Mercurial > repos > galaxyp > openms_inspectadapter
diff test-data/MetaProSIP_1_input.featureXML @ 7:1197d1a4c3f6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
| author | galaxyp |
|---|---|
| date | Fri, 17 May 2019 10:23:16 -0400 |
| parents | f2511ee20383 |
| children |
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--- a/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 15:25:11 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -<?xml version="1.0" encoding="ISO-8859-1"?> -<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"> - <dataProcessing completion_time="2017-12-08T12:44:40"> - <software name="FileFilter" version="2.3.0" /> - <processingAction name="Data filtering" /> - <UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/> - <UserParam type="string" name="parameter: in_type" value=""/> - <UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/> - <UserParam type="string" name="parameter: out_type" value=""/> - <UserParam type="string" name="parameter: rt" value=":"/> - <UserParam type="string" name="parameter: mz" value=":"/> - <UserParam type="string" name="parameter: int" value=":"/> - <UserParam type="string" name="parameter: sort" value="false"/> - <UserParam type="string" name="parameter: log" value=""/> - <UserParam type="int" name="parameter: debug" value="0"/> - <UserParam type="int" name="parameter: threads" value="1"/> - <UserParam type="string" name="parameter: no_progress" value="false"/> - <UserParam type="string" name="parameter: force" value="false"/> - <UserParam type="string" name="parameter: test" value="false"/> - <UserParam type="float" name="parameter: peak_options:sn" value="0"/> - <UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/> - <UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/> - <UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/> - <UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/> - <UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/> - <UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/> - <UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/> - <UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/> - <UserParam type="string" name="parameter: peak_options:int_precision" value="32"/> - <UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/> - <UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/> - <UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/> - <UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/> - <UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/> - <UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/> - <UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/> - <UserParam type="string" name="parameter: spectra:remove_mode" value=""/> - <UserParam type="string" name="parameter: spectra:remove_activation" value=""/> - <UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/> - <UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/> - <UserParam type="string" name="parameter: spectra:select_zoom" value="false"/> - <UserParam type="string" name="parameter: spectra:select_mode" value=""/> - <UserParam type="string" name="parameter: spectra:select_activation" value=""/> - <UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/> - <UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/> - <UserParam type="string" name="parameter: spectra:select_polarity" value=""/> - <UserParam type="string" name="parameter: feature:q" value=":"/> - <UserParam type="intList" name="parameter: consensus:map" value="[]"/> - <UserParam type="string" name="parameter: consensus:map_and" value="false"/> - <UserParam type="string" name="parameter: consensus:blackorwhitelist:blacklist" value="true"/> - <UserParam type="string" name="parameter: consensus:blackorwhitelist:file" value=""/> - <UserParam type="intList" name="parameter: consensus:blackorwhitelist:maps" value="[]"/> - <UserParam type="float" name="parameter: consensus:blackorwhitelist:rt" value="60"/> - <UserParam type="float" name="parameter: consensus:blackorwhitelist:mz" value="0.01"/> - <UserParam type="string" name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" value="false"/> - <UserParam type="string" name="parameter: f_and_c:charge" value=":"/> - <UserParam type="string" name="parameter: f_and_c:size" value=":"/> - <UserParam type="stringList" name="parameter: f_and_c:remove_meta" value="[]"/> - <UserParam type="string" name="parameter: id:remove_clashes" value="false"/> - <UserParam type="string" name="parameter: id:keep_best_score_id" value="false"/> - <UserParam type="stringList" name="parameter: id:sequences_whitelist" value="[]"/> - <UserParam type="stringList" name="parameter: id:accessions_whitelist" value="[]"/> - <UserParam type="string" name="parameter: id:remove_annotated_features" value="false"/> - <UserParam type="string" name="parameter: id:remove_unannotated_features" value="true"/> - <UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/> - <UserParam type="string" name="parameter: id:blacklist" value=""/> - <UserParam type="float" name="parameter: id:rt" value="0.1"/> - <UserParam type="float" name="parameter: id:mz" value="0.001"/> - <UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/> - <UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/> - <UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/> - <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/> - <UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/> - <UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/> - <UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/> - <UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/> - <UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/> - <UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/> - </dataProcessing> - <IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8"> - <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" > - <FixedModification name="Carbamidomethyl (C)" /> - <VariableModification name="Oxidation (M)" /> - </SearchParameters> - <ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0"> - <ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence=""> - </ProteinHit> - </ProteinIdentification> - </IdentificationRun> - <featureList count="1"> - <feature id="f_988449706551050085"> - <position dim="0">4831.43346884947</position> - <position dim="1">666.862287171363</position> - <intensity>3.25608e+06</intensity> - <quality dim="0">0</quality> - <quality dim="1">0</quality> - <overallquality>0.882314</overallquality> - <charge>2</charge> - <convexhull nr="0"> - <pt x="4803.8473" y="666.862043575291" /> - <pt x="4805.8211" y="666.862135109963" /> - </convexhull> - <convexhull nr="1"> - <pt x="4803.8473" y="667.364150217852" /> - <pt x="4805.8211" y="667.363529666672" /> - </convexhull> - <convexhull nr="2"> - <pt x="4805.8211" y="667.865608520739" /> - <pt x="4807.3928" y="667.864992849711" /> - </convexhull> - <convexhull nr="3"> - <pt x="4810.5312" y="668.364801015548" /> - <pt x="4812.1021" y="668.365292284748" /> - </convexhull> - <PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" > - <PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0"> - <UserParam type="string" name="target_decoy" value="target"/> - <UserParam type="string" name="protein_references" value="unique"/> - </PeptideHit> - </PeptideIdentification> - <UserParam type="int" name="label" value="453"/> - <UserParam type="float" name="score_fit" value="0.783165906030983"/> - <UserParam type="float" name="score_correlation" value="0.994014816652796"/> - <UserParam type="float" name="FWHM" value="23.5379981994629"/> - <UserParam type="int" name="spectrum_index" value="1569"/> - <UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/> - </feature> - </featureList> -</featureMap>