Mercurial > repos > galaxyp > openms_featurefindercentroided

comparison test-data/MetaProSIP_1_input.featureXML @ 8:d7f016292d95 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 14:40:17 -0400
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7:077ba692e138 8:d7f016292d95
1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <featureMap version="1.9" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/FeatureXML_1_9.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
3 <dataProcessing completion_time="2017-12-08T12:44:40">
4 <software name="FileFilter" version="2.3.0" />
5 <processingAction name="Data filtering" />
6 <UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>
7 <UserParam type="string" name="parameter: in_type" value=""/>
8 <UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>
9 <UserParam type="string" name="parameter: out_type" value=""/>
10 <UserParam type="string" name="parameter: rt" value=":"/>
11 <UserParam type="string" name="parameter: mz" value=":"/>
12 <UserParam type="string" name="parameter: int" value=":"/>
13 <UserParam type="string" name="parameter: sort" value="false"/>
14 <UserParam type="string" name="parameter: log" value=""/>
15 <UserParam type="int" name="parameter: debug" value="0"/>
16 <UserParam type="int" name="parameter: threads" value="1"/>
17 <UserParam type="string" name="parameter: no_progress" value="false"/>
18 <UserParam type="string" name="parameter: force" value="false"/>
19 <UserParam type="string" name="parameter: test" value="false"/>
20 <UserParam type="float" name="parameter: peak_options:sn" value="0"/>
21 <UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>
22 <UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>
23 <UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>
24 <UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>
25 <UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>
26 <UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>
27 <UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>
28 <UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>
29 <UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>
30 <UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>
31 <UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>
32 <UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>
33 <UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>
34 <UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>
35 <UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>
36 <UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>
37 <UserParam type="string" name="parameter: spectra:remove_mode" value=""/>
38 <UserParam type="string" name="parameter: spectra:remove_activation" value=""/>
39 <UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>
40 <UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>
41 <UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>
42 <UserParam type="string" name="parameter: spectra:select_mode" value=""/>
43 <UserParam type="string" name="parameter: spectra:select_activation" value=""/>
44 <UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>
45 <UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>
46 <UserParam type="string" name="parameter: spectra:select_polarity" value=""/>
47 <UserParam type="string" name="parameter: feature:q" value=":"/>
48 <UserParam type="intList" name="parameter: consensus:map" value="[]"/>
49 <UserParam type="string" name="parameter: consensus:map_and" value="false"/>
50 <UserParam type="string" name="parameter: consensus:blackorwhitelist:blacklist" value="true"/>
51 <UserParam type="string" name="parameter: consensus:blackorwhitelist:file" value=""/>
52 <UserParam type="intList" name="parameter: consensus:blackorwhitelist:maps" value="[]"/>
53 <UserParam type="float" name="parameter: consensus:blackorwhitelist:rt" value="60"/>
54 <UserParam type="float" name="parameter: consensus:blackorwhitelist:mz" value="0.01"/>
55 <UserParam type="string" name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" value="false"/>
56 <UserParam type="string" name="parameter: f_and_c:charge" value=":"/>
57 <UserParam type="string" name="parameter: f_and_c:size" value=":"/>
58 <UserParam type="stringList" name="parameter: f_and_c:remove_meta" value="[]"/>
59 <UserParam type="string" name="parameter: id:remove_clashes" value="false"/>
60 <UserParam type="string" name="parameter: id:keep_best_score_id" value="false"/>
61 <UserParam type="stringList" name="parameter: id:sequences_whitelist" value="[]"/>
62 <UserParam type="stringList" name="parameter: id:accessions_whitelist" value="[]"/>
63 <UserParam type="string" name="parameter: id:remove_annotated_features" value="false"/>
64 <UserParam type="string" name="parameter: id:remove_unannotated_features" value="true"/>
65 <UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>
66 <UserParam type="string" name="parameter: id:blacklist" value=""/>
67 <UserParam type="float" name="parameter: id:rt" value="0.1"/>
68 <UserParam type="float" name="parameter: id:mz" value="0.001"/>
69 <UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>
70 <UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>
71 <UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>
72 <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>
73 <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>
74 <UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>
75 <UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>
76 <UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>
77 <UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>
78 <UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>
79 </dataProcessing>
80 <IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">
81 <SearchParameters db="/raid/sachsenb/Jana/fasta/Zeitz_1and2_454AllContigs_HEX.fasta.psq" db_version="" taxonomy="0" mass_type="monoisotopic" charges="+2-+3" enzyme="trypsin" missed_cleavages="2" precursor_peak_tolerance="10" precursor_peak_tolerance_ppm="false" peak_mass_tolerance="0.5" peak_mass_tolerance_ppm="false" >
82 <FixedModification name="Carbamidomethyl (C)" />
83 <VariableModification name="Oxidation (M)" />
84 </SearchParameters>
85 <ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">
86 <ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">
87 </ProteinHit>
88 </ProteinIdentification>
89 </IdentificationRun>
90 <featureList count="1">
91 <feature id="f_988449706551050085">
92 <position dim="0">4831.43346884947</position>
93 <position dim="1">666.862287171363</position>
94 <intensity>3.25608e+06</intensity>
95 <quality dim="0">0</quality>
96 <quality dim="1">0</quality>
97 <overallquality>0.882314</overallquality>
98 <charge>2</charge>
99 <convexhull nr="0">
100 <pt x="4803.8473" y="666.862043575291" />
101 <pt x="4805.8211" y="666.862135109963" />
102 </convexhull>
103 <convexhull nr="1">
104 <pt x="4803.8473" y="667.364150217852" />
105 <pt x="4805.8211" y="667.363529666672" />
106 </convexhull>
107 <convexhull nr="2">
108 <pt x="4805.8211" y="667.865608520739" />
109 <pt x="4807.3928" y="667.864992849711" />
110 </convexhull>
111 <convexhull nr="3">
112 <pt x="4810.5312" y="668.364801015548" />
113 <pt x="4812.1021" y="668.365292284748" />
114 </convexhull>
115 <PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >
116 <PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">
117 <UserParam type="string" name="target_decoy" value="target"/>
118 <UserParam type="string" name="protein_references" value="unique"/>
119 </PeptideHit>
120 </PeptideIdentification>
121 <UserParam type="int" name="label" value="453"/>
122 <UserParam type="float" name="score_fit" value="0.783165906030983"/>
123 <UserParam type="float" name="score_correlation" value="0.994014816652796"/>
124 <UserParam type="float" name="FWHM" value="23.5379981994629"/>
125 <UserParam type="int" name="spectrum_index" value="1569"/>
126 <UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>
127 </feature>
128 </featureList>
129 </featureMap>