| Previous changeset 0:baa6c072fccc (2016-04-08) Next changeset 2:c9b96a178758 (2017-03-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848 |
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modified:
msconvert_macros.xml msconvert_wrapper.py 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-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 |
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removed:
tool_dependencies.xml |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 msconvert_macros.xml --- a/msconvert_macros.xml Fri Apr 08 16:08:09 2016 -0400 +++ b/msconvert_macros.xml Tue Mar 14 16:45:30 2017 -0400 |
| [ |
| b'@@ -1,34 +1,39 @@\n <macros>\n <xml name="generic_requirements">\n <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n+ <requirement type="package" version="3.0.9992">proteowizard</requirement>\n </requirements>\n </xml>\n- <token name="@VERSION@">3.0</token>\n+ <token name="@VERSION@">3.0.9992</token>\n \n <xml name="msconvertCommand">\n <command interpreter="python">\n <![CDATA[\n #import re\n #set $ext = $input.ext\n+\n+ ## sanitize display name for use as temp filename\n+ #set basename = \'pwiz_in\'\n+ \n+ #if hasattr($input, \'display_name\')\n+ ## explicit inclusion or exclusion ??\n+ #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.display_name)\n+ ##set basename = $re.sub(r\'[\\/\\\\\\;\\|\\&\\>\\<]\',\'_\',$input.display_name)\n+ #end if\n+\n msconvert_wrapper.py\n+\n #if $ext == \'wiff\':\n- #set basename = \'absciex\'\n- #if hasattr($input, \'display_name\')\n- #set basename = $re.sub(\'\\W\',\'_\',$input.display_name)\n- #end if\n- --input=${input.extra_files_path}/wiff\n- --input_name=\'${basename}.wiff\n- --implicit=${input.extra_files_path}/wiff_scan\n- --input=${input.extra_files_path}/wiff_scan\n- --input_name=\'${basename}.wiff.scan\n+ --input=\'${input.extra_files_path}/wiff\'\n+ --input_name=\'${basename}.wiff\'\n+ --implicit=\'${input.extra_files_path}/wiff_scan\'\n+ --input=\'${input.extra_files_path}/wiff_scan\'\n+ --input_name=\'${basename}.wiff.scan\'\n #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n+ --input=\'${input}\'\n+ --input_name=\'$basename\'\n #end if\n- --output=${output}\n+ --output=\'${output}\'\n ## BEGIN_VERSION_DEFAULT\n --fromextension=$ext\n ## END_VERSION_DEFAULT\n@@ -36,15 +41,10 @@\n \n ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\n #if $data_processing.precursor_refinement.use_mzrefinement\n- #set $input_ident_name = $re.sub(\'\\W\',\'_\',$data_processing.precursor_refinement.input_ident.display_name)\n- #if $data_processing.precursor_refinement.input_ident.ext == \'mzid\':\n- #set $input_ident_name = $re.sub(\'(?i)([.]?mzid)*$\',\'.mzid\',$input_ident_name)\n- #elif $data_processing.precursor_refinement.input_ident.ext == \'pepxml\':\n- #set $input_ident_name = $re.sub(\'(?i)([.]?pep[.]?xml)*$\',\'.pep.xml\',$input_ident_name)\n- #end if\n- --ident=$data_processing.precursor_refinement.input_ident\n- --ident_name=$input_ident_name\n- --refinement=$output_refinement\n+ #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))\n+ --ident=\'$data_processing.precursor_refinement.input_ident\'\n+ --ident_name=\'$input_ident_name\'\n+ --refinement=\'$output_refinement\'\n --filter "mzRefiner $input_ident_name\n msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n thresholdScore=$data_processing.precursor_refinement.thresholdScore\n@@ -54,7 +54,7 @@\n #end if\n \n #if $data_processing.peak_picking.pick_peaks\n- --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n+ --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"\n #end if\n \n #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n@@ -76,27 +76,27 @@\n #end if\n \n #for threshold_entry in $data_processing.thresholds\n- --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"\n+ --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"\n #end for\n \n #if $data_processing.fil'..b' data?" truevalue="true" falsevalue="false" checked="False" />\n <when value="false"></when>\n <when value="true">\n <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />\n- <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. \'mvh\' for MyriMatch, \'xcorr\' for Sequest, \'specevalue\' for MS-GF+" />\n- <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. \'100-\' means score equal to or greater than 100. \'-1e-10\' means less than or equal to 1e-10." />\n+ <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. \'mvh\' for MyriMatch, \'xcorr\' for Sequest, \'specevalue\' for MS-GF+">\n+ <sanitizer>\n+ <valid initial="string.letters" />\n+ </sanitizer>\n+ </param>\n+ <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. \'100-\' means score equal to or greater than 100. \'-1e-10\' means less than or equal to 1e-10.">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits">\n+ <add value="-" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />\n <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />\n <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">\n@@ -322,14 +332,14 @@\n <option value="CID">CID</option>\n <option value="SA">SA</option>\n <option value="HCD">HCD</option>\n- <option>BIRD</option>\n- <option>ECD</option>\n- <option>IRMPD</option>\n- <option>PD</option>\n- <option>PSD</option>\n- <option>PQD</option>\n- <option>SID</option>\n- <option>SORI</option>\n+ <option value="BIRD">BIRD</option>\n+ <option value="ECD">ECD</option>\n+ <option value="IRMPD">IRMPD</option>\n+ <option value="PD">PD</option>\n+ <option value="PSD">PSD</option>\n+ <option value="PQD">PQD</option>\n+ <option value="SID">SID</option>\n+ <option value="SORI">SORI</option>\n </param>\n \n <repeat name="indices" title="Filter Scan Indices">\n@@ -433,7 +443,7 @@\n <param name="output_type" value="mz5" />\n <param name="mz_encoding" value="64" />\n <param name="intensity_encoding" value="64" />\n- <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />\n+ <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n@@ -502,11 +512,11 @@\n <param name="output_type" value="mzML" />\n <param name="binary_compression" value="numpressLinearPic" />\n <param name="use_mzrefinement" value="true" />\n- <param name="input_ident" value="Rpal_01.pepXML.gz" />\n+ <param name="input_ident" value="Rpal_01.pepXML" />\n <param name="thresholdScore" value="mvh" />\n <param name="thresholdValue" value="40-" />\n <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />\n- <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />\n+ <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />\n </test>\n \n <test>\n' |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 msconvert_wrapper.py --- a/msconvert_wrapper.py Fri Apr 08 16:08:09 2016 -0400 +++ b/msconvert_wrapper.py Tue Mar 14 16:45:30 2017 -0400 |
| [ |
| @@ -7,6 +7,7 @@ import subprocess import re import logging +import shlex assert sys.version_info[:2] >= (2, 6) @@ -40,7 +41,8 @@ try: with open(tmp_stderr_name, 'wb') as tmp_stderr: with open(tmp_stdout_name, 'wb') as tmp_stdout: - proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) + args = shlex.split(command) # handle proper splitting of quoted args + proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) returncode = proc.wait() if returncode != 0: raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-activation.mzML --- a/test-data/small-activation.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-activation.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -37,7 +37,7 @@\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_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.9987" version="3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -1272,7 +1272,7 @@\n </binaryDataArray>\n </binaryDataArrayList>\n </spectrum>\n- <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion">\n+ <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">\n <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>\n <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>\n@@ -1298,17 +1298,17 @@\n </scan>\n </scanList>\n <binaryDataArrayList count="2">\n- <binaryDataArray encodedLength="3380">\n+ <binaryDataArray encodedLength="3376">\n <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\n <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>\n <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n- <binary>QWQvt'..b' scan=5">46122</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">56638</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">66007</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">76175</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=9">83264</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">95042</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">104066</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">115538</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">124822</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">135094</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=15">144578</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">152360</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">163392</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">172607</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">183897</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">193367</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">202903</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">213761</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">221676</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">230332</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">239549</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">251033</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">261182</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">270752</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">281502</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">289815</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">300177</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">311617</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">320988</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">330652</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">339520</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">347091</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">356116</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">365289</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">377574</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">386946</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">397736</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">407696</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">421227</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">432570</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">441955</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">453815</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">463594</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">472999</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">482238</offset>\n+ <offset idRef="TIC">482229</offset>\n </index>\n </indexList>\n- <indexListOffset>484188</indexListOffset>\n- <fileChecksum>e18a3d758326d6d1adb2a8f00fa69cfb1dc5b83d</fileChecksum>\n+ <indexListOffset>484179</indexListOffset>\n+ <fileChecksum>38c3d8ce41007e9ae1289c57a9448e0554d31ff1</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-analyzer-filter.mzML --- a/test-data/small-analyzer-filter.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-analyzer-filter.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -37,7 +37,7 @@\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_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.9987" version="3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -1112,7 +1112,7 @@\n </binaryDataArray>\n </binaryDataArrayList>\n </spectrum>\n- <spectrum index="18" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion">\n+ <spectrum index="18" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">\n <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>\n <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>\n@@ -1138,17 +1138,17 @@\n </scan>\n </scanList>\n <binaryDataArrayList count="2">\n- <binaryDataArray encodedLength="3380">\n+ <binaryDataArray encodedLength="3376">\n <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\n <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>\n <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n- <binary>QWQvt'..b'umber=1 scan=46">392411</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=47">402190</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=48">411595</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=2">5577</offset>\n+ <offset 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-deisotope.mzML --- a/test-data/small-deisotope.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-deisotope.mzML Tue Mar 14 16:45:30 2017 -0400 |
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| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-denoise.mzML --- a/test-data/small-denoise.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-denoise.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -1272,7 +1272,7 @@\n </binaryDataArray>\n </binaryDataArrayList>\n </spectrum>\n- <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion">\n+ <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">\n <cvParam 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-index-filter.mzML --- a/test-data/small-index-filter.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-index-filter.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/> + <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/> </sourceFile> </sourceFileList> </fileDescription> @@ -37,7 +37,7 @@ <software id="pwiz" version="3.0.8981"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> - <software id="pwiz_3.0.8990" version="3.0.8990"> + <software id="pwiz_3.0.9987" version="3.0.9987"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> </softwareList> @@ -82,10 +82,10 @@ </processingMethod> </dataProcessing> <dataProcessing id="pwiz_Reader_conversion"> - <processingMethod order="0" softwareRef="pwiz_3.0.8990"> + <processingMethod order="0" softwareRef="pwiz_3.0.9987"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> </processingMethod> - <processingMethod order="1" softwareRef="pwiz_3.0.8990"> + <processingMethod order="1" softwareRef="pwiz_3.0.9987"> <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> </processingMethod> </dataProcessing> @@ -496,18 +496,18 @@ </mzML> <indexList count="2"> <index name="spectrum"> - <offset idRef="controllerType=0 controllerNumber=1 scan=3">5577</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=4">14148</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=5">26006</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=11">36522</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=14">47993</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=15">57476</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=16">65257</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=3">5576</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=4">14147</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=5">26005</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=11">36521</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=14">47992</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=15">57475</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=16">65256</offset> </index> <index name="chromatogram"> - <offset idRef="TIC">76395</offset> + <offset idRef="TIC">76394</offset> </index> </indexList> - <indexListOffset>78345</indexListOffset> - <fileChecksum>0d5bbd9cad4ad9471eba2e80d0ddea2cddcf3db9</fileChecksum> + <indexListOffset>78344</indexListOffset> + <fileChecksum>ee644abff7e27a2bdc852562fcd0258f31fb46eb</fileChecksum> </indexedmzML> |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-ms-level-filter.mzML --- a/test-data/small-ms-level-filter.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-ms-level-filter.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -37,7 +37,7 @@\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_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.9987" version="3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -2156,45 +2156,45 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">5578</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">14149</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=5">26007</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-mzWindow.mzML --- a/test-data/small-mzWindow.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-mzWindow.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-numpressL.mzML --- a/test-data/small-numpressL.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-numpressL.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-numpressLP.mzML --- a/test-data/small-numpressLP.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-numpressLP.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-numpressLS.mzML --- a/test-data/small-numpressLS.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-numpressLS.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-numpressP.mzML --- a/test-data/small-numpressP.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-numpressP.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-numpressS.mzML --- a/test-data/small-numpressS.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-numpressS.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-peakpicking-cwt-allMS.mzML --- a/test-data/small-peakpicking-cwt-allMS.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-peakpicking-cwt-allMS.mzML Tue Mar 14 16:45:30 2017 -0400 |
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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-polarity-filter.mzML --- a/test-data/small-polarity-filter.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-polarity-filter.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-strip-it.mzML --- a/test-data/small-strip-it.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-strip-it.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -2436,52 +2436,52 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=1">5578</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">14788</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=4">23359</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-threshold.mzML --- a/test-data/small-threshold.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-threshold.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -37,7 +37,7 @@\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_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.9987" version="3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +82,10 @@\n </processingMethod>\n </dataProcessing>\n <dataProcessing id="pwiz_Reader_conversion">\n- <processingMethod order="0" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="0" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>\n </processingMethod>\n- <processingMethod order="1" softwareRef="pwiz_3.0.8990">\n+ <processingMethod order="1" softwareRef="pwiz_3.0.9987">\n <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>\n </processingMethod>\n </dataProcessing>\n@@ -2716,59 +2716,59 @@\n </mzML>\n <indexList count="2">\n <index name="spectrum">\n- <offset idRef="controllerType=0 controllerNumber=1 scan=1">5578</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=2">9950</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 scan=3">14341</offset>\n- <offset idRef="controllerType=0 controllerNumber=1 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| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-turbocharger.mzML --- a/test-data/small-turbocharger.mzML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-turbocharger.mzML Tue Mar 14 16:45:30 2017 -0400 |
| 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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n <cv id="UO" fullName="Unit Ontology" version="12:10:2011" 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scan=46">455603</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">465428</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">474880</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">484164</offset>\n+ <offset idRef="TIC">484155</offset>\n </index>\n </indexList>\n- <indexListOffset>486114</indexListOffset>\n- <fileChecksum>e7ec398af412704484453e19bd2bc7578529b5c0</fileChecksum>\n+ <indexListOffset>486105</indexListOffset>\n+ <fileChecksum>1dda3f0dfdbbd41618dd9aa7ac70fa871cbc4199</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-zlib-32.mzXML --- a/test-data/small-zlib-32.mzXML Fri Apr 08 16:08:09 2016 -0400 +++ b/test-data/small-zlib-32.mzXML Tue Mar 14 16:45:30 2017 -0400 |
| b |
| b'@@ -27,9 +27,9 @@\n <processingOperation name="Conversion to mzML"/>\n </dataProcessing>\n <dataProcessing centroided="1">\n- <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>\n+ <software type="conversion" name="ProteoWizard software" version="3.0.9987"/>\n <processingOperation name="Conversion to mzML"/>\n- <software type="processing" name="ProteoWizard software" version="3.0.8990"/>\n+ <software type="processing" name="ProteoWizard software" version="3.0.9987"/>\n </dataProcessing>\n <scan num="1"\n scanType="Full"\n@@ -483,7 +483,7 @@\n scanType="Full"\n centroided="1"\n msLevel="1"\n- peaksCount="701"\n+ peaksCount="700"\n polarity="+"\n retentionTime="PT13.0048S"\n lowMz="200.090909093618"\n@@ -493,10 +493,10 @@\n totIonCurrent="1.5974105e06"\n msInstrumentID="2">\n <peaks compressionType="zlib"\n- compressedLen="4633"\n+ compressedLen="4626"\n precision="32"\n byteOrder="network"\n- contentType="m/z-int">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'..b'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</peaks>\n </scan>\n <scan num="24"\n scanType="Full"\n@@ -1036,32 +1036,32 @@\n <offset id="21">161095</offset>\n <offset id="22">170617</offset>\n <offset id="23">176729</offset>\n- <offset id="24">183490</offset>\n- <offset id="25">189935</offset>\n- <offset id="26">199835</offset>\n- <offset id="27">208382</offset>\n- <offset id="28">215936</offset>\n- <offset id="29">225210</offset>\n- <offset id="30">231870</offset>\n- <offset id="31">240581</offset>\n- <offset id="32">250493</offset>\n- <offset id="33">257707</offset>\n- <offset id="34">265415</offset>\n- <offset id="35">271998</offset>\n- <offset id="36">277622</offset>\n- <offset id="37">284712</offset>\n- <offset id="38">291083</offset>\n- <offset id="39">302220</offset>\n- <offset id="40">309440</offset>\n- <offset id="41">318799</offset>\n- <offset id="42">327000</offset>\n- <offset id="43">340330</offset>\n- <offset id="44">350330</offset>\n- <offset id="45">357082</offset>\n- <offset id="46">367693</offset>\n- <offset id="47">375466</offset>\n- <offset id="48">382757</offset>\n+ <offset id="24">183478</offset>\n+ <offset id="25">189923</offset>\n+ <offset id="26">199823</offset>\n+ <offset id="27">208370</offset>\n+ <offset id="28">215924</offset>\n+ <offset id="29">225198</offset>\n+ <offset id="30">231858</offset>\n+ <offset id="31">240569</offset>\n+ <offset id="32">250481</offset>\n+ <offset id="33">257695</offset>\n+ <offset id="34">265403</offset>\n+ <offset id="35">271986</offset>\n+ <offset id="36">277610</offset>\n+ <offset id="37">284700</offset>\n+ <offset id="38">291071</offset>\n+ <offset id="39">302208</offset>\n+ <offset id="40">309428</offset>\n+ <offset id="41">318787</offset>\n+ <offset id="42">326988</offset>\n+ <offset id="43">340318</offset>\n+ <offset id="44">350318</offset>\n+ <offset id="45">357070</offset>\n+ <offset id="46">367681</offset>\n+ <offset id="47">375454</offset>\n+ <offset id="48">382745</offset>\n </index>\n- <indexOffset>389817</indexOffset>\n- <sha1>352d6c47e7a76389270f5e063a125ae498ad9f9c</sha1>\n+ <indexOffset>389805</indexOffset>\n+ <sha1>1b29dcc1fa98171da67734f8ac212e894ef1ce61</sha1>\n </mzXML>\n' |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 test-data/small-zlib-64.mz5 |
| b |
| Binary file test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r baa6c072fccc -r 7016f1f10f42 tool_dependencies.xml --- a/tool_dependencies.xml Fri Apr 08 16:08:09 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="proteowizard" version="3.0.9016"> - <repository changeset_revision="e9ae8f0be737" name="package_proteowizard_3_0_9016" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |