Mercurial > repos > galaxyp > openms_featurefinderidentification

annotate test-data/MetaProSIP_1_input.featureXML @ 8:3baff5ec6dab 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 14:36:31 -0400
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8
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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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">
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3 <dataProcessing completion_time="2017-12-08T12:44:40">
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4 <software name="FileFilter" version="2.3.0" />
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5 <processingAction name="Data filtering" />
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6 <UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>
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7 <UserParam type="string" name="parameter: in_type" value=""/>
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8 <UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>
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9 <UserParam type="string" name="parameter: out_type" value=""/>
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10 <UserParam type="string" name="parameter: rt" value=":"/>
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11 <UserParam type="string" name="parameter: mz" value=":"/>
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12 <UserParam type="string" name="parameter: int" value=":"/>
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13 <UserParam type="string" name="parameter: sort" value="false"/>
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14 <UserParam type="string" name="parameter: log" value=""/>
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15 <UserParam type="int" name="parameter: debug" value="0"/>
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16 <UserParam type="int" name="parameter: threads" value="1"/>
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17 <UserParam type="string" name="parameter: no_progress" value="false"/>
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18 <UserParam type="string" name="parameter: force" value="false"/>
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19 <UserParam type="string" name="parameter: test" value="false"/>
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20 <UserParam type="float" name="parameter: peak_options:sn" value="0"/>
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21 <UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>
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22 <UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>
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23 <UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>
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24 <UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>
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25 <UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>
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26 <UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>
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27 <UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>
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28 <UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>
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29 <UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>
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30 <UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>
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31 <UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>
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32 <UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>
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33 <UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>
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34 <UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>
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35 <UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>
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36 <UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>
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37 <UserParam type="string" name="parameter: spectra:remove_mode" value=""/>
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38 <UserParam type="string" name="parameter: spectra:remove_activation" value=""/>
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39 <UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>
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40 <UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>
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41 <UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>
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42 <UserParam type="string" name="parameter: spectra:select_mode" value=""/>
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43 <UserParam type="string" name="parameter: spectra:select_activation" value=""/>
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44 <UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>
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45 <UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>
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46 <UserParam type="string" name="parameter: spectra:select_polarity" value=""/>
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47 <UserParam type="string" name="parameter: feature:q" value=":"/>
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48 <UserParam type="intList" name="parameter: consensus:map" value="[]"/>
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49 <UserParam type="string" name="parameter: consensus:map_and" value="false"/>
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50 <UserParam type="string" name="parameter: consensus:blackorwhitelist:blacklist" value="true"/>
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51 <UserParam type="string" name="parameter: consensus:blackorwhitelist:file" value=""/>
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52 <UserParam type="intList" name="parameter: consensus:blackorwhitelist:maps" value="[]"/>
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53 <UserParam type="float" name="parameter: consensus:blackorwhitelist:rt" value="60"/>
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54 <UserParam type="float" name="parameter: consensus:blackorwhitelist:mz" value="0.01"/>
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55 <UserParam type="string" name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" value="false"/>
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56 <UserParam type="string" name="parameter: f_and_c:charge" value=":"/>
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57 <UserParam type="string" name="parameter: f_and_c:size" value=":"/>
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58 <UserParam type="stringList" name="parameter: f_and_c:remove_meta" value="[]"/>
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59 <UserParam type="string" name="parameter: id:remove_clashes" value="false"/>
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60 <UserParam type="string" name="parameter: id:keep_best_score_id" value="false"/>
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61 <UserParam type="stringList" name="parameter: id:sequences_whitelist" value="[]"/>
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62 <UserParam type="stringList" name="parameter: id:accessions_whitelist" value="[]"/>
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63 <UserParam type="string" name="parameter: id:remove_annotated_features" value="false"/>
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64 <UserParam type="string" name="parameter: id:remove_unannotated_features" value="true"/>
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65 <UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>
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66 <UserParam type="string" name="parameter: id:blacklist" value=""/>
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67 <UserParam type="float" name="parameter: id:rt" value="0.1"/>
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68 <UserParam type="float" name="parameter: id:mz" value="0.001"/>
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69 <UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>
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70 <UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>
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71 <UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>
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72 <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>
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73 <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>
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74 <UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>
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75 <UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>
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76 <UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>
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77 <UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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78 <UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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79 </dataProcessing>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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80 <IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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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" >
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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82 <FixedModification name="Carbamidomethyl (C)" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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83 <VariableModification name="Oxidation (M)" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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84 </SearchParameters>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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85 <ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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86 <ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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87 </ProteinHit>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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88 </ProteinIdentification>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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89 </IdentificationRun>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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90 <featureList count="1">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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91 <feature id="f_988449706551050085">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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92 <position dim="0">4831.43346884947</position>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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93 <position dim="1">666.862287171363</position>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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94 <intensity>3.25608e+06</intensity>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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95 <quality dim="0">0</quality>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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96 <quality dim="1">0</quality>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
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97 <overallquality>0.882314</overallquality>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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98 <charge>2</charge>
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99 <convexhull nr="0">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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100 <pt x="4803.8473" y="666.862043575291" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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101 <pt x="4805.8211" y="666.862135109963" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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102 </convexhull>
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103 <convexhull nr="1">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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104 <pt x="4803.8473" y="667.364150217852" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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105 <pt x="4805.8211" y="667.363529666672" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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106 </convexhull>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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107 <convexhull nr="2">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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108 <pt x="4805.8211" y="667.865608520739" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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109 <pt x="4807.3928" y="667.864992849711" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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110 </convexhull>
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111 <convexhull nr="3">
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112 <pt x="4810.5312" y="668.364801015548" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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113 <pt x="4812.1021" y="668.365292284748" />
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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114 </convexhull>
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115 <PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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116 <PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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117 <UserParam type="string" name="target_decoy" value="target"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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118 <UserParam type="string" name="protein_references" value="unique"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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119 </PeptideHit>
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120 </PeptideIdentification>
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121 <UserParam type="int" name="label" value="453"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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122 <UserParam type="float" name="score_fit" value="0.783165906030983"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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123 <UserParam type="float" name="score_correlation" value="0.994014816652796"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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124 <UserParam type="float" name="FWHM" value="23.5379981994629"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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125 <UserParam type="int" name="spectrum_index" value="1569"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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126 <UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>
3baff5ec6dab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
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127 </feature>
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128 </featureList>
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129 </featureMap>