test expect_num_outputs="3">
3060 <conditional name="adv_opts_cond">
3061 <param name="adv_opts_selector" value="advanced"/>
3062 <param name="force" value="false"/>
3063 <param name="test" value="true"/>
3064 </conditional>
3065 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
3066 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3067 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3068 <section name="algorithm">
3069 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
3070 <param name="charge" value="1:7"/>
3071 <param name="isotopes_per_peptide" value="3:8"/>
3072 <param name="rt_typical" value="50.0"/>
3073 <param name="rt_band" value="3.0"/>
3074 <param name="rt_min" value="8.0"/>
3075 <param name="mz_tolerance" value="10.0"/>
3076 <param name="mz_unit" value="ppm"/>
3077 <param name="intensity_cutoff" value="10.0"/>
3078 <param name="peptide_similarity" value="0.2"/>
3079 <param name="averagine_similarity" value="0.25"/>
3080 <param name="averagine_similarity_scaling" value="0.95"/>
3081 <param name="missed_cleavages" value="4"/>
3082 <param name="spectrum_type" value="automatic"/>
3083 <param name="averagine_type" value="peptide"/>
3084 <param name="knock_out" value="true"/>
3085 </section>
3086 <section name="labels">
3087 <param name="Arg6" value="6.0201290268"/>
3088 <param name="Arg10" value="10.0082686"/>
3089 <param name="Lys4" value="4.0251069836"/>
3090 <param name="Lys6" value="6.0201290268"/>
3091 <param name="Lys8" value="8.0141988132"/>
3092 <param name="Leu3" value="3.01883"/>
3093 <param name="Dimethyl0" value="28.0313"/>
3094 <param name="Dimethyl4" value="32.056407"/>
3095 <param name="Dimethyl6" value="34.063117"/>
3096 <param name="Dimethyl8" value="36.07567"/>
3097 <param name="ICPL0" value="105.021464"/>
3098 <param name="ICPL4" value="109.046571"/>
3099 <param name="ICPL6" value="111.041593"/>
3100 <param name="ICPL10" value="115.0667"/>
3101 </section>
3102 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3103 <output name="ctd_out" ftype="xml">
3104 <assert_contents>
3105 <is_valid_xml/>
3106 </assert_contents>
3107 </output>
3108 </test>
3109 <test expect_num_outputs="3">
3110 <conditional name="adv_opts_cond">
3111 <param name="adv_opts_selector" value="advanced"/>
3112 <param name="force" value="false"/>
3113 <param name="test" value="true"/>
3114 </conditional>
3115 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
3116 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3117 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3118 <section name="algorithm">
3119 <param name="labels" value="[0][6.03705]"/>
3120 <param name="charge" value="2:8"/>
3121 <param name="isotopes_per_peptide" value="3:8"/>
3122 <param name="rt_typical" value="40.0"/>
3123 <param name="rt_band" value="0.0"/>
3124 <param name="rt_min" value="4.0"/>
3125 <param name="mz_tolerance" value="10.0"/>
3126 <param name="mz_unit" value="ppm"/>
3127 <param name="intensity_cutoff" value="1000.0"/>
3128 <param name="peptide_similarity" value="0.5"/>
3129 <param name="averagine_similarity" value="0.4"/>
3130 <param name="averagine_similarity_scaling" value="0.95"/>
3131 <param name="missed_cleavages" value="0"/>
3132 <param name="spectrum_type" value="centroid"/>
3133 <param name="averagine_type" value="peptide"/>
3134 <param name="knock_out" value="false"/>
3135 </section>
3136 <section name="labels">
3137 <param name="Arg6" value="6.0201290268"/>
3138 <param name="Arg10" value="10.0082686"/>
3139 <param name="Lys4" value="4.0251069836"/>
3140 <param name="Lys6" value="6.0201290268"/>
3141 <param name="Lys8" value="8.0141988132"/>
3142 <param name="Leu3" value="3.01883"/>
3143 <param name="Dimethyl0" value="28.0313"/>
3144 <param name="Dimethyl4" value="32.056407"/>
3145 <param name="Dimethyl6" value="34.063117"/>
3146 <param name="Dimethyl8" value="36.07567"/>
3147 <param name="ICPL0" value="105.021464"/>
3148 <param name="ICPL4" value="109.046571"/>
3149 <param name="ICPL6" value="111.041593"/>
3150 <param name="ICPL10" value="115.0667"/>
3151 </section>
3152 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3153 <output name="ctd_out" ftype="xml">
3154 <assert_contents>
3155 <is_valid_xml/>
3156 </assert_contents>
3157 </output>
3158 </test>
3159 <test expect_num_outputs="3">
3160 <conditional name="adv_opts_cond">
3161 <param name="adv_opts_selector" value="advanced"/>
3162 <param name="force" value="false"/>
3163 <param name="test" value="true"/>
3164 </conditional>
3165 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
3166 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3167 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3168 <section name="algorithm">
3169 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
3170 <param name="charge" value="1:7"/>
3171 <param name="isotopes_per_peptide" value="3:6"/>
3172 <param name="rt_typical" value="50.0"/>
3173 <param name="rt_band" value="5.0"/>
3174 <param name="rt_min" value="8.0"/>
3175 <param name="mz_tolerance" value="6.0"/>
3176 <param name="mz_unit" value="ppm"/>
3177 <param name="intensity_cutoff" value="10.0"/>
3178 <param name="peptide_similarity" value="0.4"/>
3179 <param name="averagine_similarity" value="0.5"/>
3180 <param name="averagine_similarity_scaling" value="0.95"/>
3181 <param name="missed_cleavages" value="3"/>
3182 <param name="spectrum_type" value="profile"/>
3183 <param name="averagine_type" value="peptide"/>
3184 <param name="knock_out" value="true"/>
3185 </section>
3186 <section name="labels">
3187 <param name="Arg6" value="6.0201290268"/>
3188 <param name="Arg10" value="10.0082686"/>
3189 <param name="Lys4" value="4.0251069836"/>
3190 <param name="Lys6" value="6.0201290268"/>
3191 <param name="Lys8" value="8.0141988132"/>
3192 <param name="Leu3" value="3.01883"/>
3193 <param name="Dimethyl0" value="28.0313"/>
3194 <param name="Dimethyl4" value="32.056407"/>
3195 <param name="Dimethyl6" value="34.063117"/>
3196 <param name="Dimethyl8" value="36.07567"/>
3197 <param name="ICPL0" value="105.021464"/>
3198 <param name="ICPL4" value="109.046571"/>
3199 <param name="ICPL6" value="111.041593"/>
3200 <param name="ICPL10" value="115.0667"/>
3201 </section>
3202 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
3203 <output name="ctd_out" ftype="xml">
3204 <assert_contents>
3205 <is_valid_xml/>
3206 </assert_contents>
3207 </output>
3208 </test>
3209 <test expect_num_outputs="2">
3210 <conditional name="adv_opts_cond">
3211 <param name="adv_opts_selector" value="advanced"/>
3212 <param name="force" value="false"/>
3213 <param name="test" value="true"/>
3214 </conditional>
3215 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
3216 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3217 <section name="algorithm">
3218 <param name="labels" value="[]"/>
3219 <param name="charge" value="1:4"/>
3220 <param name="isotopes_per_peptide" value="3:6"/>
3221 <param name="rt_typical" value="1e-05"/>
3222 <param name="rt_band" value="0.0"/>
3223 <param name="rt_min" value="0.0"/>
3224 <param name="mz_tolerance" value="10.0"/>
3225 <param name="mz_unit" value="ppm"/>
3226 <param name="intensity_cutoff" value="1000.0"/>
3227 <param name="peptide_similarity" value="0.5"/>
3228 <param name="averagine_similarity" value="0.7"/>
3229 <param name="averagine_similarity_scaling" value="0.95"/>
3230 <param name="missed_cleavages" value="0"/>
3231 <param name="spectrum_type" value="automatic"/>
3232 <param name="averagine_type" value="peptide"/>
3233 <param name="knock_out" value="false"/>
3234 </section>
3235 <section name="labels">
3236 <param name="Arg6" value="6.0201290268"/>
3237 <param name="Arg10" value="10.0082686"/>
3238 <param name="Lys4" value="4.0251069836"/>
3239 <param name="Lys6" value="6.0201290268"/>
3240 <param name="Lys8" value="8.0141988132"/>
3241 <param name="Leu3" value="3.01883"/>
3242 <param name="Dimethyl0" value="28.0313"/>
3243 <param name="Dimethyl4" value="32.056407"/>
3244 <param name="Dimethyl6" value="34.063117"/>
3245 <param name="Dimethyl8" value="36.07567"/>
3246 <param name="ICPL0" value="105.021464"/>
3247 <param name="ICPL4" value="109.046571"/>
3248 <param name="ICPL6" value="111.041593"/>
3249 <param name="ICPL10" value="115.0667"/>
3250 </section>
3251 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
3252 <output name="ctd_out" ftype="xml">
3253 <assert_contents>
3254 <is_valid_xml/>
3255 </assert_contents>
3256 </output>
3257 </test>
3258 </xml>
3259 <xml name="autotest_FeatureFinderSuperHirn">
3260 <test expect_num_outputs="2">
3261 <conditional name="adv_opts_cond">
3262 <param name="adv_opts_selector" value="advanced"/>
3263 <param name="force" value="false"/>
3264 <param name="test" value="true"/>
3265 </conditional>
3266 <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/>
3267 <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3268 <section name="algorithm">
3269 <section name="centroiding">
3270 <param name="active" value="false"/>
3271 <param name="window_width" value="5"/>
3272 <param name="absolute_isotope_mass_precision" value="0.01"/>
3273 <param name="relative_isotope_mass_precision" value="10.0"/>
3274 <param name="minimal_peak_height" value="0.0"/>
3275 <param name="min_ms_signal_intensity" value="50.0"/>
3276 </section>
3277 <section name="ms1">
3278 <param name="precursor_detection_scan_levels" value="1"/>
3279 <param name="max_inter_scan_distance" value="0"/>
3280 <param name="tr_resolution" value="0.01"/>
3281 <param name="intensity_threshold" value="1000.0"/>
3282 <param name="max_inter_scan_rt_distance" value="0.1"/>
3283 <param name="min_nb_cluster_members" value="4"/>
3284 <param name="detectable_isotope_factor" value="0.05"/>
3285 <param name="intensity_cv" value="0.9"/>
3286 <param name="retention_time_tolerance" value="0.5"/>
3287 <param name="mz_tolerance" value="0.0"/>
3288 </section>
3289 <section name="ms1_feature_merger">
3290 <param name="active" value="true"/>
3291 <param name="tr_resolution" value="0.01"/>
3292 <param name="initial_apex_tr_tolerance" value="5.0"/>
3293 <param name="feature_merging_tr_tolerance" value="1.0"/>
3294 <param name="intensity_variation_percentage" value="25.0"/>
3295 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3296 </section>
3297 <section name="ms1_feature_selection_options">
3298 <param name="start_elution_window" value="0.0"/>
3299 <param name="end_elution_window" value="180.0"/>
3300 <param name="mz_range_min" value="0.0"/>
3301 <param name="mz_range_max" value="2000.0"/>
3302 <param name="chrg_range_min" value="1"/>
3303 <param name="chrg_range_max" value="5"/>
3304 </section>
3305 </section>
3306 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3307 <output name="ctd_out" ftype="xml">
3308 <assert_contents>
3309 <is_valid_xml/>
3310 </assert_contents>
3311 </output>
3312 </test>
3313 <test expect_num_outputs="2">
3314 <conditional name="adv_opts_cond">
3315 <param name="adv_opts_selector" value="advanced"/>
3316 <param name="force" value="false"/>
3317 <param name="test" value="true"/>
3318 </conditional>
3319 <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/>
3320 <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
3321 <section name="algorithm">
3322 <section name="centroiding">
3323 <param name="active" value="true"/>
3324 <param name="window_width" value="5"/>
3325 <param name="absolute_isotope_mass_precision" value="0.01"/>
3326 <param name="relative_isotope_mass_precision" value="10.0"/>
3327 <param name="minimal_peak_height" value="0.0"/>
3328 <param name="min_ms_signal_intensity" value="50.0"/>
3329 </section>
3330 <section name="ms1">
3331 <param name="precursor_detection_scan_levels" value="1"/>
3332 <param name="max_inter_scan_distance" value="0"/>
3333 <param name="tr_resolution" value="0.01"/>
3334 <param name="intensity_threshold" value="1000.0"/>
3335 <param name="max_inter_scan_rt_distance" value="0.1"/>
3336 <param name="min_nb_cluster_members" value="4"/>
3337 <param name="detectable_isotope_factor" value="0.05"/>
3338 <param name="intensity_cv" value="0.9"/>
3339 <param name="retention_time_tolerance" value="0.5"/>
3340 <param name="mz_tolerance" value="0.0"/>
3341 </section>
3342 <section name="ms1_feature_merger">
3343 <param name="active" value="true"/>
3344 <param name="tr_resolution" value="0.01"/>
3345 <param name="initial_apex_tr_tolerance" value="5.0"/>
3346 <param name="feature_merging_tr_tolerance" value="1.0"/>
3347 <param name="intensity_variation_percentage" value="25.0"/>
3348 <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
3349 </section>
3350 <section name="ms1_feature_selection_options">
3351 <param name="start_elution_window" value="0.0"/>
3352 <param name="end_elution_window" value="180.0"/>
3353 <param name="mz_range_min" value="0.0"/>
3354 <param name="mz_range_max" value="2000.0"/>
3355 <param name="chrg_range_min" value="1"/>
3356 <param name="chrg_range_max" value="5"/>
3357 </section>
3358 </section>
3359 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3360 <output name="ctd_out" ftype="xml">
3361 <assert_contents>
3362 <is_valid_xml/>
3363 </assert_contents>
3364 </output>
3365 </test>
3366 </xml>
3367 <xml name="autotest_FeatureLinkerLabeled">
3368 <test expect_num_outputs="2">
3369 <conditional name="adv_opts_cond">
3370 <param name="adv_opts_selector" value="advanced"/>
3371 <param name="force" value="false"/>
3372 <param name="test" value="true"/>
3373 </conditional>
3374 <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
3375 <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3376 <section name="algorithm">
3377 <param name="rt_estimate" value="false"/>
3378 <param name="rt_pair_dist" value="-1.0"/>
3379 <param name="rt_dev_low" value="0.4"/>
3380 <param name="rt_dev_high" value="0.4"/>
3381 <param name="mz_pair_dists" value="8.0"/>
3382 <param name="mz_dev" value="0.1"/>
3383 <param name="mrm" value="false"/>
3384 </section>
3385 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3386 <output name="ctd_out" ftype="xml">
3387 <assert_contents>
3388 <is_valid_xml/>
3389 </assert_contents>
3390 </output>
3391 </test>
3392 <test expect_num_outputs="2">
3393 <conditional name="adv_opts_cond">
3394 <param name="adv_opts_selector" value="advanced"/>
3395 <param name="force" value="false"/>
3396 <param name="test" value="true"/>
3397 </conditional>
3398 <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
3399 <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3400 <section name="algorithm">
3401 <param name="rt_estimate" value="true"/>
3402 <param name="rt_pair_dist" value="-121.0382"/>
3403 <param name="rt_dev_low" value="123.3965"/>
3404 <param name="rt_dev_high" value="123.3965"/>
3405 <param name="mz_pair_dists" value="4.0"/>
3406 <param name="mz_dev" value="0.1"/>
3407 <param name="mrm" value="false"/>
3408 </section>
3409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3410 <output name="ctd_out" ftype="xml">
3411 <assert_contents>
3412 <is_valid_xml/>
3413 </assert_contents>
3414 </output>
3415 </test>
3416 </xml>
3417 <xml name="autotest_FeatureLinkerUnlabeledKD">
3418 <test expect_num_outputs="2">
3419 <conditional name="adv_opts_cond">
3420 <param name="adv_opts_selector" value="advanced"/>
3421 <param name="force" value="false"/>
3422 <param name="test" value="true"/>
3423 </conditional>
3424 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3425 <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3426 <param name="keep_subelements" value="false"/>
3427 <section name="algorithm">
3428 <param name="mz_unit" value="Da"/>
3429 <param name="nr_partitions" value="1"/>
3430 <section name="warp">
3431 <param name="enabled" value="false"/>
3432 <param name="rt_tol" value="100.0"/>
3433 <param name="mz_tol" value="0.3"/>
3434 <param name="max_pairwise_log_fc" value="0.5"/>
3435 <param name="min_rel_cc_size" value="0.5"/>
3436 <param name="max_nr_conflicts" value="0"/>
3437 </section>
3438 <section name="link">
3439 <param name="rt_tol" value="100.0"/>
3440 <param name="mz_tol" value="0.3"/>
3441 <param name="charge_merging" value="With_charge_zero"/>
3442 <param name="adduct_merging" value="Any"/>
3443 </section>
3444 <section name="distance_RT">
3445 <param name="exponent" value="1.0"/>
3446 <param name="weight" value="1.0"/>
3447 </section>
3448 <section name="distance_MZ">
3449 <param name="exponent" value="2.0"/>
3450 <param name="weight" value="1.0"/>
3451 </section>
3452 <section name="distance_intensity">
3453 <param name="exponent" value="1.0"/>
3454 <param name="weight" value="1.0"/>
3455 <param name="log_transform" value="enabled"/>
3456 </section>
3457 <section name="LOWESS">
3458 <param name="span" value="0.666666666666667"/>
3459 <param name="num_iterations" value="3"/>
3460 <param name="delta" value="-1.0"/>
3461 <param name="interpolation_type" value="cspline"/>
3462 <param name="extrapolation_type" value="four-point-linear"/>
3463 </section>
3464 </section>
3465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3466 <output name="ctd_out" ftype="xml">
3467 <assert_contents>
3468 <is_valid_xml/>
3469 </assert_contents>
3470 </output>
3471 </test>
3472 <test expect_num_outputs="2">
3473 <conditional name="adv_opts_cond">
3474 <param name="adv_opts_selector" value="advanced"/>
3475 <param name="force" value="false"/>
3476 <param name="test" value="true"/>
3477 </conditional>
3478 <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
3479 <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3480 <param name="keep_subelements" value="true"/>
3481 <section name="algorithm">
3482 <param name="mz_unit" value="Da"/>
3483 <param name="nr_partitions" value="99999"/>
3484 <section name="warp">
3485 <param name="enabled" value="false"/>
3486 <param name="rt_tol" value="100.0"/>
3487 <param name="mz_tol" value="0.3"/>
3488 <param name="max_pairwise_log_fc" value="0.5"/>
3489 <param name="min_rel_cc_size" value="0.5"/>
3490 <param name="max_nr_conflicts" value="0"/>
3491 </section>
3492 <section name="link">
3493 <param name="rt_tol" value="100.0"/>
3494 <param name="mz_tol" value="0.3"/>
3495 <param name="charge_merging" value="With_charge_zero"/>
3496 <param name="adduct_merging" value="Any"/>
3497 </section>
3498 <section name="distance_RT">
3499 <param name="exponent" value="1.0"/>
3500 <param name="weight" value="1.0"/>
3501 </section>
3502 <section name="distance_MZ">
3503 <param name="exponent" value="2.0"/>
3504 <param name="weight" value="1.0"/>
3505 </section>
3506 <section name="distance_intensity">
3507 <param name="exponent" value="1.0"/>
3508 <param name="weight" value="1.0"/>
3509 <param name="log_transform" value="enabled"/>
3510 </section>
3511 <section name="LOWESS">
3512 <param name="span" value="0.666666666666667"/>
3513 <param name="num_iterations" value="3"/>
3514 <param name="delta" value="-1.0"/>
3515 <param name="interpolation_type" value="cspline"/>
3516 <param name="extrapolation_type" value="four-point-linear"/>
3517 </section>
3518 </section>
3519 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3520 <output name="ctd_out" ftype="xml">
3521 <assert_contents>
3522 <is_valid_xml/>
3523 </assert_contents>
3524 </output>
3525 </test>
3526 <test expect_num_outputs="2">
3527 <conditional name="adv_opts_cond">
3528 <param name="adv_opts_selector" value="advanced"/>
3529 <param name="force" value="false"/>
3530 <param name="test" value="true"/>
3531 </conditional>
3532 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3533 <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3534 <param name="keep_subelements" value="false"/>
3535 <section name="algorithm">
3536 <param name="mz_unit" value="Da"/>
3537 <param name="nr_partitions" value="100"/>
3538 <section name="warp">
3539 <param name="enabled" value="false"/>
3540 <param name="rt_tol" value="100.0"/>
3541 <param name="mz_tol" value="0.3"/>
3542 <param name="max_pairwise_log_fc" value="0.5"/>
3543 <param name="min_rel_cc_size" value="0.5"/>
3544 <param name="max_nr_conflicts" value="0"/>
3545 </section>
3546 <section name="link">
3547 <param name="rt_tol" value="100.0"/>
3548 <param name="mz_tol" value="0.3"/>
3549 <param name="charge_merging" value="With_charge_zero"/>
3550 <param name="adduct_merging" value="Any"/>
3551 </section>
3552 <section name="distance_RT">
3553 <param name="exponent" value="1.0"/>
3554 <param name="weight" value="1.0"/>
3555 </section>
3556 <section name="distance_MZ">
3557 <param name="exponent" value="2.0"/>
3558 <param name="weight" value="1.0"/>
3559 </section>
3560 <section name="distance_intensity">
3561 <param name="exponent" value="1.0"/>
3562 <param name="weight" value="1.0"/>
3563 <param name="log_transform" value="enabled"/>
3564 </section>
3565 <section name="LOWESS">
3566 <param name="span" value="0.666666666666667"/>
3567 <param name="num_iterations" value="3"/>
3568 <param name="delta" value="-1.0"/>
3569 <param name="interpolation_type" value="cspline"/>
3570 <param name="extrapolation_type" value="four-point-linear"/>
3571 </section>
3572 </section>
3573 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3574 <output name="ctd_out" ftype="xml">
3575 <assert_contents>
3576 <is_valid_xml/>
3577 </assert_contents>
3578 </output>
3579 </test>
3580 <test expect_num_outputs="2">
3581 <conditional name="adv_opts_cond">
3582 <param name="adv_opts_selector" value="advanced"/>
3583 <param name="force" value="false"/>
3584 <param name="test" value="true"/>
3585 </conditional>
3586 <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"/>
3587 <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3588 <param name="keep_subelements" value="false"/>
3589 <section name="algorithm">
3590 <param name="mz_unit" value="ppm"/>
3591 <param name="nr_partitions" value="100"/>
3592 <section name="warp">
3593 <param name="enabled" value="true"/>
3594 <param name="rt_tol" value="100.0"/>
3595 <param name="mz_tol" value="5.0"/>
3596 <param name="max_pairwise_log_fc" value="0.5"/>
3597 <param name="min_rel_cc_size" value="0.5"/>
3598 <param name="max_nr_conflicts" value="0"/>
3599 </section>
3600 <section name="link">
3601 <param name="rt_tol" value="30.0"/>
3602 <param name="mz_tol" value="10.0"/>
3603 <param name="charge_merging" value="Identical"/>
3604 <param name="adduct_merging" value="Any"/>
3605 </section>
3606 <section name="distance_RT">
3607 <param name="exponent" value="1.0"/>
3608 <param name="weight" value="1.0"/>
3609 </section>
3610 <section name="distance_MZ">
3611 <param name="exponent" value="2.0"/>
3612 <param name="weight" value="1.0"/>
3613 </section>
3614 <section name="distance_intensity">
3615 <param name="exponent" value="1.0"/>
3616 <param name="weight" value="1.0"/>
3617 <param name="log_transform" value="enabled"/>
3618 </section>
3619 <section name="LOWESS">
3620 <param name="span" value="0.666666666666667"/>
3621 <param name="num_iterations" value="3"/>
3622 <param name="delta" value="-1.0"/>
3623 <param name="interpolation_type" value="cspline"/>
3624 <param name="extrapolation_type" value="four-point-linear"/>
3625 </section>
3626 </section>
3627 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3628 <output name="ctd_out" ftype="xml">
3629 <assert_contents>
3630 <is_valid_xml/>
3631 </assert_contents>
3632 </output>
3633 </test>
3634 <test expect_num_outputs="2">
3635 <conditional name="adv_opts_cond">
3636 <param name="adv_opts_selector" value="advanced"/>
3637 <param name="force" value="false"/>
3638 <param name="test" value="true"/>
3639 </conditional>
3640 <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"/>
3641 <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3642 <param name="keep_subelements" value="false"/>
3643 <section name="algorithm">
3644 <param name="mz_unit" value="ppm"/>
3645 <param name="nr_partitions" value="100"/>
3646 <section name="warp">
3647 <param name="enabled" value="true"/>
3648 <param name="rt_tol" value="100.0"/>
3649 <param name="mz_tol" value="5.0"/>
3650 <param name="max_pairwise_log_fc" value="0.5"/>
3651 <param name="min_rel_cc_size" value="0.5"/>
3652 <param name="max_nr_conflicts" value="0"/>
3653 </section>
3654 <section name="link">
3655 <param name="rt_tol" value="30.0"/>
3656 <param name="mz_tol" value="10.0"/>
3657 <param name="charge_merging" value="With_charge_zero"/>
3658 <param name="adduct_merging" value="Any"/>
3659 </section>
3660 <section name="distance_RT">
3661 <param name="exponent" value="1.0"/>
3662 <param name="weight" value="1.0"/>
3663 </section>
3664 <section name="distance_MZ">
3665 <param name="exponent" value="2.0"/>
3666 <param name="weight" value="1.0"/>
3667 </section>
3668 <section name="distance_intensity">
3669 <param name="exponent" value="1.0"/>
3670 <param name="weight" value="1.0"/>
3671 <param name="log_transform" value="enabled"/>
3672 </section>
3673 <section name="LOWESS">
3674 <param name="span" value="0.666666666666667"/>
3675 <param name="num_iterations" value="3"/>
3676 <param name="delta" value="-1.0"/>
3677 <param name="interpolation_type" value="cspline"/>
3678 <param name="extrapolation_type" value="four-point-linear"/>
3679 </section>
3680 </section>
3681 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3682 <output name="ctd_out" ftype="xml">
3683 <assert_contents>
3684 <is_valid_xml/>
3685 </assert_contents>
3686 </output>
3687 </test>
3688 <test expect_num_outputs="2">
3689 <conditional name="adv_opts_cond">
3690 <param name="adv_opts_selector" value="advanced"/>
3691 <param name="force" value="false"/>
3692 <param name="test" value="true"/>
3693 </conditional>
3694 <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"/>
3695 <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3696 <param name="keep_subelements" value="false"/>
3697 <section name="algorithm">
3698 <param name="mz_unit" value="ppm"/>
3699 <param name="nr_partitions" value="100"/>
3700 <section name="warp">
3701 <param name="enabled" value="true"/>
3702 <param name="rt_tol" value="100.0"/>
3703 <param name="mz_tol" value="5.0"/>
3704 <param name="max_pairwise_log_fc" value="0.5"/>
3705 <param name="min_rel_cc_size" value="0.5"/>
3706 <param name="max_nr_conflicts" value="0"/>
3707 </section>
3708 <section name="link">
3709 <param name="rt_tol" value="30.0"/>
3710 <param name="mz_tol" value="10.0"/>
3711 <param name="charge_merging" value="Any"/>
3712 <param name="adduct_merging" value="With_unknown_adducts"/>
3713 </section>
3714 <section name="distance_RT">
3715 <param name="exponent" value="1.0"/>
3716 <param name="weight" value="1.0"/>
3717 </section>
3718 <section name="distance_MZ">
3719 <param name="exponent" value="2.0"/>
3720 <param name="weight" value="1.0"/>
3721 </section>
3722 <section name="distance_intensity">
3723 <param name="exponent" value="1.0"/>
3724 <param name="weight" value="1.0"/>
3725 <param name="log_transform" value="enabled"/>
3726 </section>
3727 <section name="LOWESS">
3728 <param name="span" value="0.666666666666667"/>
3729 <param name="num_iterations" value="3"/>
3730 <param name="delta" value="-1.0"/>
3731 <param name="interpolation_type" value="cspline"/>
3732 <param name="extrapolation_type" value="four-point-linear"/>
3733 </section>
3734 </section>
3735 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3736 <output name="ctd_out" ftype="xml">
3737 <assert_contents>
3738 <is_valid_xml/>
3739 </assert_contents>
3740 </output>
3741 </test>
3742 <test expect_num_outputs="2">
3743 <conditional name="adv_opts_cond">
3744 <param name="adv_opts_selector" value="advanced"/>
3745 <param name="force" value="false"/>
3746 <param name="test" value="true"/>
3747 </conditional>
3748 <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"/>
3749 <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3750 <param name="keep_subelements" value="false"/>
3751 <section name="algorithm">
3752 <param name="mz_unit" value="ppm"/>
3753 <param name="nr_partitions" value="100"/>
3754 <section name="warp">
3755 <param name="enabled" value="true"/>
3756 <param name="rt_tol" value="100.0"/>
3757 <param name="mz_tol" value="5.0"/>
3758 <param name="max_pairwise_log_fc" value="0.5"/>
3759 <param name="min_rel_cc_size" value="0.5"/>
3760 <param name="max_nr_conflicts" value="0"/>
3761 </section>
3762 <section name="link">
3763 <param name="rt_tol" value="30.0"/>
3764 <param name="mz_tol" value="10.0"/>
3765 <param name="charge_merging" value="Any"/>
3766 <param name="adduct_merging" value="Identical"/>
3767 </section>
3768 <section name="distance_RT">
3769 <param name="exponent" value="1.0"/>
3770 <param name="weight" value="1.0"/>
3771 </section>
3772 <section name="distance_MZ">
3773 <param name="exponent" value="2.0"/>
3774 <param name="weight" value="1.0"/>
3775 </section>
3776 <section name="distance_intensity">
3777 <param name="exponent" value="1.0"/>
3778 <param name="weight" value="1.0"/>
3779 <param name="log_transform" value="enabled"/>
3780 </section>
3781 <section name="LOWESS">
3782 <param name="span" value="0.666666666666667"/>
3783 <param name="num_iterations" value="3"/>
3784 <param name="delta" value="-1.0"/>
3785 <param name="interpolation_type" value="cspline"/>
3786 <param name="extrapolation_type" value="four-point-linear"/>
3787 </section>
3788 </section>
3789 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3790 <output name="ctd_out" ftype="xml">
3791 <assert_contents>
3792 <is_valid_xml/>
3793 </assert_contents>
3794 </output>
3795 </test>
3796 </xml>
3797 <xml name="autotest_FeatureLinkerUnlabeledQT">
3798 <test expect_num_outputs="2">
3799 <conditional name="adv_opts_cond">
3800 <param name="adv_opts_selector" value="advanced"/>
3801 <param name="force" value="false"/>
3802 <param name="test" value="true"/>
3803 </conditional>
3804 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3805 <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3806 <param name="keep_subelements" value="false"/>
3807 <section name="algorithm">
3808 <param name="use_identifications" value="false"/>
3809 <param name="nr_partitions" value="100"/>
3810 <param name="ignore_charge" value="false"/>
3811 <param name="ignore_adduct" value="true"/>
3812 <section name="distance_RT">
3813 <param name="max_difference" value="100.0"/>
3814 <param name="exponent" value="1.0"/>
3815 <param name="weight" value="1.0"/>
3816 </section>
3817 <section name="distance_MZ">
3818 <param name="max_difference" value="0.3"/>
3819 <param name="unit" value="Da"/>
3820 <param name="exponent" value="2.0"/>
3821 <param name="weight" value="1.0"/>
3822 </section>
3823 <section name="distance_intensity">
3824 <param name="exponent" value="1.0"/>
3825 <param name="weight" value="0.0"/>
3826 <param name="log_transform" value="disabled"/>
3827 </section>
3828 </section>
3829 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3830 <output name="ctd_out" ftype="xml">
3831 <assert_contents>
3832 <is_valid_xml/>
3833 </assert_contents>
3834 </output>
3835 </test>
3836 <test expect_num_outputs="2">
3837 <conditional name="adv_opts_cond">
3838 <param name="adv_opts_selector" value="advanced"/>
3839 <param name="force" value="false"/>
3840 <param name="test" value="true"/>
3841 </conditional>
3842 <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
3843 <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3844 <param name="keep_subelements" value="true"/>
3845 <section name="algorithm">
3846 <param name="use_identifications" value="false"/>
3847 <param name="nr_partitions" value="100"/>
3848 <param name="ignore_charge" value="false"/>
3849 <param name="ignore_adduct" value="true"/>
3850 <section name="distance_RT">
3851 <param name="max_difference" value="100.0"/>
3852 <param name="exponent" value="1.0"/>
3853 <param name="weight" value="1.0"/>
3854 </section>
3855 <section name="distance_MZ">
3856 <param name="max_difference" value="0.3"/>
3857 <param name="unit" value="Da"/>
3858 <param name="exponent" value="2.0"/>
3859 <param name="weight" value="1.0"/>
3860 </section>
3861 <section name="distance_intensity">
3862 <param name="exponent" value="1.0"/>
3863 <param name="weight" value="0.0"/>
3864 <param name="log_transform" value="disabled"/>
3865 </section>
3866 </section>
3867 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3868 <output name="ctd_out" ftype="xml">
3869 <assert_contents>
3870 <is_valid_xml/>
3871 </assert_contents>
3872 </output>
3873 </test>
3874 <test expect_num_outputs="2">
3875 <conditional name="adv_opts_cond">
3876 <param name="adv_opts_selector" value="advanced"/>
3877 <param name="force" value="false"/>
3878 <param name="test" value="true"/>
3879 </conditional>
3880 <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
3881 <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3882 <param name="keep_subelements" value="false"/>
3883 <section name="algorithm">
3884 <param name="use_identifications" value="false"/>
3885 <param name="nr_partitions" value="99999"/>
3886 <param name="ignore_charge" value="false"/>
3887 <param name="ignore_adduct" value="true"/>
3888 <section name="distance_RT">
3889 <param name="max_difference" value="100.0"/>
3890 <param name="exponent" value="1.0"/>
3891 <param name="weight" value="1.0"/>
3892 </section>
3893 <section name="distance_MZ">
3894 <param name="max_difference" value="0.3"/>
3895 <param name="unit" value="Da"/>
3896 <param name="exponent" value="2.0"/>
3897 <param name="weight" value="1.0"/>
3898 </section>
3899 <section name="distance_intensity">
3900 <param name="exponent" value="1.0"/>
3901 <param name="weight" value="0.0"/>
3902 <param name="log_transform" value="disabled"/>
3903 </section>
3904 </section>
3905 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3906 <output name="ctd_out" ftype="xml">
3907 <assert_contents>
3908 <is_valid_xml/>
3909 </assert_contents>
3910 </output>
3911 </test>
3912 <test expect_num_outputs="2">
3913 <conditional name="adv_opts_cond">
3914 <param name="adv_opts_selector" value="advanced"/>
3915 <param name="force" value="false"/>
3916 <param name="test" value="true"/>
3917 </conditional>
3918 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
3919 <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3920 <param name="keep_subelements" value="false"/>
3921 <section name="algorithm">
3922 <param name="use_identifications" value="true"/>
3923 <param name="nr_partitions" value="100"/>
3924 <param name="ignore_charge" value="false"/>
3925 <param name="ignore_adduct" value="true"/>
3926 <section name="distance_RT">
3927 <param name="max_difference" value="100.0"/>
3928 <param name="exponent" value="1.0"/>
3929 <param name="weight" value="1.0"/>
3930 </section>
3931 <section name="distance_MZ">
3932 <param name="max_difference" value="0.3"/>
3933 <param name="unit" value="Da"/>
3934 <param name="exponent" value="2.0"/>
3935 <param name="weight" value="1.0"/>
3936 </section>
3937 <section name="distance_intensity">
3938 <param name="exponent" value="1.0"/>
3939 <param name="weight" value="0.0"/>
3940 <param name="log_transform" value="disabled"/>
3941 </section>
3942 </section>
3943 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3944 <output name="ctd_out" ftype="xml">
3945 <assert_contents>
3946 <is_valid_xml/>
3947 </assert_contents>
3948 </output>
3949 </test>
3950 <test expect_num_outputs="2">
3951 <conditional name="adv_opts_cond">
3952 <param name="adv_opts_selector" value="advanced"/>
3953 <param name="force" value="false"/>
3954 <param name="test" value="true"/>
3955 </conditional>
3956 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3957 <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3958 <param name="keep_subelements" value="false"/>
3959 <section name="algorithm">
3960 <param name="use_identifications" value="false"/>
3961 <param name="nr_partitions" value="100"/>
3962 <param name="ignore_charge" value="false"/>
3963 <param name="ignore_adduct" value="true"/>
3964 <section name="distance_RT">
3965 <param name="max_difference" value="200.0"/>
3966 <param name="exponent" value="1.0"/>
3967 <param name="weight" value="1.0"/>
3968 </section>
3969 <section name="distance_MZ">
3970 <param name="max_difference" value="0.3"/>
3971 <param name="unit" value="Da"/>
3972 <param name="exponent" value="2.0"/>
3973 <param name="weight" value="1.0"/>
3974 </section>
3975 <section name="distance_intensity">
3976 <param name="exponent" value="1.0"/>
3977 <param name="weight" value="0.0"/>
3978 <param name="log_transform" value="disabled"/>
3979 </section>
3980 </section>
3981 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
3982 <output name="ctd_out" ftype="xml">
3983 <assert_contents>
3984 <is_valid_xml/>
3985 </assert_contents>
3986 </output>
3987 </test>
3988 <test expect_num_outputs="2">
3989 <conditional name="adv_opts_cond">
3990 <param name="adv_opts_selector" value="advanced"/>
3991 <param name="force" value="false"/>
3992 <param name="test" value="true"/>
3993 </conditional>
3994 <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
3995 <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
3996 <param name="keep_subelements" value="false"/>
3997 <section name="algorithm">
3998 <param name="use_identifications" value="true"/>
3999 <param name="nr_partitions" value="100"/>
4000 <param name="ignore_charge" value="false"/>
4001 <param name="ignore_adduct" value="true"/>
4002 <section name="distance_RT">
4003 <param name="max_difference" value="200.0"/>
4004 <param name="exponent" value="1.0"/>
4005 <param name="weight" value="1.0"/>
4006 </section>
4007 <section name="distance_MZ">
4008 <param name="max_difference" value="0.3"/>
4009 <param name="unit" value="Da"/>
4010 <param name="exponent" value="2.0"/>
4011 <param name="weight" value="1.0"/>
4012 </section>
4013 <section name="distance_intensity">
4014 <param name="exponent" value="1.0"/>
4015 <param name="weight" value="0.0"/>
4016 <param name="log_transform" value="disabled"/>
4017 </section>
4018 </section>
4019 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4020 <output name="ctd_out" ftype="xml">
4021 <assert_contents>
4022 <is_valid_xml/>
4023 </assert_contents>
4024 </output>
4025 </test>
4026 </xml>
4027 <xml name="autotest_FeatureLinkerUnlabeled">
4028 <test expect_num_outputs="2">
4029 <conditional name="adv_opts_cond">
4030 <param name="adv_opts_selector" value="advanced"/>
4031 <param name="force" value="false"/>
4032 <param name="test" value="true"/>
4033 </conditional>
4034 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
4035 <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4036 <param name="keep_subelements" value="false"/>
4037 <section name="algorithm">
4038 <param name="second_nearest_gap" value="2.0"/>
4039 <param name="use_identifications" value="false"/>
4040 <param name="ignore_charge" value="true"/>
4041 <param name="ignore_adduct" value="true"/>
4042 <section name="distance_RT">
4043 <param name="max_difference" value="200.0"/>
4044 <param name="exponent" value="1.0"/>
4045 <param name="weight" value="1.0"/>
4046 </section>
4047 <section name="distance_MZ">
4048 <param name="max_difference" value="0.5"/>
4049 <param name="unit" value="Da"/>
4050 <param name="exponent" value="1.0"/>
4051 <param name="weight" value="1.0"/>
4052 </section>
4053 <section name="distance_intensity">
4054 <param name="exponent" value="1.0"/>
4055 <param name="weight" value="0.0"/>
4056 <param name="log_transform" value="disabled"/>
4057 </section>
4058 </section>
4059 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4060 <output name="ctd_out" ftype="xml">
4061 <assert_contents>
4062 <is_valid_xml/>
4063 </assert_contents>
4064 </output>
4065 </test>
4066 <test expect_num_outputs="2">
4067 <conditional name="adv_opts_cond">
4068 <param name="adv_opts_selector" value="advanced"/>
4069 <param name="force" value="false"/>
4070 <param name="test" value="true"/>
4071 </conditional>
4072 <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
4073 <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4074 <param name="keep_subelements" value="false"/>
4075 <section name="algorithm">
4076 <param name="second_nearest_gap" value="2.0"/>
4077 <param name="use_identifications" value="false"/>
4078 <param name="ignore_charge" value="false"/>
4079 <param name="ignore_adduct" value="true"/>
4080 <section name="distance_RT">
4081 <param name="max_difference" value="100.0"/>
4082 <param name="exponent" value="1.0"/>
4083 <param name="weight" value="1.0"/>
4084 </section>
4085 <section name="distance_MZ">
4086 <param name="max_difference" value="0.3"/>
4087 <param name="unit" value="Da"/>
4088 <param name="exponent" value="2.0"/>
4089 <param name="weight" value="1.0"/>
4090 </section>
4091 <section name="distance_intensity">
4092 <param name="exponent" value="1.0"/>
4093 <param name="weight" value="0.5"/>
4094 <param name="log_transform" value="disabled"/>
4095 </section>
4096 </section>
4097 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4098 <output name="ctd_out" ftype="xml">
4099 <assert_contents>
4100 <is_valid_xml/>
4101 </assert_contents>
4102 </output>
4103 </test>
4104 <test expect_num_outputs="2">
4105 <conditional name="adv_opts_cond">
4106 <param name="adv_opts_selector" value="advanced"/>
4107 <param name="force" value="false"/>
4108 <param name="test" value="true"/>
4109 </conditional>
4110 <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
4111 <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4112 <param name="keep_subelements" value="false"/>
4113 <section name="algorithm">
4114 <param name="second_nearest_gap" value="1.5"/>
4115 <param name="use_identifications" value="false"/>
4116 <param name="ignore_charge" value="true"/>
4117 <param name="ignore_adduct" value="true"/>
4118 <section name="distance_RT">
4119 <param name="max_difference" value="30.0"/>
4120 <param name="exponent" value="1.0"/>
4121 <param name="weight" value="1.0"/>
4122 </section>
4123 <section name="distance_MZ">
4124 <param name="max_difference" value="0.3"/>
4125 <param name="unit" value="Da"/>
4126 <param name="exponent" value="2.0"/>
4127 <param name="weight" value="1.0"/>
4128 </section>
4129 <section name="distance_intensity">
4130 <param name="exponent" value="1.0"/>
4131 <param name="weight" value="0.0"/>
4132 <param name="log_transform" value="disabled"/>
4133 </section>
4134 </section>
4135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4136 <output name="ctd_out" ftype="xml">
4137 <assert_contents>
4138 <is_valid_xml/>
4139 </assert_contents>
4140 </output>
4141 </test>
4142 <test expect_num_outputs="2">
4143 <conditional name="adv_opts_cond">
4144 <param name="adv_opts_selector" value="advanced"/>
4145 <param name="force" value="false"/>
4146 <param name="test" value="true"/>
4147 </conditional>
4148 <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
4149 <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4150 <param name="keep_subelements" value="false"/>
4151 <section name="algorithm">
4152 <param name="second_nearest_gap" value="2.0"/>
4153 <param name="use_identifications" value="true"/>
4154 <param name="ignore_charge" value="true"/>
4155 <param name="ignore_adduct" value="true"/>
4156 <section name="distance_RT">
4157 <param name="max_difference" value="200.0"/>
4158 <param name="exponent" value="2.0"/>
4159 <param name="weight" value="1.0"/>
4160 </section>
4161 <section name="distance_MZ">
4162 <param name="max_difference" value="0.5"/>
4163 <param name="unit" value="Da"/>
4164 <param name="exponent" value="2.0"/>
4165 <param name="weight" value="1.0"/>
4166 </section>
4167 <section name="distance_intensity">
4168 <param name="exponent" value="1.0"/>
4169 <param name="weight" value="0.0"/>
4170 <param name="log_transform" value="disabled"/>
4171 </section>
4172 </section>
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 </xml>
4181 <xml name="autotest_FFEval">
4182 </xml>
4183 <xml name="autotest_FidoAdapter">
4184 <test expect_num_outputs="2">
4185 <conditional name="adv_opts_cond">
4186 <param name="adv_opts_selector" value="advanced"/>
4187 <param name="keep_zero_group" value="false"/>
4188 <param name="accuracy" value=""/>
4189 <param name="log2_states_precalc" value="0"/>
4190 <param name="force" value="false"/>
4191 <param name="test" value="true"/>
4192 </conditional>
4193 <param name="in" value="FidoAdapter_1_input.idXML"/>
4194 <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4195 <param name="separate_runs" value="false"/>
4196 <param name="greedy_group_resolution" value="false"/>
4197 <param name="no_cleanup" value="false"/>
4198 <param name="all_PSMs" value="false"/>
4199 <param name="group_level" value="false"/>
4200 <param name="log2_states" value="0"/>
4201 <section name="prob">
4202 <param name="protein" value="0.0"/>
4203 <param name="peptide" value="0.0"/>
4204 <param name="spurious" value="0.0"/>
4205 </section>
4206 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4207 <output name="ctd_out" ftype="xml">
4208 <assert_contents>
4209 <is_valid_xml/>
4210 </assert_contents>
4211 </output>
4212 </test>
4213 <test expect_num_outputs="2">
4214 <conditional name="adv_opts_cond">
4215 <param name="adv_opts_selector" value="advanced"/>
4216 <param name="keep_zero_group" value="false"/>
4217 <param name="accuracy" value=""/>
4218 <param name="log2_states_precalc" value="0"/>
4219 <param name="force" value="false"/>
4220 <param name="test" value="true"/>
4221 </conditional>
4222 <param name="in" value="FidoAdapter_1_input.idXML"/>
4223 <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4224 <param name="separate_runs" value="true"/>
4225 <param name="greedy_group_resolution" value="false"/>
4226 <param name="no_cleanup" value="false"/>
4227 <param name="all_PSMs" value="false"/>
4228 <param name="group_level" value="false"/>
4229 <param name="log2_states" value="0"/>
4230 <section name="prob">
4231 <param name="protein" value="0.0"/>
4232 <param name="peptide" value="0.0"/>
4233 <param name="spurious" value="0.0"/>
4234 </section>
4235 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4236 <output name="ctd_out" ftype="xml">
4237 <assert_contents>
4238 <is_valid_xml/>
4239 </assert_contents>
4240 </output>
4241 </test>
4242 <test expect_num_outputs="2">
4243 <conditional name="adv_opts_cond">
4244 <param name="adv_opts_selector" value="advanced"/>
4245 <param name="keep_zero_group" value="false"/>
4246 <param name="accuracy" value=""/>
4247 <param name="log2_states_precalc" value="0"/>
4248 <param name="force" value="false"/>
4249 <param name="test" value="true"/>
4250 </conditional>
4251 <param name="in" value="FidoAdapter_1_input.idXML"/>
4252 <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4253 <param name="separate_runs" value="false"/>
4254 <param name="greedy_group_resolution" value="false"/>
4255 <param name="no_cleanup" value="false"/>
4256 <param name="all_PSMs" value="true"/>
4257 <param name="group_level" value="true"/>
4258 <param name="log2_states" value="0"/>
4259 <section name="prob">
4260 <param name="protein" value="0.0"/>
4261 <param name="peptide" value="0.0"/>
4262 <param name="spurious" value="0.0"/>
4263 </section>
4264 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4265 <output name="ctd_out" ftype="xml">
4266 <assert_contents>
4267 <is_valid_xml/>
4268 </assert_contents>
4269 </output>
4270 </test>
4271 <test expect_num_outputs="2">
4272 <conditional name="adv_opts_cond">
4273 <param name="adv_opts_selector" value="advanced"/>
4274 <param name="keep_zero_group" value="false"/>
4275 <param name="accuracy" value=""/>
4276 <param name="log2_states_precalc" value="0"/>
4277 <param name="force" value="false"/>
4278 <param name="test" value="true"/>
4279 </conditional>
4280 <param name="in" value="FidoAdapter_4_input.idXML"/>
4281 <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4282 <param name="separate_runs" value="false"/>
4283 <param name="greedy_group_resolution" value="false"/>
4284 <param name="no_cleanup" value="false"/>
4285 <param name="all_PSMs" value="false"/>
4286 <param name="group_level" value="false"/>
4287 <param name="log2_states" value="0"/>
4288 <section name="prob">
4289 <param name="protein" value="0.0"/>
4290 <param name="peptide" value="0.0"/>
4291 <param name="spurious" value="0.0"/>
4292 </section>
4293 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4294 <output name="ctd_out" ftype="xml">
4295 <assert_contents>
4296 <is_valid_xml/>
4297 </assert_contents>
4298 </output>
4299 </test>
4300 <test expect_num_outputs="2">
4301 <conditional name="adv_opts_cond">
4302 <param name="adv_opts_selector" value="advanced"/>
4303 <param name="keep_zero_group" value="false"/>
4304 <param name="accuracy" value=""/>
4305 <param name="log2_states_precalc" value="0"/>
4306 <param name="force" value="false"/>
4307 <param name="test" value="true"/>
4308 </conditional>
4309 <param name="in" value="FidoAdapter_5_input.idXML"/>
4310 <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4311 <param name="separate_runs" value="false"/>
4312 <param name="greedy_group_resolution" value="true"/>
4313 <param name="no_cleanup" value="false"/>
4314 <param name="all_PSMs" value="false"/>
4315 <param name="group_level" value="false"/>
4316 <param name="log2_states" value="0"/>
4317 <section name="prob">
4318 <param name="protein" value="0.0"/>
4319 <param name="peptide" value="0.0"/>
4320 <param name="spurious" value="0.0"/>
4321 </section>
4322 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4323 <output name="ctd_out" ftype="xml">
4324 <assert_contents>
4325 <is_valid_xml/>
4326 </assert_contents>
4327 </output>
4328 </test>
4329 <test expect_num_outputs="2">
4330 <conditional name="adv_opts_cond">
4331 <param name="adv_opts_selector" value="advanced"/>
4332 <param name="keep_zero_group" value="false"/>
4333 <param name="accuracy" value=""/>
4334 <param name="log2_states_precalc" value="0"/>
4335 <param name="force" value="false"/>
4336 <param name="test" value="true"/>
4337 </conditional>
4338 <param name="in" value="FidoAdapter_1_input.idXML"/>
4339 <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
4340 <param name="separate_runs" value="false"/>
4341 <param name="greedy_group_resolution" value="false"/>
4342 <param name="no_cleanup" value="false"/>
4343 <param name="all_PSMs" value="false"/>
4344 <param name="group_level" value="false"/>
4345 <param name="log2_states" value="0"/>
4346 <section name="prob">
4347 <param name="protein" value="0.9"/>
4348 <param name="peptide" value="0.01"/>
4349 <param name="spurious" value="0.0"/>
4350 </section>
4351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4352 <output name="ctd_out" ftype="xml">
4353 <assert_contents>
4354 <is_valid_xml/>
4355 </assert_contents>
4356 </output>
4357 </test>
4358 </xml>
4359 <xml name="autotest_FileConverter">
4360 <test expect_num_outputs="2">
4361 <conditional name="adv_opts_cond">
4362 <param name="adv_opts_selector" value="advanced"/>
4363 <param name="UID_postprocessing" value="ensure"/>
4364 <param name="TIC_DTA2D" value="false"/>
4365 <param name="MGF_compact" value="false"/>
4366 <param name="force_MaxQuant_compatibility" value="false"/>
4367 <param name="convert_to_chromatograms" value="false"/>
4368 <param name="force_TPP_compatibility" value="false"/>
4369 <param name="change_im_format" value="none"/>
4370 <param name="write_scan_index" value="true"/>
4371 <param name="lossy_compression" value="false"/>
4372 <param name="lossy_mass_accuracy" value="-1.0"/>
4373 <param name="process_lowmemory" value="false"/>
4374 <param name="no_peak_picking" value="false"/>
4375 <param name="force" value="false"/>
4376 <param name="test" value="true"/>
4377 </conditional>
4378 <param name="in" value="FileConverter_1_input.mzData"/>
4379 <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4380 <param name="out_type" value="mzML"/>
4381 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4382 <output name="ctd_out" ftype="xml">
4383 <assert_contents>
4384 <is_valid_xml/>
4385 </assert_contents>
4386 </output>
4387 </test>
4388 <test expect_num_outputs="2">
4389 <conditional name="adv_opts_cond">
4390 <param name="adv_opts_selector" value="advanced"/>
4391 <param name="UID_postprocessing" value="ensure"/>
4392 <param name="TIC_DTA2D" value="false"/>
4393 <param name="MGF_compact" value="false"/>
4394 <param name="force_MaxQuant_compatibility" value="false"/>
4395 <param name="convert_to_chromatograms" value="false"/>
4396 <param name="force_TPP_compatibility" value="false"/>
4397 <param name="change_im_format" value="none"/>
4398 <param name="write_scan_index" value="true"/>
4399 <param name="lossy_compression" value="false"/>
4400 <param name="lossy_mass_accuracy" value="-1.0"/>
4401 <param name="process_lowmemory" value="false"/>
4402 <param name="no_peak_picking" value="false"/>
4403 <param name="force" value="false"/>
4404 <param name="test" value="true"/>
4405 </conditional>
4406 <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
4407 <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4408 <param name="out_type" value="mzML"/>
4409 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4410 <output name="ctd_out" ftype="xml">
4411 <assert_contents>
4412 <is_valid_xml/>
4413 </assert_contents>
4414 </output>
4415 </test>
4416 <test expect_num_outputs="2">
4417 <conditional name="adv_opts_cond">
4418 <param name="adv_opts_selector" value="advanced"/>
4419 <param name="UID_postprocessing" value="ensure"/>
4420 <param name="TIC_DTA2D" value="false"/>
4421 <param name="MGF_compact" value="false"/>
4422 <param name="force_MaxQuant_compatibility" value="false"/>
4423 <param name="convert_to_chromatograms" value="false"/>
4424 <param name="force_TPP_compatibility" value="false"/>
4425 <param name="change_im_format" value="none"/>
4426 <param name="write_scan_index" value="true"/>
4427 <param name="lossy_compression" value="false"/>
4428 <param name="lossy_mass_accuracy" value="-1.0"/>
4429 <param name="process_lowmemory" value="false"/>
4430 <param name="no_peak_picking" value="false"/>
4431 <param name="force" value="false"/>
4432 <param name="test" value="true"/>
4433 </conditional>
4434 <param name="in" value="FileConverter_3_input.featureXML"/>
4435 <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4436 <param name="out_type" value="mzML"/>
4437 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4438 <output name="ctd_out" ftype="xml">
4439 <assert_contents>
4440 <is_valid_xml/>
4441 </assert_contents>
4442 </output>
4443 </test>
4444 <test expect_num_outputs="2">
4445 <conditional name="adv_opts_cond">
4446 <param name="adv_opts_selector" value="advanced"/>
4447 <param name="UID_postprocessing" value="ensure"/>
4448 <param name="TIC_DTA2D" value="false"/>
4449 <param name="MGF_compact" value="false"/>
4450 <param name="force_MaxQuant_compatibility" value="false"/>
4451 <param name="convert_to_chromatograms" value="false"/>
4452 <param name="force_TPP_compatibility" value="false"/>
4453 <param name="change_im_format" value="none"/>
4454 <param name="write_scan_index" value="true"/>
4455 <param name="lossy_compression" value="false"/>
4456 <param name="lossy_mass_accuracy" value="-1.0"/>
4457 <param name="process_lowmemory" value="false"/>
4458 <param name="no_peak_picking" value="false"/>
4459 <param name="force" value="false"/>
4460 <param name="test" value="true"/>
4461 </conditional>
4462 <param name="in" value="FileConverter_4_input.mzXML"/>
4463 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4464 <param name="out_type" value="mzML"/>
4465 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4466 <output name="ctd_out" ftype="xml">
4467 <assert_contents>
4468 <is_valid_xml/>
4469 </assert_contents>
4470 </output>
4471 </test>
4472 <test expect_num_outputs="2">
4473 <conditional name="adv_opts_cond">
4474 <param name="adv_opts_selector" value="advanced"/>
4475 <param name="UID_postprocessing" value="ensure"/>
4476 <param name="TIC_DTA2D" value="false"/>
4477 <param name="MGF_compact" value="false"/>
4478 <param name="force_MaxQuant_compatibility" value="false"/>
4479 <param name="convert_to_chromatograms" value="false"/>
4480 <param name="force_TPP_compatibility" value="false"/>
4481 <param name="change_im_format" value="none"/>
4482 <param name="write_scan_index" value="true"/>
4483 <param name="lossy_compression" value="false"/>
4484 <param name="lossy_mass_accuracy" value="-1.0"/>
4485 <param name="process_lowmemory" value="false"/>
4486 <param name="no_peak_picking" value="false"/>
4487 <param name="force" value="false"/>
4488 <param name="test" value="true"/>
4489 </conditional>
4490 <param name="in" value="FileConverter_5_input.mzML"/>
4491 <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4492 <param name="out_type" value="mzXML"/>
4493 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4494 <output name="ctd_out" ftype="xml">
4495 <assert_contents>
4496 <is_valid_xml/>
4497 </assert_contents>
4498 </output>
4499 </test>
4500 <test expect_num_outputs="2">
4501 <conditional name="adv_opts_cond">
4502 <param name="adv_opts_selector" value="advanced"/>
4503 <param name="UID_postprocessing" value="ensure"/>
4504 <param name="TIC_DTA2D" value="false"/>
4505 <param name="MGF_compact" value="false"/>
4506 <param name="force_MaxQuant_compatibility" value="false"/>
4507 <param name="convert_to_chromatograms" value="false"/>
4508 <param name="force_TPP_compatibility" value="false"/>
4509 <param name="change_im_format" value="none"/>
4510 <param name="write_scan_index" value="true"/>
4511 <param name="lossy_compression" value="false"/>
4512 <param name="lossy_mass_accuracy" value="-1.0"/>
4513 <param name="process_lowmemory" value="false"/>
4514 <param name="no_peak_picking" value="false"/>
4515 <param name="force" value="false"/>
4516 <param name="test" value="true"/>
4517 </conditional>
4518 <param name="in" value="FileConverter_6_input.mzML"/>
4519 <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
4520 <param name="out_type" value="mzXML"/>
4521 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4522 <output name="ctd_out" ftype="xml">
4523 <assert_contents>
4524 <is_valid_xml/>
4525 </assert_contents>
4526 </output>
4527 </test>
4528 <test expect_num_outputs="2">
4529 <conditional name="adv_opts_cond">
4530 <param name="adv_opts_selector" value="advanced"/>
4531 <param name="UID_postprocessing" value="ensure"/>
4532 <param name="TIC_DTA2D" value="false"/>
4533 <param name="MGF_compact" value="false"/>
4534 <param name="force_MaxQuant_compatibility" value="false"/>
4535 <param name="convert_to_chromatograms" value="false"/>
4536 <param name="force_TPP_compatibility" value="false"/>
4537 <param name="change_im_format" value="none"/>
4538 <param name="write_scan_index" value="true"/>
4539 <param name="lossy_compression" value="false"/>
4540 <param name="lossy_mass_accuracy" value="-1.0"/>
4541 <param name="process_lowmemory" value="false"/>
4542 <param name="no_peak_picking" value="false"/>
4543 <param name="force" value="false"/>
4544 <param name="test" value="true"/>
4545 </conditional>
4546 <param name="in" value="FileConverter_7_input.consensusXML"/>
4547 <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4548 <param name="out_type" value="featureXML"/>
4549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4550 <output name="ctd_out" ftype="xml">
4551 <assert_contents>
4552 <is_valid_xml/>
4553 </assert_contents>
4554 </output>
4555 </test>
4556 <test expect_num_outputs="2">
4557 <conditional name="adv_opts_cond">
4558 <param name="adv_opts_selector" value="advanced"/>
4559 <param name="UID_postprocessing" value="ensure"/>
4560 <param name="TIC_DTA2D" value="false"/>
4561 <param name="MGF_compact" value="false"/>
4562 <param name="force_MaxQuant_compatibility" value="false"/>
4563 <param name="convert_to_chromatograms" value="false"/>
4564 <param name="force_TPP_compatibility" value="false"/>
4565 <param name="change_im_format" value="none"/>
4566 <param name="write_scan_index" value="true"/>
4567 <param name="lossy_compression" value="false"/>
4568 <param name="lossy_mass_accuracy" value="-1.0"/>
4569 <param name="process_lowmemory" value="false"/>
4570 <param name="no_peak_picking" value="false"/>
4571 <param name="force" value="false"/>
4572 <param name="test" value="true"/>
4573 </conditional>
4574 <param name="in" value="FileConverter_8_input.mzML"/>
4575 <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
4576 <param name="out_type" value="mzData"/>
4577 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4578 <output name="ctd_out" ftype="xml">
4579 <assert_contents>
4580 <is_valid_xml/>
4581 </assert_contents>
4582 </output>
4583 </test>
4584 <test expect_num_outputs="2">
4585 <conditional name="adv_opts_cond">
4586 <param name="adv_opts_selector" value="advanced"/>
4587 <param name="UID_postprocessing" value="ensure"/>
4588 <param name="TIC_DTA2D" value="false"/>
4589 <param name="MGF_compact" value="false"/>
4590 <param name="force_MaxQuant_compatibility" value="false"/>
4591 <param name="convert_to_chromatograms" value="false"/>
4592 <param name="force_TPP_compatibility" value="false"/>
4593 <param name="change_im_format" value="none"/>
4594 <param name="write_scan_index" value="true"/>
4595 <param name="lossy_compression" value="false"/>
4596 <param name="lossy_mass_accuracy" value="-1.0"/>
4597 <param name="process_lowmemory" value="false"/>
4598 <param name="no_peak_picking" value="false"/>
4599 <param name="force" value="false"/>
4600 <param name="test" value="true"/>
4601 </conditional>
4602 <param name="in" value="FileConverter_9_input.consensusXML"/>
4603 <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4604 <param name="out_type" value="featureXML"/>
4605 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4606 <output name="ctd_out" ftype="xml">
4607 <assert_contents>
4608 <is_valid_xml/>
4609 </assert_contents>
4610 </output>
4611 </test>
4612 <test expect_num_outputs="2">
4613 <conditional name="adv_opts_cond">
4614 <param name="adv_opts_selector" value="advanced"/>
4615 <param name="UID_postprocessing" value="ensure"/>
4616 <param name="TIC_DTA2D" value="false"/>
4617 <param name="MGF_compact" value="false"/>
4618 <param name="force_MaxQuant_compatibility" value="false"/>
4619 <param name="convert_to_chromatograms" value="false"/>
4620 <param name="force_TPP_compatibility" value="false"/>
4621 <param name="change_im_format" value="none"/>
4622 <param name="write_scan_index" value="true"/>
4623 <param name="lossy_compression" value="false"/>
4624 <param name="lossy_mass_accuracy" value="-1.0"/>
4625 <param name="process_lowmemory" value="false"/>
4626 <param name="no_peak_picking" value="false"/>
4627 <param name="force" value="false"/>
4628 <param name="test" value="true"/>
4629 </conditional>
4630 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4631 <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4632 <param name="out_type" value="featureXML"/>
4633 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4634 <output name="ctd_out" ftype="xml">
4635 <assert_contents>
4636 <is_valid_xml/>
4637 </assert_contents>
4638 </output>
4639 </test>
4640 <test expect_num_outputs="2">
4641 <conditional name="adv_opts_cond">
4642 <param name="adv_opts_selector" value="advanced"/>
4643 <param name="UID_postprocessing" value="ensure"/>
4644 <param name="TIC_DTA2D" value="false"/>
4645 <param name="MGF_compact" value="false"/>
4646 <param name="force_MaxQuant_compatibility" value="false"/>
4647 <param name="convert_to_chromatograms" value="false"/>
4648 <param name="force_TPP_compatibility" value="false"/>
4649 <param name="change_im_format" value="none"/>
4650 <param name="write_scan_index" value="true"/>
4651 <param name="lossy_compression" value="false"/>
4652 <param name="lossy_mass_accuracy" value="-1.0"/>
4653 <param name="process_lowmemory" value="false"/>
4654 <param name="no_peak_picking" value="false"/>
4655 <param name="force" value="false"/>
4656 <param name="test" value="true"/>
4657 </conditional>
4658 <param name="in" value="FileConverter_11_input.peplist"/>
4659 <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4660 <param name="out_type" value="featureXML"/>
4661 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4662 <output name="ctd_out" ftype="xml">
4663 <assert_contents>
4664 <is_valid_xml/>
4665 </assert_contents>
4666 </output>
4667 </test>
4668 <test expect_num_outputs="2">
4669 <conditional name="adv_opts_cond">
4670 <param name="adv_opts_selector" value="advanced"/>
4671 <param name="UID_postprocessing" value="ensure"/>
4672 <param name="TIC_DTA2D" value="false"/>
4673 <param name="MGF_compact" value="false"/>
4674 <param name="force_MaxQuant_compatibility" value="false"/>
4675 <param name="convert_to_chromatograms" value="false"/>
4676 <param name="force_TPP_compatibility" value="false"/>
4677 <param name="change_im_format" value="none"/>
4678 <param name="write_scan_index" value="true"/>
4679 <param name="lossy_compression" value="false"/>
4680 <param name="lossy_mass_accuracy" value="-1.0"/>
4681 <param name="process_lowmemory" value="false"/>
4682 <param name="no_peak_picking" value="false"/>
4683 <param name="force" value="false"/>
4684 <param name="test" value="true"/>
4685 </conditional>
4686 <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
4687 <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4688 <param name="out_type" value="featureXML"/>
4689 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4690 <output name="ctd_out" ftype="xml">
4691 <assert_contents>
4692 <is_valid_xml/>
4693 </assert_contents>
4694 </output>
4695 </test>
4696 <test expect_num_outputs="2">
4697 <conditional name="adv_opts_cond">
4698 <param name="adv_opts_selector" value="advanced"/>
4699 <param name="UID_postprocessing" value="ensure"/>
4700 <param name="TIC_DTA2D" value="false"/>
4701 <param name="MGF_compact" value="false"/>
4702 <param name="force_MaxQuant_compatibility" value="false"/>
4703 <param name="convert_to_chromatograms" value="false"/>
4704 <param name="force_TPP_compatibility" value="false"/>
4705 <param name="change_im_format" value="none"/>
4706 <param name="write_scan_index" value="true"/>
4707 <param name="lossy_compression" value="false"/>
4708 <param name="lossy_mass_accuracy" value="-1.0"/>
4709 <param name="process_lowmemory" value="false"/>
4710 <param name="no_peak_picking" value="false"/>
4711 <param name="force" value="false"/>
4712 <param name="test" value="true"/>
4713 </conditional>
4714 <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
4715 <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4716 <param name="out_type" value="featureXML"/>
4717 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4718 <output name="ctd_out" ftype="xml">
4719 <assert_contents>
4720 <is_valid_xml/>
4721 </assert_contents>
4722 </output>
4723 </test>
4724 <test expect_num_outputs="2">
4725 <conditional name="adv_opts_cond">
4726 <param name="adv_opts_selector" value="advanced"/>
4727 <param name="UID_postprocessing" value="ensure"/>
4728 <param name="TIC_DTA2D" value="false"/>
4729 <param name="MGF_compact" value="false"/>
4730 <param name="force_MaxQuant_compatibility" value="false"/>
4731 <param name="convert_to_chromatograms" value="false"/>
4732 <param name="force_TPP_compatibility" value="false"/>
4733 <param name="change_im_format" value="none"/>
4734 <param name="write_scan_index" value="true"/>
4735 <param name="lossy_compression" value="false"/>
4736 <param name="lossy_mass_accuracy" value="-1.0"/>
4737 <param name="process_lowmemory" value="false"/>
4738 <param name="no_peak_picking" value="false"/>
4739 <param name="force" value="false"/>
4740 <param name="test" value="true"/>
4741 </conditional>
4742 <param name="in" value="FileConverter_9_output.featureXML"/>
4743 <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4744 <param name="out_type" value="consensusXML"/>
4745 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4746 <output name="ctd_out" ftype="xml">
4747 <assert_contents>
4748 <is_valid_xml/>
4749 </assert_contents>
4750 </output>
4751 </test>
4752 <test expect_num_outputs="2">
4753 <conditional name="adv_opts_cond">
4754 <param name="adv_opts_selector" value="advanced"/>
4755 <param name="UID_postprocessing" value="ensure"/>
4756 <param name="TIC_DTA2D" value="false"/>
4757 <param name="MGF_compact" value="false"/>
4758 <param name="force_MaxQuant_compatibility" value="false"/>
4759 <param name="convert_to_chromatograms" value="false"/>
4760 <param name="force_TPP_compatibility" value="false"/>
4761 <param name="change_im_format" value="none"/>
4762 <param name="write_scan_index" value="true"/>
4763 <param name="lossy_compression" value="false"/>
4764 <param name="lossy_mass_accuracy" value="-1.0"/>
4765 <param name="process_lowmemory" value="false"/>
4766 <param name="no_peak_picking" value="false"/>
4767 <param name="force" value="false"/>
4768 <param name="test" value="true"/>
4769 </conditional>
4770 <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
4771 <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4772 <param name="out_type" value="consensusXML"/>
4773 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4774 <output name="ctd_out" ftype="xml">
4775 <assert_contents>
4776 <is_valid_xml/>
4777 </assert_contents>
4778 </output>
4779 </test>
4780 <test expect_num_outputs="2">
4781 <conditional name="adv_opts_cond">
4782 <param name="adv_opts_selector" value="advanced"/>
4783 <param name="UID_postprocessing" value="ensure"/>
4784 <param name="TIC_DTA2D" value="false"/>
4785 <param name="MGF_compact" value="false"/>
4786 <param name="force_MaxQuant_compatibility" value="false"/>
4787 <param name="convert_to_chromatograms" value="false"/>
4788 <param name="force_TPP_compatibility" value="false"/>
4789 <param name="change_im_format" value="none"/>
4790 <param name="write_scan_index" value="true"/>
4791 <param name="lossy_compression" value="false"/>
4792 <param name="lossy_mass_accuracy" value="-1.0"/>
4793 <param name="process_lowmemory" value="false"/>
4794 <param name="no_peak_picking" value="false"/>
4795 <param name="force" value="false"/>
4796 <param name="test" value="true"/>
4797 </conditional>
4798 <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
4799 <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
4800 <param name="out_type" value="consensusXML"/>
4801 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4802 <output name="ctd_out" ftype="xml">
4803 <assert_contents>
4804 <is_valid_xml/>
4805 </assert_contents>
4806 </output>
4807 </test>
4808 <test expect_num_outputs="2">
4809 <conditional name="adv_opts_cond">
4810 <param name="adv_opts_selector" value="advanced"/>
4811 <param name="UID_postprocessing" value="ensure"/>
4812 <param name="TIC_DTA2D" value="false"/>
4813 <param name="MGF_compact" value="false"/>
4814 <param name="force_MaxQuant_compatibility" value="false"/>
4815 <param name="convert_to_chromatograms" value="false"/>
4816 <param name="force_TPP_compatibility" value="false"/>
4817 <param name="change_im_format" value="none"/>
4818 <param name="write_scan_index" value="true"/>
4819 <param name="lossy_compression" value="false"/>
4820 <param name="lossy_mass_accuracy" value="-1.0"/>
4821 <param name="process_lowmemory" value="false"/>
4822 <param name="no_peak_picking" value="false"/>
4823 <param name="force" value="false"/>
4824 <param name="test" value="true"/>
4825 </conditional>
4826 <param name="in" value="FileConverter_17_input.consensusXML"/>
4827 <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
4828 <param name="out_type" value="csv"/>
4829 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4830 <output name="ctd_out" ftype="xml">
4831 <assert_contents>
4832 <is_valid_xml/>
4833 </assert_contents>
4834 </output>
4835 </test>
4836 <test expect_num_outputs="2">
4837 <conditional name="adv_opts_cond">
4838 <param name="adv_opts_selector" value="advanced"/>
4839 <param name="UID_postprocessing" value="ensure"/>
4840 <param name="TIC_DTA2D" value="false"/>
4841 <param name="MGF_compact" value="false"/>
4842 <param name="force_MaxQuant_compatibility" value="false"/>
4843 <param name="convert_to_chromatograms" value="false"/>
4844 <param name="force_TPP_compatibility" value="false"/>
4845 <param name="change_im_format" value="none"/>
4846 <param name="write_scan_index" value="true"/>
4847 <param name="lossy_compression" value="false"/>
4848 <param name="lossy_mass_accuracy" value="-1.0"/>
4849 <param name="process_lowmemory" value="false"/>
4850 <param name="no_peak_picking" value="false"/>
4851 <param name="force" value="false"/>
4852 <param name="test" value="true"/>
4853 </conditional>
4854 <param name="in" value="FileConverter_17_input.consensusXML"/>
4855 <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
4856 <param name="out_type" value="csv"/>
4857 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4858 <output name="ctd_out" ftype="xml">
4859 <assert_contents>
4860 <is_valid_xml/>
4861 </assert_contents>
4862 </output>
4863 </test>
4864 <test expect_num_outputs="2">
4865 <conditional name="adv_opts_cond">
4866 <param name="adv_opts_selector" value="advanced"/>
4867 <param name="UID_postprocessing" value="ensure"/>
4868 <param name="TIC_DTA2D" value="false"/>
4869 <param name="MGF_compact" value="false"/>
4870 <param name="force_MaxQuant_compatibility" value="false"/>
4871 <param name="convert_to_chromatograms" value="false"/>
4872 <param name="force_TPP_compatibility" value="false"/>
4873 <param name="change_im_format" value="none"/>
4874 <param name="write_scan_index" value="true"/>
4875 <param name="lossy_compression" value="false"/>
4876 <param name="lossy_mass_accuracy" value="-1.0"/>
4877 <param name="process_lowmemory" value="true"/>
4878 <param name="no_peak_picking" value="false"/>
4879 <param name="force" value="false"/>
4880 <param name="test" value="true"/>
4881 </conditional>
4882 <param name="in" value="FileFilter_1_input.mzML"/>
4883 <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4884 <param name="out_type" value="mzML"/>
4885 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4886 <output name="ctd_out" ftype="xml">
4887 <assert_contents>
4888 <is_valid_xml/>
4889 </assert_contents>
4890 </output>
4891 </test>
4892 <test expect_num_outputs="2">
4893 <conditional name="adv_opts_cond">
4894 <param name="adv_opts_selector" value="advanced"/>
4895 <param name="UID_postprocessing" value="ensure"/>
4896 <param name="TIC_DTA2D" value="false"/>
4897 <param name="MGF_compact" value="false"/>
4898 <param name="force_MaxQuant_compatibility" value="false"/>
4899 <param name="convert_to_chromatograms" value="false"/>
4900 <param name="force_TPP_compatibility" value="false"/>
4901 <param name="change_im_format" value="none"/>
4902 <param name="write_scan_index" value="true"/>
4903 <param name="lossy_compression" value="false"/>
4904 <param name="lossy_mass_accuracy" value="-1.0"/>
4905 <param name="process_lowmemory" value="false"/>
4906 <param name="no_peak_picking" value="false"/>
4907 <param name="force" value="false"/>
4908 <param name="test" value="true"/>
4909 </conditional>
4910 <param name="in" value="FileConverter_20_input.featureXML"/>
4911 <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
4912 <param name="out_type" value="featureXML"/>
4913 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4914 <output name="ctd_out" ftype="xml">
4915 <assert_contents>
4916 <is_valid_xml/>
4917 </assert_contents>
4918 </output>
4919 </test>
4920 <test expect_num_outputs="2">
4921 <conditional name="adv_opts_cond">
4922 <param name="adv_opts_selector" value="advanced"/>
4923 <param name="UID_postprocessing" value="ensure"/>
4924 <param name="TIC_DTA2D" value="false"/>
4925 <param name="MGF_compact" value="false"/>
4926 <param name="force_MaxQuant_compatibility" value="false"/>
4927 <param name="convert_to_chromatograms" value="false"/>
4928 <param name="force_TPP_compatibility" value="false"/>
4929 <param name="change_im_format" value="none"/>
4930 <param name="write_scan_index" value="true"/>
4931 <param name="lossy_compression" value="false"/>
4932 <param name="lossy_mass_accuracy" value="-1.0"/>
4933 <param name="process_lowmemory" value="true"/>
4934 <param name="no_peak_picking" value="false"/>
4935 <param name="force" value="false"/>
4936 <param name="test" value="true"/>
4937 </conditional>
4938 <param name="in" value="FileConverter_4_input.mzXML"/>
4939 <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4940 <param name="out_type" value="mzML"/>
4941 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4942 <output name="ctd_out" ftype="xml">
4943 <assert_contents>
4944 <is_valid_xml/>
4945 </assert_contents>
4946 </output>
4947 </test>
4948 <test expect_num_outputs="2">
4949 <conditional name="adv_opts_cond">
4950 <param name="adv_opts_selector" value="advanced"/>
4951 <param name="UID_postprocessing" value="ensure"/>
4952 <param name="TIC_DTA2D" value="false"/>
4953 <param name="MGF_compact" value="false"/>
4954 <param name="force_MaxQuant_compatibility" value="false"/>
4955 <param name="convert_to_chromatograms" value="false"/>
4956 <param name="force_TPP_compatibility" value="false"/>
4957 <param name="change_im_format" value="none"/>
4958 <param name="write_scan_index" value="true"/>
4959 <param name="lossy_compression" value="false"/>
4960 <param name="lossy_mass_accuracy" value="-1.0"/>
4961 <param name="process_lowmemory" value="false"/>
4962 <param name="no_peak_picking" value="false"/>
4963 <param name="force" value="false"/>
4964 <param name="test" value="true"/>
4965 </conditional>
4966 <param name="in" value="FileConverter_23_input.mzML"/>
4967 <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4968 <param name="out_type" value="mzML"/>
4969 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4970 <output name="ctd_out" ftype="xml">
4971 <assert_contents>
4972 <is_valid_xml/>
4973 </assert_contents>
4974 </output>
4975 </test>
4976 <test expect_num_outputs="2">
4977 <conditional name="adv_opts_cond">
4978 <param name="adv_opts_selector" value="advanced"/>
4979 <param name="UID_postprocessing" value="ensure"/>
4980 <param name="TIC_DTA2D" value="false"/>
4981 <param name="MGF_compact" value="false"/>
4982 <param name="force_MaxQuant_compatibility" value="false"/>
4983 <param name="convert_to_chromatograms" value="false"/>
4984 <param name="force_TPP_compatibility" value="false"/>
4985 <param name="change_im_format" value="none"/>
4986 <param name="write_scan_index" value="true"/>
4987 <param name="lossy_compression" value="true"/>
4988 <param name="lossy_mass_accuracy" value="0.0001"/>
4989 <param name="process_lowmemory" value="true"/>
4990 <param name="no_peak_picking" value="false"/>
4991 <param name="force" value="false"/>
4992 <param name="test" value="true"/>
4993 </conditional>
4994 <param name="in" value="FileFilter_1_input.mzML"/>
4995 <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
4996 <param name="out_type" value="mzML"/>
4997 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
4998 <output name="ctd_out" ftype="xml">
4999 <assert_contents>
5000 <is_valid_xml/>
5001 </assert_contents>
5002 </output>
5003 </test>
5004 <test expect_num_outputs="2">
5005 <conditional name="adv_opts_cond">
5006 <param name="adv_opts_selector" value="advanced"/>
5007 <param name="UID_postprocessing" value="ensure"/>
5008 <param name="TIC_DTA2D" value="false"/>
5009 <param name="MGF_compact" value="false"/>
5010 <param name="force_MaxQuant_compatibility" value="false"/>
5011 <param name="convert_to_chromatograms" value="false"/>
5012 <param name="force_TPP_compatibility" value="false"/>
5013 <param name="change_im_format" value="none"/>
5014 <param name="write_scan_index" value="true"/>
5015 <param name="lossy_compression" value="true"/>
5016 <param name="lossy_mass_accuracy" value="-1.0"/>
5017 <param name="process_lowmemory" value="true"/>
5018 <param name="no_peak_picking" value="false"/>
5019 <param name="force" value="false"/>
5020 <param name="test" value="true"/>