Mercurial > repos > galaxyp > msconvert_nix
changeset 1:7016f1f10f42 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
| author | galaxyp |
|---|---|
| date | Tue, 14 Mar 2017 16:45:30 -0400 |
| parents | baa6c072fccc |
| children | c9b96a178758 |
| files | 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 tool_dependencies.xml |
| diffstat | 23 files changed, 1116 insertions(+), 1110 deletions(-) [+] |
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--- a/msconvert_macros.xml Fri Apr 08 16:08:09 2016 -0400 +++ b/msconvert_macros.xml Tue Mar 14 16:45:30 2017 -0400 @@ -1,34 +1,39 @@ <macros> <xml name="generic_requirements"> <requirements> - <requirement type="package" version="3.0.9016">proteowizard</requirement> + <requirement type="package" version="3.0.9992">proteowizard</requirement> </requirements> </xml> - <token name="@VERSION@">3.0</token> + <token name="@VERSION@">3.0.9992</token> <xml name="msconvertCommand"> <command interpreter="python"> <![CDATA[ #import re #set $ext = $input.ext + + ## sanitize display name for use as temp filename + #set basename = 'pwiz_in' + + #if hasattr($input, 'display_name') + ## explicit inclusion or exclusion ?? + #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name) + ##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name) + #end if + msconvert_wrapper.py + #if $ext == 'wiff': - #set basename = 'absciex' - #if hasattr($input, 'display_name') - #set basename = $re.sub('\W','_',$input.display_name) - #end if - --input=${input.extra_files_path}/wiff - --input_name='${basename}.wiff - --implicit=${input.extra_files_path}/wiff_scan - --input=${input.extra_files_path}/wiff_scan - --input_name='${basename}.wiff.scan + --input='${input.extra_files_path}/wiff' + --input_name='${basename}.wiff' + --implicit='${input.extra_files_path}/wiff_scan' + --input='${input.extra_files_path}/wiff_scan' + --input_name='${basename}.wiff.scan' #else - --input=${input} - #if hasattr($input, 'display_name') - --input_name='${input.display_name}' - #end if + --input='${input}' + --input_name='$basename' #end if - --output=${output} + --output='${output}' ## BEGIN_VERSION_DEFAULT --fromextension=$ext ## END_VERSION_DEFAULT @@ -36,15 +41,10 @@ ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) #if $data_processing.precursor_refinement.use_mzrefinement - #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name) - #if $data_processing.precursor_refinement.input_ident.ext == 'mzid': - #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name) - #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml': - #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name) - #end if - --ident=$data_processing.precursor_refinement.input_ident - --ident_name=$input_ident_name - --refinement=$output_refinement + #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext)) + --ident='$data_processing.precursor_refinement.input_ident' + --ident_name='$input_ident_name' + --refinement='$output_refinement' --filter "mzRefiner $input_ident_name msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels thresholdScore=$data_processing.precursor_refinement.thresholdScore @@ -54,7 +54,7 @@ #end if #if $data_processing.peak_picking.pick_peaks - --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" + --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" #end if #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" @@ -76,27 +76,27 @@ #end if #for threshold_entry in $data_processing.thresholds - --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" + --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" #end for #if $data_processing.filter_mz_windows.do_mzwindow_filter - --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" + --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" #end if #if $data_processing.etd_filtering.do_etd_filtering - --filter "ETDFilter $data_processing.etd_filtering.remove_precursor - $data_processing.etd_filtering.remove_charge_reduced - $data_processing.etd_filtering.remove_neutral_loss - $data_processing.etd_filtering.blanket_removal - $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units" + --filter "ETDFilter $data_processing.etd_filtering.remove_precursor + $data_processing.etd_filtering.remove_charge_reduced + $data_processing.etd_filtering.remove_neutral_loss + $data_processing.etd_filtering.blanket_removal + $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units" #end if #if $data_processing.ms2denoise.denoise - --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" + --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" #end if #if str($data_processing.ms2deisotope) == "true" - --filter "MS2Deisotope" + --filter "MS2Deisotope" #end if @@ -106,35 +106,35 @@ #end if #if len($filtering.indices) > 0 - --filter "index - #for $index in $filtering.indices - [${index.from},${index.to}] - #end for - " + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " #end if #if len($filtering.scan_numbers) > 0 - --filter "scanNumber - #for $scan_number in $filtering.scan_numbers - [${scan_number.from},${scan_number.to}] - #end for - " + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " #end if #if $filtering.strip_it.value - --filter "stripIT" + --filter "stripIT" #end if #if $filtering.filter_ms_levels.do_ms_level_filter - --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" + --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" #end if #if str($filtering.polarity) != "false" - --filter "polarity $filtering.polarity" + --filter "polarity $filtering.polarity" #end if #if str($filtering.analyzer) != "false" - --filter "analyzer $filtering.analyzer" + --filter "analyzer $filtering.analyzer" #end if ## OUTPUT ENCODING @@ -154,21 +154,21 @@ #set binary_compression = str($settings.binary_compression) #if $binary_compression == "zlib" - --zlib + --zlib #else if $binary_compression == "numpressLinearPic" - --numpressLinear --numpressPic + --numpressLinear --numpressPic #else if $binary_compression == "numpressLinearSlof" - --numpressLinear --numpressSlof + --numpressLinear --numpressSlof #else if $binary_compression == "numpressLinear" - --numpressLinear + --numpressLinear #else if $binary_compression == "numpressPic" - --numpressPic + --numpressPic #else if $binary_compression == "numpressSlof" - --numpressSlof + --numpressSlof #end if #if $settings.gzip_compression - --gzip + --gzip #end if ]]> @@ -203,13 +203,23 @@ </when> </conditional> - <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true"> + <conditional name="precursor_refinement"> <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" /> <when value="false"></when> <when value="true"> <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" /> - <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+" /> - <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." /> + <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+"> + <sanitizer> + <valid initial="string.letters" /> + </sanitizer> + </param> + <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."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="-" /> + </valid> + </sanitizer> + </param> <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)." /> <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" /> <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels"> @@ -322,14 +332,14 @@ <option value="CID">CID</option> <option value="SA">SA</option> <option value="HCD">HCD</option> - <option>BIRD</option> - <option>ECD</option> - <option>IRMPD</option> - <option>PD</option> - <option>PSD</option> - <option>PQD</option> - <option>SID</option> - <option>SORI</option> + <option value="BIRD">BIRD</option> + <option value="ECD">ECD</option> + <option value="IRMPD">IRMPD</option> + <option value="PD">PD</option> + <option value="PSD">PSD</option> + <option value="PQD">PQD</option> + <option value="SID">SID</option> + <option value="SORI">SORI</option> </param> <repeat name="indices" title="Filter Scan Indices"> @@ -433,7 +443,7 @@ <param name="output_type" value="mz5" /> <param name="mz_encoding" value="64" /> <param name="intensity_encoding" value="64" /> - <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> + <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" /> </test> <test> <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> @@ -502,11 +512,11 @@ <param name="output_type" value="mzML" /> <param name="binary_compression" value="numpressLinearPic" /> <param name="use_mzrefinement" value="true" /> - <param name="input_ident" value="Rpal_01.pepXML.gz" /> + <param name="input_ident" value="Rpal_01.pepXML" /> <param name="thresholdScore" value="mvh" /> <param name="thresholdValue" value="40-" /> <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> - <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> + <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> </test> <test>
--- 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()))
--- 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 @@ -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> @@ -1272,7 +1272,7 @@ </binaryDataArray> </binaryDataArrayList> </spectrum> - <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion"> + <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion"> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/> <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> @@ -1298,17 +1298,17 @@ </scan> </scanList> <binaryDataArrayList count="2"> - <binaryDataArray encodedLength="3380"> + <binaryDataArray encodedLength="3376"> <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> - 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--- 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 @@ -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" 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--- 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 @@ -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" 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--- 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 @@ -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" 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--- 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 @@ -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>
--- 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 @@ -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:///"> - 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--- 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 @@ -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> @@ -2716,59 +2716,59 @@ </mzML> <indexList count="2"> <index name="spectrum"> - 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--- 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 @@ -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" 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--- 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 @@ -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" 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--- 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 @@ -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" 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--- 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 @@ -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> @@ -2436,52 +2436,52 @@ </mzML> <indexList count="2"> <index name="spectrum"> - 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<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> @@ -2716,59 +2716,59 @@ </mzML> <indexList count="2"> <index name="spectrum"> - 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--- 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 @@ -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" 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</binaryDataArray> </binaryDataArrayList> </spectrum> @@ -2753,59 +2753,59 @@ </mzML> <indexList count="2"> <index name="spectrum"> - <offset idRef="controllerType=0 controllerNumber=1 scan=1">5578</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=2">14788</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=3">25694</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=4">34311</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=5">46215</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=6">56777</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=7">66192</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=8">76768</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=9">83857</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=10">95635</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=11">104705</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=12">116223</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=13">125553</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=14">135871</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=15">145401</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=16">153183</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=17">164215</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=18">173476</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=19">184812</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=20">194329</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=21">203911</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=22">214815</offset> - <offset idRef="controllerType=0 controllerNumber=1 scan=23">222730</offset> - <offset idRef="controllerType=0 controllerNumber=1 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controllerNumber=1 scan=40">388550</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=41">399386</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=42">409393</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=43">422924</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=44">434267</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=45">443697</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=46">455603</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=47">465428</offset> + <offset idRef="controllerType=0 controllerNumber=1 scan=48">474880</offset> </index> <index name="chromatogram"> - <offset idRef="TIC">484164</offset> + <offset idRef="TIC">484155</offset> </index> </indexList> - <indexListOffset>486114</indexListOffset> - <fileChecksum>e7ec398af412704484453e19bd2bc7578529b5c0</fileChecksum> + <indexListOffset>486105</indexListOffset> + <fileChecksum>1dda3f0dfdbbd41618dd9aa7ac70fa871cbc4199</fileChecksum> </indexedmzML>
--- 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 @@ -27,9 +27,9 @@ <processingOperation name="Conversion to mzML"/> </dataProcessing> <dataProcessing centroided="1"> - <software type="conversion" name="ProteoWizard software" version="3.0.8990"/> + <software type="conversion" name="ProteoWizard software" version="3.0.9987"/> <processingOperation name="Conversion to mzML"/> - <software type="processing" name="ProteoWizard software" version="3.0.8990"/> + <software type="processing" name="ProteoWizard software" version="3.0.9987"/> </dataProcessing> <scan num="1" scanType="Full" @@ -483,7 +483,7 @@ scanType="Full" centroided="1" msLevel="1" - peaksCount="701" + peaksCount="700" polarity="+" retentionTime="PT13.0048S" lowMz="200.090909093618" @@ -493,10 +493,10 @@ totIonCurrent="1.5974105e06" msInstrumentID="2"> <peaks compressionType="zlib" - compressedLen="4633" + compressedLen="4626" precision="32" byteOrder="network" - contentType="m/z-int">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--- a/tool_dependencies.xml Fri Apr 08 16:08:09 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>