| Previous changeset 5:ae772e47d635 (2018-02-12) Next changeset 7:6f22beeb9f32 (2019-05-15) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb |
|
modified:
readme.md |
|
added:
test-data/FileFilter_1_input.mzML test-data/MetaProSIP_1_input.fasta test-data/MetaProSIP_1_input.featureXML test-data/MetaProSIP_1_input.mzML test-data/MetaProSIP_1_output_1.csv test-data/MetaProSIP_1_output_2.csv test-data/MzMLSplitter_output_part1.mzML test-data/MzMLSplitter_output_part2.mzML |
| b |
| diff -r ae772e47d635 -r 241674ffc642 readme.md --- a/readme.md Mon Feb 12 12:53:38 2018 -0500 +++ b/readme.md Tue Mar 20 14:33:46 2018 -0400 |
| b |
| @@ -170,16 +170,6 @@ </tests> ``` - - * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `tools_blacklist.txt`: - * SeedListGenerator - * SpecLibSearcher - * MapAlignerIdentification - * MapAlignerPoseClustering - * MapAlignerSpectrum - * MapAlignerRTTransformer - * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: * OMSSAAdapter * MyrimatchAdapter |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/FileFilter_1_input.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FileFilter_1_input.mzML Tue Mar 20 14:33:46 2018 -0400 |
| b |
| b'@@ -0,0 +1,336 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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">\n+\t<cvList count="2">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<contact>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n+\t\t</contact>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="12">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n+\t\t\t\t</analyzer>\n+\t\t\t\t<detector order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000026" name="detector type" />\n+\t\t\t\t</detector>\n+\t\t\t</componentList>\n+\t\t\t<softwareRef ref="so_in_0" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="10">\n+\t\t<dataProcessing id="dp_sp_0">\n+\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000543" name="data processing action" />\n+\t\t\t</processingMethod>\n+\t\t\t<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:10'..b'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</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n' |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MetaProSIP_1_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.fasta Tue Mar 20 14:33:46 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>contig23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 +GGIPNEENWNFGSSDGSGLPVRGSGQRRDVLGRLCRRNFTSSIGQSVNVRDVEASGFAGG +MSRYHFKYGGAVDPTVLGGVKLGTWFVKEGFAGWSGYPDWCKYFGFYTDFSYHRFYTRDN +RISGTDFFAAYGGGSAALGDVGFMKTEGMVATWAFMLAARYGFFQDSEVPFGRLQPYVAV +GPAIMFSSMKPKIWTQFNEPNVGFPNPDLVYSPGNQSSTDLGLAVDTGIRYMCLKNVSLD +ISFKYRYAQPHYNFSGQDGSVMVPAHMSLSPALNLYSFQAGVAYHF |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MetaProSIP_1_input.featureXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.featureXML Tue Mar 20 14:33:46 2018 -0400 |
| [ |
| b'@@ -0,0 +1,129 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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">\n+\t<dataProcessing completion_time="2017-12-08T12:44:40">\n+\t\t<software name="FileFilter" version="2.3.0" />\n+\t\t<processingAction name="Data filtering" />\n+\t\t<UserParam type="string" name="parameter: in" value="MetaProSIP_1_input.featureXML"/>\n+\t\t<UserParam type="string" name="parameter: in_type" value=""/>\n+\t\t<UserParam type="string" name="parameter: out" value="MetaProSIP_1_input.featureXML"/>\n+\t\t<UserParam type="string" name="parameter: out_type" value=""/>\n+\t\t<UserParam type="string" name="parameter: rt" value=":"/>\n+\t\t<UserParam type="string" name="parameter: mz" value=":"/>\n+\t\t<UserParam type="string" name="parameter: int" value=":"/>\n+\t\t<UserParam type="string" name="parameter: sort" value="false"/>\n+\t\t<UserParam type="string" name="parameter: log" value=""/>\n+\t\t<UserParam type="int" name="parameter: debug" value="0"/>\n+\t\t<UserParam type="int" name="parameter: threads" value="1"/>\n+\t\t<UserParam type="string" name="parameter: no_progress" value="false"/>\n+\t\t<UserParam type="string" name="parameter: force" value="false"/>\n+\t\t<UserParam type="string" name="parameter: test" value="false"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:sn" value="0"/>\n+\t\t<UserParam type="intList" name="parameter: peak_options:rm_pc_charge" value="[]"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:pc_mz_range" value=":"/>\n+\t\t<UserParam type="floatList" name="parameter: peak_options:pc_mz_list" value="[]"/>\n+\t\t<UserParam type="intList" name="parameter: peak_options:level" value="[1, 2, 3]"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:sort_peaks" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:no_chromatograms" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:remove_chromatograms" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:mz_precision" value="64"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:int_precision" value="32"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:indexed_file" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:zlib_compression" value="false"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:numpress:masstime" value="none"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:numpress:masstime_error" value="0.0001"/>\n+\t\t<UserParam type="string" name="parameter: peak_options:numpress:intensity" value="none"/>\n+\t\t<UserParam type="float" name="parameter: peak_options:numpress:intensity_error" value="0.0001"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_zoom" value="false"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_mode" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_activation" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_collision_energy" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:remove_isolation_window_width" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_zoom" value="false"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_mode" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_activation" value=""/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_collision_energy" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_isolation_window_width" value=":"/>\n+\t\t<UserParam type="string" name="parameter: spectra:select_polarity" value=""/>\n+\t\t<UserParam type="string" name="parameter: feature:q" value=":"/>\n+\t\t<UserParam type="intList" name="parameter: consensus:map" value="[]"/>\n+\t\t<UserParam type="string" name="parameter: consensus:map_and" value="false"/>\n+\t\t<UserParam type="string" name="parameter: consensus:blackorwhitelist:bl'..b'id:remove_unannotated_features" value="true"/>\n+\t\t<UserParam type="string" name="parameter: id:remove_unassigned_ids" value="false"/>\n+\t\t<UserParam type="string" name="parameter: id:blacklist" value=""/>\n+\t\t<UserParam type="float" name="parameter: id:rt" value="0.1"/>\n+\t\t<UserParam type="float" name="parameter: id:mz" value="0.001"/>\n+\t\t<UserParam type="string" name="parameter: id:blacklist_imperfect" value="false"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:max_intensity" value="-1"/>\n+\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" value="3"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_max_percentile" value="95"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:auto_mode" value="0"/>\n+\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:win_len" value="200"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:bin_count" value="30"/>\n+\t\t<UserParam type="int" name="parameter: algorithm:SignalToNoise:min_required_elements" value="10"/>\n+\t\t<UserParam type="float" name="parameter: algorithm:SignalToNoise:noise_for_empty_window" value="1e+20"/>\n+\t\t<UserParam type="string" name="parameter: algorithm:SignalToNoise:write_log_messages" value="true"/>\n+\t</dataProcessing>\n+\t<IdentificationRun id="PI_0" date="2011-03-11T14:53:29" search_engine="OMSSA" search_engine_version="2.1.8">\n+\t\t<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" >\n+\t\t\t<FixedModification name="Carbamidomethyl (C)" />\n+\t\t\t<VariableModification name="Oxidation (M)" />\n+\t\t</SearchParameters>\n+\t\t<ProteinIdentification score_type="OMSSA" higher_score_better="false" significance_threshold="0">\n+\t\t\t<ProteinHit id="PH_0" accession="contig23640_802236" score="0" sequence="">\n+\t\t\t</ProteinHit>\n+\t\t</ProteinIdentification>\n+\t</IdentificationRun>\n+\t<featureList count="1">\n+\t\t<feature id="f_988449706551050085">\n+\t\t\t<position dim="0">4831.43346884947</position>\n+\t\t\t<position dim="1">666.862287171363</position>\n+\t\t\t<intensity>3.25608e+06</intensity>\n+\t\t\t<quality dim="0">0</quality>\n+\t\t\t<quality dim="1">0</quality>\n+\t\t\t<overallquality>0.882314</overallquality>\n+\t\t\t<charge>2</charge>\n+\t\t\t<convexhull nr="0">\n+\t\t\t\t<pt x="4803.8473" y="666.862043575291" />\n+\t\t\t\t<pt x="4805.8211" y="666.862135109963" />\n+\t\t\t</convexhull>\n+\t\t\t<convexhull nr="1">\n+\t\t\t\t<pt x="4803.8473" y="667.364150217852" />\n+\t\t\t\t<pt x="4805.8211" y="667.363529666672" />\n+\t\t\t</convexhull>\n+\t\t\t<convexhull nr="2">\n+\t\t\t\t<pt x="4805.8211" y="667.865608520739" />\n+\t\t\t\t<pt x="4807.3928" y="667.864992849711" />\n+\t\t\t</convexhull>\n+\t\t\t<convexhull nr="3">\n+\t\t\t\t<pt x="4810.5312" y="668.364801015548" />\n+\t\t\t\t<pt x="4812.1021" y="668.365292284748" />\n+\t\t\t</convexhull>\n+\t\t\t<PeptideIdentification identification_run_ref="PI_0" score_type="OMSSA" higher_score_better="false" significance_threshold="0" MZ="666.861999511719" RT="4808.4946" >\n+\t\t\t\t<PeptideHit score="0.174659044235501" sequence="YGGAVDPTVLGGVK" charge="2" aa_before="K" aa_after="L" protein_refs="PH_0">\n+\t\t\t\t\t<UserParam type="string" name="target_decoy" value="target"/>\n+\t\t\t\t\t<UserParam type="string" name="protein_references" value="unique"/>\n+\t\t\t\t</PeptideHit>\n+\t\t\t</PeptideIdentification>\n+\t\t\t<UserParam type="int" name="label" value="453"/>\n+\t\t\t<UserParam type="float" name="score_fit" value="0.783165906030983"/>\n+\t\t\t<UserParam type="float" name="score_correlation" value="0.994014816652796"/>\n+\t\t\t<UserParam type="float" name="FWHM" value="23.5379981994629"/>\n+\t\t\t<UserParam type="int" name="spectrum_index" value="1569"/>\n+\t\t\t<UserParam type="string" name="spectrum_native_id" value="controllerType=0 controllerNumber=1 scan=6112"/>\n+\t\t</feature>\n+\t</featureList>\n+</featureMap>\n' |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MetaProSIP_1_input.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_input.mzML Tue Mar 20 14:33:46 2018 -0400 |
| b |
| b'@@ -0,0 +1,2621 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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">\n+<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">\n+\t<cvList count="5">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n+\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n+\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<sourceFileList count="1">\n+\t\t\t<sourceFile id="sf_ru_0" name="Zeitz_SIP_13-II_020_picked.mzML" location="file:///nfs/wsi/abi/old-data/sachsenb/OpenMS_IDE/MetaProSIP/Zeitz">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="cda64713a3466f7bf74af2a42da97351aaff691b" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />\n+\t\t\t</sourceFile>\n+\t\t</sourceFileList>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="5">\n+\t\t<software id="so_in_0" version="2.5.5" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_0" version="2.0.1885" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_1" version="1.8.0" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000763" name="PeakPicker" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_2" version="2.3.0" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="SpectrumCanvas" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000556" name="LTQ Orbitrap XL" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN01757B"/>\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="2">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unit'..b'ntrollerType=0 controllerNumber=1 scan=6072">32939</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6074">35910</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6075">50741</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6077">53845</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6078">56980</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6079">72151</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6081">75306</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6083">78505</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6086">81862</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6089">85432</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6093">89366</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6095">93424</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6097">97550</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6100">101763</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6104">106419</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6107">111284</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6112">116083</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6114">121096</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6116">125835</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6117">141040</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6118">145957</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6119">150825</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6123">166221</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6125">171358</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6128">176225</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6130">181237</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6131">197169</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6132">201908</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6135">217825</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6138">222882</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6140">227623</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6144">231990</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6145">247361</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6147">252112</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6150">256418</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6155">260869</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6157">275807</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6163">280291</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6165">284708</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6169">300162</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6170">304804</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6173">320528</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6179">325158</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6182">329574</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6184">333979</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6188">338637</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6191">343073</offset>\n+\t\t<offset idRef="controllerType=0 controllerNumber=1 scan=6194">357613</offset>\n+\t</index>\n+</indexList>\n+<indexListOffset>362032</indexListOffset>\n+<fileChecksum>0</fileChecksum>\n+</indexedmzML>\n\\ No newline at end of file\n' |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MetaProSIP_1_output_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_output_1.csv Tue Mar 20 14:33:46 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +Group 1 # Distinct Peptides # Unambigous Proteins Median Global LR median RIA 1 median RIA 2 + 1 1 0.269627132474428 0.603333333333335 36.4733333333347 + Protein Accession Description # Unique Peptides Median Global LR median RIA 1 median RIA 2 + CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 0.269627132474428 0.603333333333335 36.4733333333347 + Peptide Sequence RT Exp. m/z Theo. m/z Charge Score TIC fraction #non-natural weights RIA 1 INT 1 Cor. 1 RIA 2 INT 2 Cor. 2 Peak intensities Global LR + YGGAVDPTVLGGVK 80.52 666.8623 666.861538013921 2 0.174659044235501 0.831887919884233 7 0.6 1432379 1.00 36.5 146376 0.87 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 +Non-Unique Peptides Accessions Peptide Sequence Descriptions Score RT Exp. m/z Theo. m/z Charge #non-natural weights Peak intensities Global LR |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MetaProSIP_1_output_2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MetaProSIP_1_output_2.csv Tue Mar 20 14:33:46 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Peptide Sequence Feature Quality Report Spectrum Quality report scores Sample Name Protein Accessions Description Unique #Ambiguity members Score RT Exp. m/z Theo. m/z Charge TIC fraction #non-natural weights Peak intensities Group Global Peptide LR RIA 1 LR of RIA 1 INT 1 Cor. 1 RIA 2 LR of RIA 2 INT 2 Cor. 2 RIA 3 LR of RIA 3 INT 3 Cor. 3 RIA 4 LR of RIA 4 INT 4 Cor. 4 RIA 5 LR of RIA 5 INT 5 Cor. 5 RIA 6 LR of RIA 6 INT 6 Cor. 6 RIA 7 LR of RIA 7 INT 7 Cor. 7 RIA 8 LR of RIA 8 INT 8 Cor. 8 RIA 9 LR of RIA 9 INT 9 Cor. 9 RIA 10 LR of RIA 10 INT 10 Cor. 10 +YGGAVDPTVLGGVK feature test_mode_enabled.mzML CONTIG23640_802236 length=2326 numreads=28 strand:-1 frame:0 orf_location:136:990 1 1 0.174659044235501 80.52 666.8623 666.8615 2 0.831887919884232 7 659720 461384 165174 49177 14782 11728 6541 7410 10868 8404 9437 9556 10203 12619 12159 15831 16288 19847 19258 22222 21275 21576 21294 22006 24019 19046 17493 19060 17884 15631 15769 13964 14131 10090 9445 9216 7297 6670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.269627132474428 0.6 1.0 1432378.6 1.0 36.5 0.0 146375.7 0.9 + |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MzMLSplitter_output_part1.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MzMLSplitter_output_part1.mzML Tue Mar 20 14:33:46 2018 -0400 |
| b |
| b'@@ -0,0 +1,222 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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">\n+<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">\n+\t<cvList count="5">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n+\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n+\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<contact>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n+\t\t</contact>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="4">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n+\t\t\t\t</analyzer>\n+\t\t\t\t<detector order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName='..b'" unitName="number of detector counts" unitCvRef="MS"/>\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n+\t\t\t\t\t\t<binary>Q1AYQ2XIvEL9I51D</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="spectrum=4" index="3" defaultArrayLength="5">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />\n+\t\t\t\t\t<scan >\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="27.8168" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="56">\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n+\t\t\t\t\t\t<binary>AAAAAAA4gEAAAACg76CHQAAAAGByuIdAAAAAAADIh0AAAABg+26IQA==</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="28">\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n+\t\t\t\t\t\t<binary>cnq9QXJQmEPn4JFCfnq9QY1f/0E=</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="spectrum=5" index="4" defaultArrayLength="8">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000525" name="spectrum representation" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />\n+\t\t\t\t\t<scan >\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="25.3972" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="88">\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n+\t\t\t\t\t\t<binary>AAAAgGlaf0AAAAAAxmp/QAAAAKAOin9AAAAAQKXDf0AAAABAsjOAQAAAAAAfeoBAAAAAAJQigUAAAAAg0/aJQA==</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="44">\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" />\n+\t\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />\n+\t\t\t\t\t\t<binary>dFNiQxQQLkIcK5ZCCBdQQ2L91UOKGBVDhPZcQ0KtHUM=</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n+<indexList count="1">\n+\t<index name="spectrum">\n+\t\t<offset idRef="spectrum=1">4899</offset>\n+\t\t<offset idRef="spectrum=2">19011</offset>\n+\t\t<offset idRef="spectrum=3">31431</offset>\n+\t\t<offset idRef="spectrum=4">32961</offset>\n+\t\t<offset idRef="spectrum=5">34527</offset>\n+\t</index>\n+</indexList>\n+<indexListOffset>36171</indexListOffset>\n+<fileChecksum>0</fileChecksum>\n+</indexedmzML>\n\\ No newline at end of file\n' |
| b |
| diff -r ae772e47d635 -r 241674ffc642 test-data/MzMLSplitter_output_part2.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MzMLSplitter_output_part2.mzML Tue Mar 20 14:33:46 2018 -0400 |
| b |
| b'@@ -0,0 +1,222 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<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">\n+<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">\n+\t<cvList count="5">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n+\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n+\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<contact>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=", " />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="" />\n+\t\t</contact>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="4">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_dp_sp_0_pm_1" version="version_string" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000756" name="FileConverter" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<componentList count="3">\n+\t\t\t\t<source order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000008" name="ionization type" />\n+\t\t\t\t</source>\n+\t\t\t\t<analyzer order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000443" name="mass analyzer type" />\n+\t\t\t\t</analyzer>\n+\t\t\t\t<detector order="0">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName='..b'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</binary>\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n+<indexList count="1">\n+\t<index name="spectrum">\n+\t\t<offset idRef="spectrum=6">4899</offset>\n+\t\t<offset idRef="spectrum=7">20575</offset>\n+\t\t<offset idRef="spectrum=8">22141</offset>\n+\t\t<offset idRef="spectrum=9">23739</offset>\n+\t\t<offset idRef="spectrum=10">25269</offset>\n+\t</index>\n+</indexList>\n+<indexListOffset>39000</indexListOffset>\n+<fileChecksum>0</fileChecksum>\n+</indexedmzML>\n\\ No newline at end of file\n' |