| Previous changeset 14:3cf310697624 (2020-11-16) Next changeset 16:545054b15d7c (2024-03-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877" |
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modified:
msconvert.xml msconvert_macros.xml test-data/AgilentMassHunterTest.mzXML test-data/BrukerBafTest.mzML test-data/MassLynxTest.mzML test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML test-data/SciexTest-HPINalone-srmAsSpectra.mzXML test-data/SciexTest-HPINalone.mzML test-data/ThyroglobMRM000003.mzML test-data/small-activation.mzML test-data/small-analyzer-filter.mzML test-data/small-chargeStatePredictor.mzML test-data/small-deisotope.mzML test-data/small-denoise.mzML test-data/small-index-filter.mzML test-data/small-ms-level-filter.mzML test-data/small-mzWindow.mzML test-data/small-numpressL.mzML test-data/small-numpressLP.mzML test-data/small-numpressLS.mzML test-data/small-numpressP.mzML test-data/small-numpressS.mzML test-data/small-peakpicking-cwt-allMS.mzML test-data/small-peakpicking-vendor-allMS.mzML test-data/small-polarity-filter.mzML test-data/small-strip-it.mzML test-data/small-threshold.mzML test-data/small-turbocharger.mzML test-data/small-zlib-32.mzXML test-data/small-zlib-64.mz5 |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee msconvert.xml --- a/msconvert.xml Mon Nov 16 17:25:12 2020 +0000 +++ b/msconvert.xml Mon Nov 30 16:01:10 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="msconvert" name="msconvert" version="@VERSION@.1"> +<tool id="msconvert" name="msconvert" version="@VERSION@.2"> <description>Convert and/or filter mass spectrometry files</description> <macros> <import>msconvert_macros.xml</import> @@ -6,6 +6,9 @@ <requirements> <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container> </requirements> + <stdio> + <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." /> + </stdio> <expand macro="msconvertCommand" /> <inputs> <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" /> |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee msconvert_macros.xml --- a/msconvert_macros.xml Mon Nov 16 17:25:12 2020 +0000 +++ b/msconvert_macros.xml Mon Nov 30 16:01:10 2020 +0000 |
| [ |
| b'@@ -1,7 +1,6 @@\n <macros>\n- <token name="@VERSION@">3.0.19052</token>\n- <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n-\n+ <token name="@VERSION@">3.0.20287</token>\n+ <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>\n <xml name="msconvertCommand">\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -39,18 +38,17 @@\n ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n #end if\n \n-\n- CAN_SUDO=\\$(sudo -n -l 2> /dev/null; echo \\$?) &&\n+ CAN_SUDO=\\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) &&\n if [ "\\$CAN_SUDO" -eq "0" ]; then\n- uid=`id -u` &&\n- gid=`id -g` && \n- WINE="wine64_anyuser";\n+ uid=`id -u` &&\n+ gid=`id -g` && \n+ WINE="wine64_anyuser";\n else\n- WINE="wine64" &&\n- ## create a writable copy of wine prefix (since copying fails for some html\n- ## stderr and exit code is swallowed)\n- export WINEPREFIX=\\$(mktemp -d) &&\n- (cp -a /wineprefix64/* \\$WINEPREFIX 2> /dev/null || true);\n+ WINE="wine64" &&\n+ ## create a writable copy of wine prefix (since copying fails for some html\n+ ## stderr and exit code is swallowed)\n+ export WINEPREFIX=\\$(mktemp -d) &&\n+ (cp -a /wineprefix64/* \\$WINEPREFIX 2> /dev/null || true);\n fi\n &&\n \\$WINE msconvert ${inputmask}\n@@ -214,21 +212,25 @@\n \n #if $general_options.multi_run_output.do_multi_run_output == \'false\':\n --outfile \'${os.path.splitext($basename)[0]}\'\n- && \n- if [ "\\$CAN_SUDO" -eq "0" ]; then\n- sudo chown \\$uid:\\$gid \'outputs/${os.path.splitext($basename)[0]}.${output_type}\' && \n- sudo mv \'outputs/${os.path.splitext($basename)[0]}.${output_type}\' \'${output}\';\n- else\n- mv \'outputs/${os.path.splitext($basename)[0]}.${output_type}\' \'${output}\';\n- fi\n+ #end if\n+ && \n+ if [ "\\$CAN_SUDO" -eq "0" ]; then\n+ sudo chown -R \\$uid:\\$gid \'./\';\n+ fi\n+ #if $general_options.multi_run_output.do_multi_run_output == \'false\':\n+ && mv \'outputs/${os.path.splitext($basename)[0]}.${output_type}\' \'${output}\'\n #else\n- && ls -la outputs/\n+ ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file\n+ ## TODO this won\'t be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803\n+ #if $output_type == \'mzML\' or $output_type == \'mzXML\'\n+ && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c \'mv FILE outputs/\\$(basename FILE .$output_type).#echo str($output_type).lower()\n+ ## a newline is needed after `#echo ...` therefore the `;\'` on the next line\n+;\'\n+ #end if\n #end if\n \n #if $data_processing.precursor_refinement.use_mzrefinement\n- && if [ "\\$CAN_SUDO" -ne "0" ]; then\n- mv \'$output_refinement_name\' \'$output_refinement\';\n- fi\n+ && mv \'$output_refinement_name\' \'$output_refinement\';\n #end if\n ]]>\n </command>\n@@ -543,13 +545,13 @@\n \n <xml name="msconvert_tests">\n <test>\n- <param name="input" value="small.mzML" />\n+ <param name="input" value="small.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="pick_peaks" value="true" />\n <param name="pick_peaks_algorithm" value="cwt" />\n <param name="pick_peaks_ms_levels" value="1-" />\n- <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />\n+ <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />\n </test>\n <test>\n <param name="input" value="small.RAW" ftype="thermo.raw" />\n@@ -558,47 +560,47 @@\n <param name="pick_peaks" value="true" />\n <param name="pick_peaks_algorithm" value="vendor" />\n <param name="pick_peaks_ms_levels" value="1-" />\n- <output name="output" file="small-peakp'..b'am name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="indices_0|from" value="2" />\n@@ -844,44 +846,44 @@\n <param name="indices_2|from" value="13" />\n <param name="indices_2|to" value="15" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />\n </test>\n <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="strip_it" value="true" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n+ <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />\n </test>\n <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="do_ms_level_filter" value="true" />\n <param name="ms_level_from" value="2" />\n <param name="ms_level_to" value="2" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n+ <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />\n </test>\n <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="polarity" value="positive" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n+ <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />\n </test>\n <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="analyzer" value="IT" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n+ <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />\n </test>\n <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />\n <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="scan_numbers_0|from" value="3" />\n@@ -891,7 +893,7 @@\n <param name="scan_numbers_2|from" value="14" />\n <param name="scan_numbers_2|to" value="16" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n+ <output name="output" file="small-index-filter.mzML" lines_diff="86" ftype="mzml"/> <!-- the scan numbers here produce the same output as the index test above -->\n </test>\n <!--<test>\n <param name="input" value="small.mzML" />\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/AgilentMassHunterTest.mzXML --- a/test-data/AgilentMassHunterTest.mzXML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/AgilentMassHunterTest.mzXML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| @@ -12,7 +12,7 @@ <software type="acquisition" name="MassHunter Data Acquisition" version="8.0"/> </msInstrument> <dataProcessing> - <software type="conversion" name="ProteoWizard software" version="3.0.19044"/> + <software type="conversion" name="ProteoWizard software" version="3.0.20287"/> <processingOperation name="Conversion to mzML"/> </dataProcessing> <scan num="676" @@ -4259,5 +4259,5 @@ <offset id="209716">686056</offset> </index> <indexOffset>689294</indexOffset> - <sha1>012aa0944f6d6b54d2001d1198d42d91c4d5d84f</sha1> + <sha1>919d9f6aaa20533cbe9c75398a139a36bec4b6b0</sha1> </mzXML> |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/BrukerBafTest.mzML --- a/test-data/BrukerBafTest.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/BrukerBafTest.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| @@ -2,7 +2,7 @@ <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/mzML1.1.2_idx.xsd"> <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" id="BrukerBafTest" version="1.1.0"> <cvList count="2"> - <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/> </cvList> <fileDescription> @@ -30,13 +30,14 @@ <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)"> <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/> </software> - <software id="pwiz_Reader_Bruker" version="3.0.19044"> + <software id="pwiz_Reader_Bruker" version="3.0.20287"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> </softwareList> <instrumentConfigurationList count="1"> <instrumentConfiguration id="IC1"> <referenceableParamGroupRef ref="CommonInstrumentParams"/> + <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="-1.3"/> <componentList count="3"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/> @@ -99,15 +100,65 @@ </binaryDataArrayList> </spectrum> </spectrumList> + <chromatogramList count="2" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion"> + <chromatogram index="0" id="TIC" defaultArrayLength="1"> + <cvParam cvRef="MS" accession="MS:1000235" name="total ion current chromatogram" value=""/> + <binaryDataArrayList count="3"> + <binaryDataArray encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000595" name="time array" value="" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/> + <binary>eJxjYIAAAAAIAAE=</binary> + </binaryDataArray> + <binaryDataArray encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/> + <binary>eJzT/rfSHwAFSwIi</binary> + </binaryDataArray> + <binaryDataArray arrayLength="1" encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000522" name="64-bit integer" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000786" name="non-standard data array" value="ms level" unitCvRef="UO" unitAccession="UO:0000186" unitName="dimensionless unit"/> + <binary>eJxjZIAAAAAQAAI=</binary> + </binaryDataArray> + </binaryDataArrayList> + </chromatogram> + <chromatogram index="1" id="BPC" defaultArrayLength="1"> + <cvParam cvRef="MS" accession="MS:1000628" name="basepeak chromatogram" value=""/> + <binaryDataArrayList count="3"> + <binaryDataArray encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000595" name="time array" value="" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"/> + <binary>eJxjYIAAAAAIAAE=</binary> + </binaryDataArray> + <binaryDataArray encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/> + <binary>eJwTCLLyAwAB/ADr</binary> + </binaryDataArray> + <binaryDataArray arrayLength="1" encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000522" name="64-bit integer" value=""/> + <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000786" name="non-standard data array" value="ms level" unitCvRef="UO" unitAccession="UO:0000186" unitName="dimensionless unit"/> + <binary>eJxjZIAAAAAQAAI=</binary> + </binaryDataArray> + </binaryDataArrayList> + </chromatogram> + </chromatogramList> </run> </mzML> <indexList count="2"> <index name="spectrum"> - <offset idRef="scan=1">4166</offset> + <offset idRef="scan=1">4264</offset> </index> <index name="chromatogram"> + <offset idRef="TIC">7765</offset> + <offset idRef="BPC">9468</offset> </index> </indexList> - <indexListOffset>7590</indexListOffset> - <fileChecksum>e6b4d51fdbe306f0823fe1cb583e7ec52629303f</fileChecksum> + <indexListOffset>11203</indexListOffset> + <fileChecksum>913c285a998996d2707f6f242bf7a0c00bd6468b</fileChecksum> </indexedmzML> |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/MassLynxTest.mzML --- a/test-data/MassLynxTest.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/MassLynxTest.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="MassLynxTest" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -391,7 +391,7 @@\n <software id="MassLynx" version="4.1">\n <cvParam cvRef="MS" accession="MS:1000534" name="MassLynx" value=""/>\n </software>\n- <software id="pwiz_Reader_Waters" version="3.0.19044">\n+ <software id="pwiz_Reader_Waters" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -421,7 +421,7 @@\n <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\n <scan>\n <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="17"/>\n- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="22.488966" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="22.488965988159" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n <scanWindowList count="1">\n <scanWindow>\n <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="50.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n@@ -473,7 +473,7 @@\n <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\n <scan>\n <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="17"/>\n- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="23.8005009" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="23.800500869751" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n <scanWindowList count="1">\n <scanWindow>\n <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="50.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n@@ -525,7 +525,7 @@\n <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\n <scan>\n <cvParam cvRef="MS" accession="MS:1000616" name="preset scan configuration" value="19"/>\n- <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="28.0034008" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n+ <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="28.003400802612" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/>\n <scanWindowList count="1">\n <scanWindow>\n <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="50.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n@@ -577,7 +577,7 @@\n <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>\n <scan'..b'0">211731</offset>\n- <offset idRef="SRM SIC Q1=582.318 Q3=951.471 function=4 offset=1">217047</offset>\n- <offset idRef="SRM SIC Q1=602.795 Q3=792.346 function=5 offset=0">222505</offset>\n- <offset idRef="SRM SIC Q1=602.795 Q3=921.387 function=5 offset=1">226575</offset>\n- <offset idRef="SRM SIC Q1=618.336 Q3=478.26 function=6 offset=0">230634</offset>\n- <offset idRef="SRM SIC Q1=618.336 Q3=759.433 function=6 offset=1">236512</offset>\n- <offset idRef="SRM SIC Q1=629.836 Q3=832.437 function=7 offset=0">242386</offset>\n- <offset idRef="SRM SIC Q1=629.836 Q3=1017.52 function=7 offset=1">248286</offset>\n- <offset idRef="SRM SIC Q1=643.86 Q3=745.458 function=8 offset=0">254274</offset>\n- <offset idRef="SRM SIC Q1=643.86 Q3=1073.57 function=8 offset=1">258764</offset>\n- <offset idRef="SRM SIC Q1=644.862 Q3=834.448 function=9 offset=0">263200</offset>\n- <offset idRef="SRM SIC Q1=644.862 Q3=947.527 function=9 offset=1">266979</offset>\n- <offset idRef="SRM SIC Q1=721.853 Q3=856.372 function=10 offset=0">270740</offset>\n- <offset idRef="SRM SIC Q1=721.853 Q3=1067.48 function=10 offset=1">276349</offset>\n- <offset idRef="SRM SIC Q1=724.407 Q3=778.393 function=11 offset=0">281950</offset>\n- <offset idRef="SRM SIC Q1=724.407 Q3=1079.56 function=11 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offset=0">223358</offset>\n+ <offset idRef="SRM SIC Q1=602.795 Q3=921.387 function=5 offset=1">227428</offset>\n+ <offset idRef="SRM SIC Q1=618.336 Q3=478.26 function=6 offset=0">231487</offset>\n+ <offset idRef="SRM SIC Q1=618.336 Q3=759.433 function=6 offset=1">237365</offset>\n+ <offset idRef="SRM SIC Q1=629.836 Q3=832.437 function=7 offset=0">243239</offset>\n+ <offset idRef="SRM SIC Q1=629.836 Q3=1017.52 function=7 offset=1">249139</offset>\n+ <offset idRef="SRM SIC Q1=643.86 Q3=745.458 function=8 offset=0">255127</offset>\n+ <offset idRef="SRM SIC Q1=643.86 Q3=1073.57 function=8 offset=1">259617</offset>\n+ <offset idRef="SRM SIC Q1=644.862 Q3=834.448 function=9 offset=0">264053</offset>\n+ <offset idRef="SRM SIC Q1=644.862 Q3=947.527 function=9 offset=1">267832</offset>\n+ <offset idRef="SRM SIC Q1=721.853 Q3=856.372 function=10 offset=0">271593</offset>\n+ <offset idRef="SRM SIC Q1=721.853 Q3=1067.48 function=10 offset=1">277202</offset>\n+ <offset idRef="SRM SIC Q1=724.407 Q3=778.393 function=11 offset=0">282803</offset>\n+ <offset idRef="SRM SIC Q1=724.407 Q3=1079.56 function=11 offset=1">288055</offset>\n+ <offset idRef="SRM SIC Q1=759.426 Q3=761.435 function=12 offset=0">293231</offset>\n+ <offset idRef="SRM SIC Q1=759.426 Q3=832.471 function=12 offset=1">297102</offset>\n </index>\n </indexList>\n- <indexListOffset>300205</indexListOffset>\n- <fileChecksum>dd6223a8d7fcf64e7b1270ed861077758703acd7</fileChecksum>\n+ <indexListOffset>301058</indexListOffset>\n+ <fileChecksum>4458a8c91171a5d1f242564986152d5e914567f9</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML --- a/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -15,12 +15,12 @@\n <software type="acquisition" name="Analyst" version="unknown"/>\n </msInstrument>\n <dataProcessing>\n- <software type="conversion" name="ProteoWizard software" version="3.0.19044"/>\n+ <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>\n <processingOperation name="Conversion to mzML"/>\n </dataProcessing>\n <scan num="1"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -30,14 +30,14 @@\n totIonCurrent="40.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="107"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdzDEOgkAQQFFKSwsLCwpDjDHGGEFBQYVlT8aRPQL1vGkmb34yRRFn+kcnetrgLd7hPS7xAVf4yD7Rz/iCr/jGvzu9xg1+4Cdu4z119Bd+4x4P+IO/+IdHPOGkl+iZPtMzPce+Ajw5E4I=</peaks>\n+ compressedLen="284"\n+ precision="64"\n+ byteOrder="network"\n+ contentType="m/z-int">eJxzqDjEr75b/w0DFDhUbHa5ILxSC84vnRQUkrAqFSe/PvhDfqZLOpzfWKTCXcHsDufXXkoDAYT5aPZ1KLX4MlpNhvNbujaEGiXWwPmFk9LOO34SdlCB8jsXG/5YMEEPLt/0y+zRaxlnOB9dHqofzi9+eHqSleZxuHn1Rs7/YiZeRJhnlbFc9tlsOL/90ZK7+lIL4PzerofCDn5L4fwCZ42e58wbEHyj/hiNr4cdTGDmXzoYcrL1A1y+4RVH6pT1/nB+2yTU8O6xamRTuasP55c1z4hn+zYFzk9XNgYBnOHbEvnjyt/P2+D8LiZTbmCI43R/bXIFqnrjNTdf2DnB+ZMOCS1mDVZDmN9dgBrfTEeMToWvwCUPAK6ah78=</peaks>\n </scan>\n <scan num="2"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -47,14 +47,14 @@\n totIonCurrent="40.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="111"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdzrsOgkAQQFFKSgsKCgtDiDHGEF4+QIGFL/OT/QQbmj3bTE7uZLJJEr/lFzvQQ4oPOMM5PuITLnCJz/iCr/iGK1zjBre4wz3zvs/93+HB/hO/8IBH/Ob+hz7hGS846G/slb7SN/oW9z+zqhOC</peaks>\n+ compressedLen="282"\n+ precision="64"\n+ byteOrder="network"\n+ contentType="m/z-int">eJxzqDjEr75b/w0DFDhUbHa5ILxSC84vnRQUkrAqFSe/PvhDfqZLOpzfWKTCXcHsDufXXkoDAYT5aPZ1KLX4MlpNhvNbujaEGiXWwPmFk9LOO34ShvM7Fxv+WDBBD85v+mX26LWMM055dP3FD09PstI8jnC/kfO/mIkXEeZZZSyXfTYbzm9/tOSuvtQCOL+366Gwg99SOL/AWaPnOfMGBxMY36g/RuPrYQcVmPmXDoacbP0AV9/wiiN1ynp/OL9tEmp491g1sqnc1Yfzy5pnxLN9mwLnpysbgwDcfPTwbYn8ceXv521wfheTKTcwxHG6vza5AlW98ZqbL+yc4PxJh4QWswarIczvLkCNb6YjRqfCV+CSBwAmGoe/</peaks>\n </scan>\n <scan num="3"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -64,14 +64,14 @@\n totIonCurrent="40.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="109"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdzjsOglAURVFKSwsKCwtjCDHEEFQ+AgIPRuaQHYINzVu3OVnZzU2S+JZf7EAPB3zEKT7hM77gK872rffN6Tdc4DsucYUf+IlfuMYN/7b0Dr9xjwc84g+e8IwXHPQ39kpf6Rt9i/sfyx4TLg==</peaks>\n+ compressedLen="284"\n+ precision="64"\n+ byteOrder="network"\n+ contentType="m/z-int">eJxzqDjEr75b/w0DFDhUbHa5ILxSC84vnRQUkrAqFSe/PvhDfqZLOpzfWKTCXcHsDufXXkoDAYT5aPZ1KLX4MlpNhvNbujaEGiXWwPmFk9LOO34SdjCB8jsXG/5YMEEPLt/0y+zRaxlnOB9dHqofzi9+eHqSleZxhPuNnP/FTLyIMM8qY7nss9lwfvujJXf1pRbA+b1dD4Ud/JbC+QXOGj3PmTcg+Eb9MRpfD8PdW3/pYMjJ1g9w+YZXHKlT1vvD+W2TUMO7x6qRTeWuPpxf1jwjnu3bFDg/XdkYBOB89PBtifxx5e/nbXB+F5MpNzDEcbq/NrkCVb3xmpsv7Jzg/EmHhBazBqshzO8uQI1vpiNGp8JX4JIHAD2Oh2s=</peaks>\n </scan>\n <scan num="4"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -81,14 +81,14 @@\n totIonCurrent="30.0"\n msInstrumentID="1">\n <peaks compre'..b't id="401">350617</offset>\n+ <offset id="402">351523</offset>\n+ <offset id="403">352428</offset>\n+ <offset id="404">353329</offset>\n+ <offset id="405">354234</offset>\n+ <offset id="406">355135</offset>\n+ <offset id="407">356040</offset>\n+ <offset id="408">356954</offset>\n+ <offset id="409">357867</offset>\n+ <offset id="410">358772</offset>\n+ <offset 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/SciexTest-HPINalone-srmAsSpectra.mzXML --- a/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -15,12 +15,12 @@\n <software type="acquisition" name="Analyst" version="unknown"/>\n </msInstrument>\n <dataProcessing>\n- <software type="conversion" name="ProteoWizard software" version="3.0.19044"/>\n+ <software type="conversion" name="ProteoWizard software" version="3.0.20287"/>\n <processingOperation name="Conversion to mzML"/>\n </dataProcessing>\n <scan num="1"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -30,14 +30,14 @@\n totIonCurrent="40.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="107"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdzDEOglAQRVFKSwsLCwpDjDHGGEFBQYXPXxlLdgnUc6Y7uZNXFPGmf3Sipw3e4h3e4xIfcIWP+ITP+IKv+BZ30x3X/Df4gZ+4Za+jv/Ab93hg70P/4h8e8YSTXqJn+kzP9Bz7Ck4FE9Y=</peaks>\n+ compressedLen="279"\n+ precision="64"\n+ byteOrder="network"\n+ contentType="m/z-int">eJxzqDjEr75b/w0DFDhUbHa5ILxSC84vnRQUkrAqFSe/PvhDfqZLOpzfWKTCXcHsDufXXkoDAYT5aPZ1KLX4MlpNhvNbujaEGiXWwPmFk9LOO34ShvM7Fxv+WDBBD85v+mX26LWMM055dP3FD09PstI87qACc7+R87+YiRfh/CarjOWyz2bD1bc/WnJXX2oBnN/b9VDYwW8pnF/grNHznHkDgm/UH6Px9TDC/EsHQ062foDLN7ziSJ2y3h/Ob5uEGt49Vo1sKnf14fyy5hnxbN+mwM1LVzYGAZzh2xL548rfz9vg/C4mU25giON0f21yBap64zU3X9g5wfmTDgktZg1WQ5jfXYAa30xHjE6Fr8AlDwDAZogT</peaks>\n </scan>\n <scan num="2"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -47,14 +47,14 @@\n totIonCurrent="30.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="106"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdyTEOgkAARFFKSgsKCwpDiDGGGBUQUIGFk3lkj0BDs2+ayctPknjzP3aghxQfcIaPOMcnXOASn/EFX3GFb/iOH/iJa9zsP+3f0l+4wz0e8Bt/8BePeMIzDvoXe6Ev9JW+xn0DFhgSxA==</peaks>\n+ compressedLen="279"\n+ precision="64"\n+ byteOrder="network"\n+ contentType="m/z-int">eJxzqDjEr75b/w0DFDhUbHa5ILxSC84vnRQUkrAqFSe/PvhDfqZLOpzfWKTCXcHsDufXXkoDAYT5aPZ1KLX4MlpNhvNbujaEGiXWwPmFk9LOO34ShvM7Fxv+WDBBD85v+mX26LWMM055dP3FD09PstI8jnC/kfO/mIkXEeZZZSyXfTYbzm9/tOSuvtQCOL+366Gwg99SOL/AWaPnOfMGBzsY36g/RuPrYYT5lw6GnGz9AOc3vOJInbLeH85vm4Qa3j1WjWwqd/Xh/LLmGfFs36bA+enKxiAA56OHb0vkjyt/P2+D87uYTLmBIY7T/bXJFajqjdfcfGHnBOdPOiS0mDVYDWF+dwFqfDMdMToVvgKXPACIeYcB</peaks>\n </scan>\n <scan num="3"\n scanType="SRM"\n- centroided="0"\n+ centroided="1"\n msLevel="1"\n peaksCount="38"\n polarity="+"\n@@ -64,14 +64,14 @@\n totIonCurrent="40.0"\n msInstrumentID="1">\n <peaks compressionType="zlib"\n- compressedLen="108"\n- precision="64"\n- byteOrder="network"\n- contentType="m/z-int">eJxdzjEOgkAQQFFKSwsLCwpDjDHGGEFBQYVlT8aRPQL1vO3e/MlkiyK+6R+d6GmDt3iH97jEB1zhIz7hM77gK77hO65xgx/4Gf+ZWuYd+y/8xj0euP+hf/EPj3jCSS/RM32mZ3qOfQW46hOC</peaks>\n+ compressedLen="280"\n+ precision="64"\n+ byteOrder="network"\n+ 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| diff -r 3cf310697624 -r 6153e8ada1ee test-data/SciexTest-HPINalone.mzML --- a/test-data/SciexTest-HPINalone.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/SciexTest-HPINalone.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/ThyroglobMRM000003.mzML --- a/test-data/ThyroglobMRM000003.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/ThyroglobMRM000003.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="ThyroglobMRM000003" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-activation.mzML --- a/test-data/small-activation.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-activation.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>\n </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n@@ -2719,59 +2717,59 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=2">14908</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">25814</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">34385</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">46243</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=6">56759</offset>\n- <offset idRef="controllerType=0 controll'..b' scan=5">46159</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">56675</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">66044</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">76212</offset>\n+ <offset 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scan=21">202940</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">213798</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">221713</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">230369</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">239586</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">251070</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">261219</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">270789</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">281539</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">289852</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">300214</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">311654</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">321025</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">330689</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">339557</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">347128</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">356145</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">365318</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">377603</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">386975</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">397765</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">407725</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">421264</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">432607</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">441992</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">453852</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">463631</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">473036</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">482350</offset>\n+ <offset idRef="TIC">482266</offset>\n </index>\n </indexList>\n- <indexListOffset>484300</indexListOffset>\n- <fileChecksum>843aa9bf79a1bc9eb78f452273992425b1620ee9</fileChecksum>\n+ <indexListOffset>484216</indexListOffset>\n+ <fileChecksum>8b12e89899d385d5ef0b007114bc36001c18198e</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-analyzer-filter.mzML --- a/test-data/small-analyzer-filter.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-analyzer-filter.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>\n </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n@@ -2439,52 +2437,52 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=2">5698</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">16604</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">25175</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">37033</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=6">47549</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=7">56918</offset>\n- <offset idRef="controllerType=0 controll'..b'umber=1 scan=46">392515</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=47">402294</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=48">411699</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=2">5614</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=3">16520</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=4">25091</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=5">36949</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">47465</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">56834</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=9">67002</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">78780</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">87804</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">99275</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">108558</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">118830</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">128314</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">139346</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">148561</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">159851</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">169321</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">178857</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">189715</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">198371</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">207588</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">219072</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">229221</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">238791</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">249541</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">259903</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">271343</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">280714</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">290378</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">299246</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">308263</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">317436</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">329721</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">339093</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">349883</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">359843</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">371186</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">380571</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">392431</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">402210</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">411615</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">420929</offset>\n+ <offset idRef="TIC">420845</offset>\n </index>\n </indexList>\n- <indexListOffset>422879</indexListOffset>\n- <fileChecksum>66d97ae40f2d7213e35aa35794484007ee40ce1a</fileChecksum>\n+ <indexListOffset>422795</indexListOffset>\n+ <fileChecksum>e9998c0aa79067dc7935ea57633613380f9eef85</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-chargeStatePredictor.mzML --- a/test-data/small-chargeStatePredictor.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-chargeStatePredictor.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" 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scan=46">466185</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">476372</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">486185</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">495592</offset>\n+ <offset idRef="TIC">495508</offset>\n </index>\n </indexList>\n- <indexListOffset>497542</indexListOffset>\n- <fileChecksum>4a570796813708eca1754ccf46e25355eae4a2b4</fileChecksum>\n+ <indexListOffset>497458</indexListOffset>\n+ <fileChecksum>820300fdfbf32732fca84c471e7509c5cfee54de</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-deisotope.mzML --- a/test-data/small-deisotope.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-deisotope.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-denoise.mzML --- a/test-data/small-denoise.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-denoise.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" 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scan=46">348837</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">355417</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">361875</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">368743</offset>\n+ <offset idRef="TIC">368659</offset>\n </index>\n </indexList>\n- <indexListOffset>370693</indexListOffset>\n- <fileChecksum>c8898ce9bf2f20b5934353cec6f9703268b79e6e</fileChecksum>\n+ <indexListOffset>370609</indexListOffset>\n+ <fileChecksum>3bb136dddbbf1dbe75414cfeb9b330cbc887d232</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-index-filter.mzML --- a/test-data/small-index-filter.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-index-filter.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| @@ -2,7 +2,7 @@ <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/mzML1.1.2_idx.xsd"> <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" id="small" version="1.1.0"> <cvList count="2"> - <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/> </cvList> <fileDescription> @@ -20,7 +20,7 @@ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/> </sourceFile> <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///"> - <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/> + <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/> </sourceFile> </sourceFileList> </fileDescription> @@ -30,17 +30,14 @@ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/> </referenceableParamGroup> </referenceableParamGroupList> - <softwareList count="4"> + <softwareList count="3"> <software id="Xcalibur" version="1.1 Beta 7"> <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/> </software> <software id="pwiz" version="3.0.8981"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> - <software id="pwiz_3.0.19038" version="3.0.19038"> - <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> - </software> - <software id="pwiz_3.0.19044" version="3.0.19044"> + <software id="pwiz_3.0.20287" version="3.0.20287"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> </softwareList> @@ -85,11 +82,12 @@ </processingMethod> </dataProcessing> <dataProcessing id="pwiz_Reader_conversion"> - <processingMethod order="0" softwareRef="pwiz_3.0.19038"> + <processingMethod order="0" softwareRef="pwiz_3.0.20287"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> </processingMethod> - <processingMethod order="1" softwareRef="pwiz_3.0.19038"> + <processingMethod order="1" softwareRef="pwiz_3.0.20287"> <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> + <userParam name="CantWaiT (continuous wavelet transform) peak picker"/> </processingMethod> </dataProcessing> </dataProcessingList> @@ -499,18 +497,18 @@ </mzML> <indexList count="2"> <index name="spectrum"> - <offset idRef="controllerType=0 controllerNumber=1 scan=3">5697</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=4">14268</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=5">26126</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=11">36642</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=14">48113</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=15">57596</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=16">65377</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=3">5613</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=4">14184</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=5">26042</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=11">36558</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=14">48029</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=15">57512</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=16">65293</offset> </index> <index name="chromatogram"> - <offset idRef="TIC">76515</offset> + <offset idRef="TIC">76431</offset> </index> </indexList> - <indexListOffset>78465</indexListOffset> - <fileChecksum>0671bee5b37c6f8cc8afde991309fd96af7f5c3d</fileChecksum> + <indexListOffset>78381</indexListOffset> + <fileChecksum>190e7438359420dfb1a9b11d5829700a34ec36bd</fileChecksum> </indexedmzML> |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-ms-level-filter.mzML --- a/test-data/small-ms-level-filter.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-ms-level-filter.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>\n </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n@@ -2159,45 +2157,45 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">5698</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">14269</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">26127</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=6">36643</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=7">46012</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=10">56180</offset>\n- <offset idRef="controllerType=0 control'..b'ber=1 scan=37">246594</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=38">255767</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=39">268052</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=40">277424</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=41">288214</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=44">298174</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=45">307559</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=46">319419</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=47">329198</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=48">338603</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=3">5614</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=4">14185</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=5">26043</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">36559</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">45928</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">56096</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">65120</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">76591</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">85874</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">96145</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">105628</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">114843</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">126133</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">135603</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">145139</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">155997</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">165214</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">176698</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">186847</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">196417</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">207167</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">218607</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">227978</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">237642</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">246510</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">255683</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">267968</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">277340</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">288130</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">298090</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">307475</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">319335</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">329114</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">338519</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">347833</offset>\n+ <offset idRef="TIC">347749</offset>\n </index>\n </indexList>\n- <indexListOffset>349783</indexListOffset>\n- <fileChecksum>b37853cea35a8233460f48bc42abefd34f982729</fileChecksum>\n+ <indexListOffset>349699</indexListOffset>\n+ <fileChecksum>4fc5cbcd6dd3aef49694e162339328aa1da1ac72</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-mzWindow.mzML --- a/test-data/small-mzWindow.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-mzWindow.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ 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<offset idRef="controllerType=0 controllerNumber=1 scan=9">57757</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">62854</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">69894</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">77550</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">84770</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">92198</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=15">99626</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">105164</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">110451</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">117486</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">125120</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">132330</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 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scan=46">308086</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">315337</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">322694</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">330136</offset>\n+ <offset idRef="TIC">330052</offset>\n </index>\n </indexList>\n- <indexListOffset>332086</indexListOffset>\n- <fileChecksum>4c52055cc16e42e05ef5a8eae5df244ea6ead1ac</fileChecksum>\n+ <indexListOffset>332002</indexListOffset>\n+ <fileChecksum>c854b1b0a8acbad401bff243741e2b6e87b59921</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-numpressL.mzML --- a/test-data/small-numpressL.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-numpressL.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-numpressLP.mzML --- a/test-data/small-numpressLP.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-numpressLP.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-numpressLS.mzML --- a/test-data/small-numpressLS.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-numpressLS.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-numpressP.mzML --- a/test-data/small-numpressP.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-numpressP.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-numpressS.mzML --- a/test-data/small-numpressS.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-numpressS.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-peakpicking-cwt-allMS.mzML --- a/test-data/small-peakpicking-cwt-allMS.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-peakpicking-cwt-allMS.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-peakpicking-vendor-allMS.mzML --- a/test-data/small-peakpicking-vendor-allMS.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-peakpicking-vendor-allMS.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-polarity-filter.mzML --- a/test-data/small-polarity-filter.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-polarity-filter.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n 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scan=46">453852</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">463631</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">473036</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">482350</offset>\n+ <offset idRef="TIC">482266</offset>\n </index>\n </indexList>\n- <indexListOffset>484300</indexListOffset>\n- <fileChecksum>843aa9bf79a1bc9eb78f452273992425b1620ee9</fileChecksum>\n+ <indexListOffset>484216</indexListOffset>\n+ <fileChecksum>8b12e89899d385d5ef0b007114bc36001c18198e</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-strip-it.mzML --- a/test-data/small-strip-it.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-strip-it.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-threshold.mzML --- a/test-data/small-threshold.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-threshold.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>\n </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n@@ -2719,59 +2717,59 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=2">10070</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">14461</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">20485</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">26507</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=6">32496</offset>\n- <offset idRef="controllerType=0 controll'..b'Number=1 scan=5">26423</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">32412</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">38398</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">44419</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=9">48782</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">53141</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">59170</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">65195</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">71176</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">77165</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=15">83158</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">87534</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">91919</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">97951</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">103974</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">109953</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">115950</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">121949</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">126322</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">130660</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">136690</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">142719</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">148697</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">154688</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">160703</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">165074</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">169474</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">175499</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">181471</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">187456</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">193402</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">197779</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">202154</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">208184</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">214217</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">220202</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">226205</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">232182</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">236546</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">240942</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">246968</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">252984</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">258952</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">264930</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">271077</offset>\n+ <offset idRef="TIC">270993</offset>\n </index>\n </indexList>\n- <indexListOffset>273027</indexListOffset>\n- <fileChecksum>b1908e0016bbf6bf4fc21daa511924db77237312</fileChecksum>\n+ <indexListOffset>272943</indexListOffset>\n+ <fileChecksum>95a42b81dbc77e94be64a5f6577fe211616e6069</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-turbocharger.mzML --- a/test-data/small-turbocharger.mzML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-turbocharger.mzML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| b'@@ -2,7 +2,7 @@\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/mzML1.1.2_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" id="small" version="1.1.0">\n <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n </sourceFile>\n <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,17 +30,14 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="4">\n+ <softwareList count="3">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.19038" version="3.0.19038">\n- <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n- </software>\n- <software id="pwiz_3.0.19044" version="3.0.19044">\n+ <software id="pwiz_3.0.20287" version="3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -85,11 +82,12 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.19038">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.20287">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n+ <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>\n </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n@@ -2756,59 +2754,59 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=2">14908</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">25814</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">34431</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">46335</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=6">56897</offset>\n- <offset idRef="controllerType=0 controll'..b' scan=5">46251</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">56813</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">66228</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">76804</offset>\n+ <offset 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| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-zlib-32.mzXML --- a/test-data/small-zlib-32.mzXML Mon Nov 16 17:25:12 2020 +0000 +++ b/test-data/small-zlib-32.mzXML Mon Nov 30 16:01:10 2020 +0000 |
| b |
| @@ -27,12 +27,13 @@ <processingOperation name="Conversion to mzML"/> </dataProcessing> <dataProcessing> - <software type="conversion" name="ProteoWizard software" version="3.0.19038"/> + <software type="conversion" name="ProteoWizard software" version="3.0.20287"/> <processingOperation name="Conversion to mzML"/> </dataProcessing> <dataProcessing centroided="1"> - <software type="processing" name="ProteoWizard software" version="3.0.19038"/> + <software type="processing" name="ProteoWizard software" version="3.0.20287"/> <processingOperation name="peak picking"/> + <comment>CantWaiT (continuous wavelet transform) peak picker</comment> </dataProcessing> <scan num="1" scanType="Full" @@ -1016,55 +1017,55 @@ </scan> </msRun> <index name="scan"> - <offset id="1">2139</offset> - <offset id="2">9724</offset> - <offset id="3">19203</offset> - <offset id="4">24723</offset> - <offset id="5">35301</offset> - <offset id="6">44300</offset> - <offset id="7">51480</offset> - <offset id="8">59736</offset> - <offset id="9">64740</offset> - <offset id="10">75655</offset> - <offset id="11">81834</offset> - <offset id="12">91749</offset> - <offset id="13">98784</offset> - <offset id="14">107337</offset> - <offset id="15">114704</offset> - <offset id="16">120598</offset> - <offset id="17">130214</offset> - <offset id="18">136659</offset> - <offset id="19">146356</offset> - <offset id="20">153734</offset> - <offset id="21">161154</offset> - <offset id="22">170676</offset> - <offset id="23">176788</offset> - <offset id="24">183537</offset> - <offset id="25">189982</offset> - <offset id="26">199882</offset> - <offset id="27">208429</offset> - <offset id="28">215983</offset> - <offset id="29">225257</offset> - <offset id="30">231917</offset> - <offset id="31">240628</offset> - <offset id="32">250540</offset> - <offset id="33">257754</offset> - <offset id="34">265462</offset> - <offset id="35">272045</offset> - <offset id="36">277669</offset> - <offset id="37">284751</offset> - <offset id="38">291122</offset> - <offset id="39">302259</offset> - <offset id="40">309479</offset> - <offset id="41">318838</offset> - <offset id="42">327039</offset> - <offset id="43">340377</offset> - <offset id="44">350377</offset> - <offset id="45">357129</offset> - <offset id="46">367740</offset> - <offset id="47">375513</offset> - <offset id="48">382804</offset> + <offset id="1">2216</offset> + <offset id="2">9801</offset> + <offset id="3">19280</offset> + <offset id="4">24800</offset> + <offset id="5">35378</offset> + <offset id="6">44377</offset> + <offset id="7">51557</offset> + <offset id="8">59813</offset> + <offset id="9">64817</offset> + <offset id="10">75732</offset> + <offset id="11">81911</offset> + <offset id="12">91826</offset> + <offset id="13">98861</offset> + <offset id="14">107414</offset> + <offset id="15">114781</offset> + <offset id="16">120675</offset> + <offset id="17">130291</offset> + <offset id="18">136736</offset> + <offset id="19">146433</offset> + <offset id="20">153811</offset> + <offset id="21">161231</offset> + <offset id="22">170753</offset> + <offset id="23">176865</offset> + <offset id="24">183614</offset> + <offset id="25">190059</offset> + <offset id="26">199959</offset> + <offset id="27">208506</offset> + <offset id="28">216060</offset> + <offset id="29">225334</offset> + <offset id="30">231994</offset> + <offset id="31">240705</offset> + <offset id="32">250617</offset> + <offset id="33">257831</offset> + <offset id="34">265539</offset> + <offset id="35">272122</offset> + <offset id="36">277746</offset> + <offset id="37">284828</offset> + <offset id="38">291199</offset> + <offset id="39">302336</offset> + <offset id="40">309556</offset> + <offset id="41">318915</offset> + <offset id="42">327116</offset> + <offset id="43">340454</offset> + <offset id="44">350454</offset> + <offset id="45">357206</offset> + <offset id="46">367817</offset> + <offset id="47">375590</offset> + <offset id="48">382881</offset> </index> - <indexOffset>389864</indexOffset> - <sha1>22755d784c31491eb1a1f5f2dd9db13dd5e52277</sha1> + <indexOffset>389941</indexOffset> + <sha1>031f5f799e75da3c5f997d718cfdd7ccdc1b5672</sha1> </mzXML> |
| b |
| diff -r 3cf310697624 -r 6153e8ada1ee test-data/small-zlib-64.mz5 |
| b |
| Binary file test-data/small-zlib-64.mz5 has changed |