Mercurial > repos > galaxyp > openms_metaprosip
diff test-data/MetaProSIP_1_input.featureXML @ 6:96cc79adfadb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
| author | galaxyp |
|---|---|
| date | Tue, 20 Mar 2018 14:37:53 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 14:37:53 2018 -0400 @@ -0,0 +1,129 @@ +<?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>