Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison test-data/examples/CHROMATOGRAMS/Spyogenes.chrom.mzML @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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17:6f6c1cb968a0 18:6daaa75ccb99
1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">
3 <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
4 <cvList count="5">
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6 <cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
7 <cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
8 <cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
9 <cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
10 </cvList>
11 <fileDescription>
12 <fileContent>
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56 <userParam name="parameter: tr" type="xsd:string" value="../data/strep/lib/strep_iRT_small.TraML"/>
57 <userParam name="parameter: tr_type" type="xsd:string" value=""/>
58 <userParam name="parameter: tr_irt" type="xsd:string" value="../data/strep/lib/strep_iRT_small.TraML"/>
59 <userParam name="parameter: rt_norm" type="xsd:string" value=""/>
60 <userParam name="parameter: swath_windows_file" type="xsd:string" value="strep_win.txt"/>
61 <userParam name="parameter: sort_swath_maps" type="xsd:string" value="true"/>
62 <userParam name="parameter: use_ms1_traces" type="xsd:string" value="true"/>
63 <userParam name="parameter: enable_uis_scoring" type="xsd:string" value="false"/>
64 <userParam name="parameter: out_features" type="xsd:string" value=""/>
65 <userParam name="parameter: out_tsv" type="xsd:string" value="/localscratch/hroest.4041515.0/output.tsv"/>
66 <userParam name="parameter: out_osw" type="xsd:string" value=""/>
67 <userParam name="parameter: out_chrom" type="xsd:string" value="/localscratch/hroest.4041515.0/output.chrom.mzML"/>
68 <userParam name="parameter: min_upper_edge_dist" type="xsd:double" value="0"/>
69 <userParam name="parameter: rt_extraction_window" type="xsd:double" value="450"/>
70 <userParam name="parameter: extra_rt_extraction_window" type="xsd:double" value="100"/>
71 <userParam name="parameter: mz_extraction_window" type="xsd:double" value="50"/>
72 <userParam name="parameter: ppm" type="xsd:string" value="true"/>
73 <userParam name="parameter: sonar" type="xsd:string" value="false"/>
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75 <userParam name="parameter: min_coverage" type="xsd:double" value="0.6"/>
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80 <userParam name="parameter: irt_mz_extraction_window" type="xsd:double" value="0.05"/>
81 <userParam name="parameter: ppm_irtwindow" type="xsd:string" value="false"/>
82 <userParam name="parameter: tempDirectory" type="xsd:string" value="/localscratch/hroest.4041515.0/"/>
83 <userParam name="parameter: extraction_function" type="xsd:string" value="tophat"/>
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87 <userParam name="parameter: threads" type="xsd:integer" value="4"/>
88 <userParam name="parameter: no_progress" type="xsd:string" value="false"/>
89 <userParam name="parameter: force" type="xsd:string" value="false"/>
90 <userParam name="parameter: test" type="xsd:string" value="false"/>
91 <userParam name="parameter: Debugging:irt_mzml" type="xsd:string" value=""/>
92 <userParam name="parameter: Debugging:irt_trafo" type="xsd:string" value=""/>
93 <userParam name="parameter: Library:retentionTimeInterpretation" type="xsd:string" value="iRT"/>
94 <userParam name="parameter: Library:override_group_label_check" type="xsd:string" value="false"/>
95 <userParam name="parameter: Library:force_invalid_mods" type="xsd:string" value="false"/>
96 <userParam name="parameter: RTNormalization:alignmentMethod" type="xsd:string" value="linear"/>
97 <userParam name="parameter: RTNormalization:outlierMethod" type="xsd:string" value="iter_residual"/>
98 <userParam name="parameter: RTNormalization:useIterativeChauvenet" type="xsd:string" value="false"/>
99 <userParam name="parameter: RTNormalization:RANSACMaxIterations" type="xsd:integer" value="1000"/>
100 <userParam name="parameter: RTNormalization:RANSACMaxPercentRTThreshold" type="xsd:integer" value="3"/>
101 <userParam name="parameter: RTNormalization:RANSACSamplingSize" type="xsd:integer" value="10"/>
102 <userParam name="parameter: RTNormalization:estimateBestPeptides" type="xsd:string" value="false"/>
103 <userParam name="parameter: RTNormalization:InitialQualityCutoff" type="xsd:double" value="0.5"/>
104 <userParam name="parameter: RTNormalization:OverallQualityCutoff" type="xsd:double" value="5.5"/>
105 <userParam name="parameter: RTNormalization:NrRTBins" type="xsd:integer" value="10"/>
106 <userParam name="parameter: RTNormalization:MinPeptidesPerBin" type="xsd:integer" value="1"/>
107 <userParam name="parameter: RTNormalization:MinBinsFilled" type="xsd:integer" value="8"/>
108 <userParam name="parameter: RTNormalization:lowess:span" type="xsd:double" value="0.666666666666667"/>
109 <userParam name="parameter: RTNormalization:b_spline:num_nodes" type="xsd:integer" value="5"/>
110 <userParam name="parameter: Scoring:stop_report_after_feature" type="xsd:integer" value="5"/>
111 <userParam name="parameter: Scoring:rt_normalization_factor" type="xsd:double" value="100"/>
112 <userParam name="parameter: Scoring:quantification_cutoff" type="xsd:double" value="0"/>
113 <userParam name="parameter: Scoring:write_convex_hull" type="xsd:string" value="false"/>
114 <userParam name="parameter: Scoring:uis_threshold_sn" type="xsd:integer" value="0"/>
115 <userParam name="parameter: Scoring:uis_threshold_peak_area" type="xsd:integer" value="0"/>
116 <userParam name="parameter: Scoring:TransitionGroupPicker:stop_after_feature" type="xsd:integer" value="-1"/>
117 <userParam name="parameter: Scoring:TransitionGroupPicker:min_peak_width" type="xsd:double" value="7"/>
118 <userParam name="parameter: Scoring:TransitionGroupPicker:peak_integration" type="xsd:string" value="original"/>
119 <userParam name="parameter: Scoring:TransitionGroupPicker:background_subtraction" type="xsd:string" value="none"/>
120 <userParam name="parameter: Scoring:TransitionGroupPicker:recalculate_peaks" type="xsd:string" value="true"/>
121 <userParam name="parameter: Scoring:TransitionGroupPicker:use_precursors" type="xsd:string" value="false"/>
122 <userParam name="parameter: Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="xsd:double" value="0.75"/>
123 <userParam name="parameter: Scoring:TransitionGroupPicker:minimal_quality" type="xsd:double" value="-1.5"/>
124 <userParam name="parameter: Scoring:TransitionGroupPicker:resample_boundary" type="xsd:double" value="15"/>
125 <userParam name="parameter: Scoring:TransitionGroupPicker:compute_peak_quality" type="xsd:string" value="true"/>
126 <userParam name="parameter: Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="xsd:string" value="false"/>
127 <userParam name="parameter: Scoring:TransitionGroupPicker:boundary_selection_method" type="xsd:string" value="largest"/>
128 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length" type="xsd:integer" value="11"/>
129 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order" type="xsd:integer" value="3"/>
130 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width" type="xsd:double" value="30"/>
131 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="xsd:string" value="false"/>
132 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width" type="xsd:double" value="-1"/>
133 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise" type="xsd:double" value="0.1"/>
134 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="xsd:string" value="false"/>
135 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="xsd:string" value="true"/>
136 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakPickerMRM:method" type="xsd:string" value="corrected"/>
137 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakIntegrator:integration_type" type="xsd:string" value="intensity_sum"/>
138 <userParam name="parameter: Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type" type="xsd:string" value="base_to_base"/>
139 <userParam name="parameter: Scoring:DIAScoring:dia_extraction_window" type="xsd:double" value="0.05"/>
140 <userParam name="parameter: Scoring:DIAScoring:dia_extraction_unit" type="xsd:string" value="Th"/>
141 <userParam name="parameter: Scoring:DIAScoring:dia_centroided" type="xsd:string" value="false"/>
142 <userParam name="parameter: Scoring:DIAScoring:dia_byseries_intensity_min" type="xsd:double" value="300"/>
143 <userParam name="parameter: Scoring:DIAScoring:dia_byseries_ppm_diff" type="xsd:double" value="10"/>
144 <userParam name="parameter: Scoring:DIAScoring:dia_nr_isotopes" type="xsd:integer" value="4"/>
145 <userParam name="parameter: Scoring:DIAScoring:dia_nr_charges" type="xsd:integer" value="4"/>
146 <userParam name="parameter: Scoring:DIAScoring:peak_before_mono_max_ppm_diff" type="xsd:double" value="20"/>
147 <userParam name="parameter: Scoring:EMGScoring:max_iteration" type="xsd:integer" value="10"/>
148 <userParam name="parameter: Scoring:Scores:use_shape_score" type="xsd:string" value="true"/>
149 <userParam name="parameter: Scoring:Scores:use_coelution_score" type="xsd:string" value="true"/>
150 <userParam name="parameter: Scoring:Scores:use_rt_score" type="xsd:string" value="true"/>
151 <userParam name="parameter: Scoring:Scores:use_library_score" type="xsd:string" value="true"/>
152 <userParam name="parameter: Scoring:Scores:use_intensity_score" type="xsd:string" value="true"/>
153 <userParam name="parameter: Scoring:Scores:use_nr_peaks_score" type="xsd:string" value="true"/>
154 <userParam name="parameter: Scoring:Scores:use_total_xic_score" type="xsd:string" value="true"/>
155 <userParam name="parameter: Scoring:Scores:use_sn_score" type="xsd:string" value="true"/>
156 <userParam name="parameter: Scoring:Scores:use_dia_scores" type="xsd:string" value="true"/>
157 <userParam name="parameter: Scoring:Scores:use_ms1_correlation" type="xsd:string" value="false"/>
158 <userParam name="parameter: Scoring:Scores:use_sonar_scores" type="xsd:string" value="false"/>
159 <userParam name="parameter: Scoring:Scores:use_ms1_fullscan" type="xsd:string" value="false"/>
160 <userParam name="parameter: Scoring:Scores:use_uis_scores" type="xsd:string" value="false"/>
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166 <userParam name="parameter: log" type="xsd:string" value=""/>
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171 <userParam name="parameter: test" type="xsd:string" value="false"/>
172 <userParam name="parameter: in_type" type="xsd:string" value=""/>
173 <userParam name="parameter: out" type="xsd:string" value="/tmp/Spyogenes.chrom.mzML"/>
174 <userParam name="parameter: out_type" type="xsd:string" value=""/>
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176 <userParam name="parameter: mz" type="xsd:string" value=":"/>
177 <userParam name="parameter: int" type="xsd:string" value=":"/>
178 <userParam name="parameter: sort" type="xsd:string" value="false"/>
179 <userParam name="parameter: peak_options:sn" type="xsd:double" value="0"/>
180 <userParam name="parameter: peak_options:rm_pc_charge" type="xsd:string" value="[]"/>
181 <userParam name="parameter: peak_options:pc_mz_range" type="xsd:string" value=":"/>
182 <userParam name="parameter: peak_options:pc_mz_list" type="xsd:string" value="[]"/>
183 <userParam name="parameter: peak_options:level" type="xsd:string" value="[1, 2, 3]"/>
184 <userParam name="parameter: peak_options:sort_peaks" type="xsd:string" value="false"/>
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188 <userParam name="parameter: peak_options:int_precision" type="xsd:string" value="32"/>
189 <userParam name="parameter: peak_options:indexed_file" type="xsd:string" value="true"/>
190 <userParam name="parameter: peak_options:zlib_compression" type="xsd:string" value="true"/>
191 <userParam name="parameter: peak_options:numpress:masstime" type="xsd:string" value="none"/>
192 <userParam name="parameter: peak_options:numpress:masstime_error" type="xsd:double" value="0.0001"/>
193 <userParam name="parameter: peak_options:numpress:intensity" type="xsd:string" value="none"/>
194 <userParam name="parameter: peak_options:numpress:intensity_error" type="xsd:double" value="0.0001"/>
195 <userParam name="parameter: spectra:remove_zoom" type="xsd:string" value="false"/>
196 <userParam name="parameter: spectra:remove_mode" type="xsd:string" value=""/>
197 <userParam name="parameter: spectra:remove_activation" type="xsd:string" value=""/>
198 <userParam name="parameter: spectra:remove_collision_energy" type="xsd:string" value=":"/>
199 <userParam name="parameter: spectra:remove_isolation_window_width" type="xsd:string" value=":"/>
200 <userParam name="parameter: spectra:select_zoom" type="xsd:string" value="false"/>
201 <userParam name="parameter: spectra:select_mode" type="xsd:string" value=""/>
202 <userParam name="parameter: spectra:select_activation" type="xsd:string" value=""/>
203 <userParam name="parameter: spectra:select_collision_energy" type="xsd:string" value=":"/>
204 <userParam name="parameter: spectra:select_isolation_window_width" type="xsd:string" value=":"/>
205 <userParam name="parameter: spectra:select_polarity" type="xsd:string" value=""/>
206 <userParam name="parameter: feature:q" type="xsd:string" value=":"/>
207 <userParam name="parameter: consensus:map" type="xsd:string" value="[]"/>
208 <userParam name="parameter: consensus:map_and" type="xsd:string" value="false"/>
209 <userParam name="parameter: consensus:blackorwhitelist:blacklist" type="xsd:string" value="true"/>
210 <userParam name="parameter: consensus:blackorwhitelist:file" type="xsd:string" value=""/>
211 <userParam name="parameter: consensus:blackorwhitelist:maps" type="xsd:string" value="[]"/>
212 <userParam name="parameter: consensus:blackorwhitelist:rt" type="xsd:double" value="60"/>
213 <userParam name="parameter: consensus:blackorwhitelist:mz" type="xsd:double" value="0.01"/>
214 <userParam name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" type="xsd:string" value="false"/>
215 <userParam name="parameter: f_and_c:charge" type="xsd:string" value=":"/>
216 <userParam name="parameter: f_and_c:size" type="xsd:string" value=":"/>
217 <userParam name="parameter: f_and_c:remove_meta" type="xsd:string" value="[]"/>
218 <userParam name="parameter: id:remove_clashes" type="xsd:string" value="false"/>
219 <userParam name="parameter: id:keep_best_score_id" type="xsd:string" value="false"/>
220 <userParam name="parameter: id:sequences_whitelist" type="xsd:string" value="[]"/>
221 <userParam name="parameter: id:accessions_whitelist" type="xsd:string" value="[]"/>
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223 <userParam name="parameter: id:remove_unannotated_features" type="xsd:string" value="false"/>
224 <userParam name="parameter: id:remove_unassigned_ids" type="xsd:string" value="false"/>
225 <userParam name="parameter: id:blacklist" type="xsd:string" value=""/>
226 <userParam name="parameter: id:rt" type="xsd:double" value="0.1"/>
227 <userParam name="parameter: id:mz" type="xsd:double" value="0.001"/>
228 <userParam name="parameter: id:blacklist_imperfect" type="xsd:string" value="false"/>
229 <userParam name="parameter: algorithm:SignalToNoise:max_intensity" type="xsd:integer" value="-1"/>
230 <userParam name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" type="xsd:double" value="3"/>
231 <userParam name="parameter: algorithm:SignalToNoise:auto_max_percentile" type="xsd:integer" value="95"/>
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234 <userParam name="parameter: algorithm:SignalToNoise:bin_count" type="xsd:integer" value="30"/>
235 <userParam name="parameter: algorithm:SignalToNoise:min_required_elements" type="xsd:integer" value="10"/>
236 <userParam name="parameter: algorithm:SignalToNoise:noise_for_empty_window" type="xsd:double" value="1e+20"/>
237 <userParam name="parameter: algorithm:SignalToNoise:write_log_messages" type="xsd:string" value="true"/>
238 </processingMethod>
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249 </isolationWindow>
250 <activation>
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252 <userParam name="peptide_sequence" type="xsd:string" value="AAGGISSLEDAK"/>
253 </activation>
254 </precursor>
255 <product>
256 <isolationWindow>
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258 </isolationWindow>
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