| Previous changeset 9:dd4ba10d0c45 (2016-12-07) Next changeset 11:cc5ccfa8ee28 (2019-02-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292 |
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modified:
README.md msconvert.xml msconvert_macros.xml test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML test-data/Rpal_01-mzRefinement.mzML test-data/Rpal_01.pepXML.mzRefinement.tsv 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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added:
msconvert_macros.xml.orig test-data/AgilentMassHunterTest.d.tar test-data/AgilentMassHunterTest.mzXML test-data/BrukerBafTest.d.tar test-data/BrukerBafTest.mzML test-data/MassLynxTest.mzML test-data/MassLynxTest.raw.tar test-data/SciexTest-HPINalone-NE-srmAsSpectra.mzXML test-data/SciexTest-HPINalone-NE.mzML test-data/SciexTest-HPINalone-srmAsSpectra.mzXML test-data/SciexTest-HPINalone.mzML test-data/SciexTest.mzML test-data/SciexTest.wiff.tar test-data/ThyroglobMRM000003.d.tar test-data/ThyroglobMRM000003.mzML test-data/small-peakpicking-vendor-allMS.mzML test-data/small.RAW |
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removed:
idconvert/idconvert.xml idconvert/msconvert_macros.xml idconvert/test-data/Rpal_01.mzid idconvert/test-data/Rpal_01.pepXML idconvert/tool_dependencies.xml msconvert_nix/msconvert_macros.xml msconvert_nix/msconvert_nix.xml msconvert_nix/msconvert_wrapper.py msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 msconvert_nix/test-data/Rpal_01-mzRefinement.mzML msconvert_nix/test-data/Rpal_01.mz5 msconvert_nix/test-data/Rpal_01.pepXML msconvert_nix/test-data/Rpal_01.pepXML.mzRefinement.tsv msconvert_nix/test-data/small-activation.mzML msconvert_nix/test-data/small-analyzer-filter.mzML msconvert_nix/test-data/small-chargeStatePredictor.mzML msconvert_nix/test-data/small-deisotope-poisson.mzML msconvert_nix/test-data/small-deisotope.mzML msconvert_nix/test-data/small-denoise.mzML msconvert_nix/test-data/small-index-filter.mzML msconvert_nix/test-data/small-ms-level-filter.mzML msconvert_nix/test-data/small-mzWindow.mzML msconvert_nix/test-data/small-numpressL.mzML msconvert_nix/test-data/small-numpressLP.mzML msconvert_nix/test-data/small-numpressLS.mzML msconvert_nix/test-data/small-numpressP.mzML msconvert_nix/test-data/small-numpressS.mzML msconvert_nix/test-data/small-peakpicking-cwt-allMS.mzML msconvert_nix/test-data/small-polarity-filter.mzML msconvert_nix/test-data/small-strip-it.mzML msconvert_nix/test-data/small-threshold.mzML msconvert_nix/test-data/small-turbocharger.mzML msconvert_nix/test-data/small-zlib-32.mzXML msconvert_nix/test-data/small-zlib-64.mz5 msconvert_nix/test-data/small.mzML msconvert_nix/tool_dependencies.xml msconvert_raw.xml msconvert_raw_wrapper.py msconvert_subset.xml msconvert_win/README msconvert_win/job_conf.xml.sample msconvert_win/msconvert_macros.xml msconvert_win/msconvert_win.xml msconvert_win/msconvert_wrapper.py msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 msconvert_win/test-data/Rpal_01-mzRefinement.mzML msconvert_win/test-data/Rpal_01.mz5 msconvert_win/test-data/Rpal_01.pepXML msconvert_win/test-data/Rpal_01.pepXML.mzRefinement.tsv msconvert_win/test-data/small-activation.mzML msconvert_win/test-data/small-analyzer-filter.mzML msconvert_win/test-data/small-chargeStatePredictor.mzML msconvert_win/test-data/small-deisotope-poisson.mzML msconvert_win/test-data/small-deisotope.mzML msconvert_win/test-data/small-denoise.mzML msconvert_win/test-data/small-index-filter.mzML msconvert_win/test-data/small-ms-level-filter.mzML msconvert_win/test-data/small-mzWindow.mzML msconvert_win/test-data/small-numpressL.mzML msconvert_win/test-data/small-numpressLP.mzML msconvert_win/test-data/small-numpressLS.mzML msconvert_win/test-data/small-numpressP.mzML msconvert_win/test-data/small-numpressS.mzML msconvert_win/test-data/small-peakpicking-cwt-allMS.mzML msconvert_win/test-data/small-peakpicking-vendor-ms1.mgf msconvert_win/test-data/small-polarity-filter.mzML msconvert_win/test-data/small-strip-it.mzML msconvert_win/test-data/small-threshold.mzML msconvert_win/test-data/small-turbocharger.mzML msconvert_win/test-data/small-zlib-32.mzXML msconvert_win/test-data/small-zlib-64.mz5 msconvert_win/test-data/small.RAW msconvert_win/test-data/small.mzML msconvert_wrapper.py repository_dependencies.xml |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 README.md --- a/README.md Wed Dec 07 16:43:07 2016 -0500 +++ b/README.md Sat Feb 23 06:25:48 2019 -0500 |
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| @@ -65,3 +65,4 @@ * Fred Sadler * John Chilton <jmchilton@gmail.com> * Minnesota Supercomputing Institute, Univeristy of Minnesota +* Jeremy Volkening, University of Wisconsin-Madison |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 idconvert/idconvert.xml --- a/idconvert/idconvert.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,123 +0,0 @@ -<tool id="idconvert" name="idconvert" version="@VERSION@.0"> - <description>Convert mass spectrometry identification files</description> - <macros> - <import>msconvert_macros.xml</import> - </macros> - <expand macro="generic_requirements" /> - <stdio> - <exit_code range="1:" /> - <regex match="Error" - source="both" - level="fatal" - description="Error" /> - </stdio> - <command> -<![CDATA[ -#import os.path -#set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')]) -ln -s "$from.input" "$input_name" && -idconvert $input_name -#if str($to_format) == 'pep.xml': ---pepXML -#elif str($to_format) == 'text': ---text -#end if ---outdir outdir -&& cp outdir/* $output -]]> - </command> - <inputs> - <conditional name="from"> - <param name="from_format" type="select" label="Convert from"> - <option value="mzid">mzIdentML (mzid)</option> - <option value="pepxml">pepXML (pepxml)</option> - <option value="protxml">protXML (protxml)</option> - </param> - <when value="mzid"> - <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" /> - </when> - <when value="protxml"> - <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" /> - <param name="pepxml" type="data" format="pepxml" multiple="true" label="MS Identification" /> - </when> - <when value="pepxml"> - <param name="input" type="data" format="pepxml" label="MS Identification" /> - </when> - </conditional> - <param name="to_format" type="select" label="Convert to"> - <option value="mzid">mzIdentML (mzid)</option> - <option value="pep.xml">pepXML (pepxml)</option> - <option value="text">text</option> - </param> - </inputs> - <outputs> - <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}"> - <change_format> - <when input="to_format" value="pep.xml" format="pepxml" /> - <when input="to_format" value="text" format="txt" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input" value="Rpal_01.pepXML" /> - <param name="from_format" value="pepxml" /> - <param name="to_format" value="mzid" /> - <output name="output_psms"> - <assert_contents> - <has_text text="MzIdentML" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - <test> - <param name="input" value="Rpal_01.mzid" /> - <param name="from_format" value="mzid" /> - <param name="to_format" value="pep.xml" /> - <output name="output_psms"> - <assert_contents> - <has_text text="msms_pipeline_analysis" /> - <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" /> - </assert_contents> - </output> - </test> - </tests> - <help> -<![CDATA[ -idconvert [options] [filemasks] -Convert mass spec identification file formats. - -Return value: # of failed files. - -Options: - -f [ --filelist ] arg : specify text file containing filenames - -o [ --outdir ] arg (=.) : set output directory ('-' for stdout) [.] - -c [ --config ] arg : configuration file (optionName=value) - -e [ --ext ] arg : set extension for output files [mzid|pepXML|txt] - --mzIdentML : write mzIdentML format [default] - --pepXML : write pepXML format - --text : write hierarchical text format - -v [ --verbose ] : display detailed progress information -Examples: - -# convert sequest.pepXML to sequest.mzid -idconvert sequest.pepXML - -# convert sequest.protXML to sequest.mzid -# Also reads any pepXML file referenced in the -# protXML file if available. If the protXML -# file has been moved from its original location, -# the pepXML will still be found if it has also -# been moved to the same position relative to the -# protXML file. This relative position is determined -# by reading the protXML protein_summary:summary_xml -# and protein_summary_header:source_files values. -idconvert sequest.protXML - -# convert mascot.mzid to mascot.pepXML -idconvert mascot.mzid --pepXML - -]]> - </help> - <expand macro="citations" /> -</tool> |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 idconvert/msconvert_macros.xml --- a/idconvert/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,675 +0,0 @@\n-<macros>\n- <xml name="generic_requirements">\n- <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n- </requirements>\n- </xml>\n- <token name="@VERSION@">3.0</token>\n- \n- <xml name="msconvertCommand">\n- <command interpreter="python">\n-<![CDATA[\n- #import re\n- #set $ext = $input.ext\n- msconvert_wrapper.py\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=\'${basename}.wiff.scan\n- #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n- --toextension=${output_type}\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- --filter "mzRefiner $input_ident_name\n- msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n- thresholdScore=$data_processing.precursor_refinement.thresholdScore\n- thresholdValue=$data_processing.precursor_refinement.thresholdValue\n- thresholdStep=$data_processing.precursor_refinement.thresholdStep\n- maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"\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- #end if\n-\n- #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n- --filter "chargeStatePredictor\n- overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n- minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n- maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n- singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n- maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"\n- #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"\n- --filter "turbocharger\n- minCharge=$data_processing.charge_state_calculation.minCharge\n- maxCharge=$data_processing.charge_state_calculation.maxCharge\n- precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore\n- precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter\n- halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth\n- defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge\n- defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"\n- #end if\n-\n- #for threshold_entry in $data_processing.thresholds\n- --filter "threshold $threshold_entry.threshold_type $thres'..b'e="mzML" />\n- <param name="activation" value="CID" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-activation.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="indices_0|from" value="2" />\n- <param name="indices_0|to" value="4" />\n- <param name="indices_1|from" value="10" />\n- <param name="indices_1|to" value="10" />\n- <param name="indices_2|from" value="13" />\n- <param name="indices_2|to" value="15" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->\n- </test>\n- <!--<test>\n- <param name="input" value="small.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-deisotope-poisson.mzML" />\n- </test>-->\n- </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btn323</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n- year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n- </citations>\n- </xml>\n-\n-</macros>\n' |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 idconvert/test-data/Rpal_01.mzid --- a/idconvert/test-data/Rpal_01.mzid Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,78943 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<MzIdentML id="" creationDate="2011-10-31T11:08:11" version="1.1.0" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://psidev.info/files/mzIdentML1.1.0.xsd" xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">\n- <cvList>\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="UNIMOD" fullName="UNIMOD" version="2016-07-01" uri="http://www.unimod.org/obo/unimod.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- <AnalysisSoftwareList>\n- <AnalysisSoftware id="AS_MyriMatch_2.1.101" name="MyriMatch" version="2.1.101">\n- <SoftwareName><cvParam cvRef="MS" accession="MS:1001585" name="MyriMatch" value=""/></SoftwareName>\n- </AnalysisSoftware>\n- <AnalysisSoftware id="pwiz_3.0.9934" name="ProteoWizard MzIdentML" version="3.0.9934">\n- <ContactRole contact_ref="ORG_PWIZ">\n- <Role><cvParam cvRef="MS" accession="MS:1001267" name="software vendor" value=""/></Role>\n- </ContactRole>\n- <SoftwareName><cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/></SoftwareName>\n- </AnalysisSoftware>\n- </AnalysisSoftwareList>\n- <AuditCollection>\n- <Organization id="ORG_PWIZ" name="ProteoWizard">\n- <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="support@proteowizard.org"/>\n- </Organization>\n- </AuditCollection>\n- <SequenceCollection>\n- <DBSequence id="DBSeq_rev_RPA0498" accession="rev_RPA0498" searchDatabase_ref="SDB"/>\n- <DBSequence id="DBSeq_RPA1332" accession="RPA1332" searchDatabase_ref="SDB"/>\n- <DBSequence id="DBSeq_rev_RPA3341" accession="rev_RPA3341" searchDatabase_ref="SDB"/>\n- <DBSequence 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<cvParam cvRef="MS" accession="MS:1001590" name="MyriMatch:mzFidelity" value="29.849243245154"/>\n- <userParam name="number of matched peaks" value="4" type="xsd:float"/>\n- <userParam name="number of unmatched peaks" value="14" type="xsd:float"/>\n- <userParam name="xcorr" value="0.67468716832110653" type="xsd:float"/>\n- </SpectrumIdentificationItem>\n- <userParam name="num_target_comparisons" value="109"/>\n- <userParam name="num_decoy_comparisons" value="122"/>\n- </SpectrumIdentificationResult>\n- <SpectrumIdentificationResult id="SIR_1937" name="Rpal_01.2436.2436" spectrumID="controllerType=0 controllerNumber=1 scan=2436" spectraData_ref="SD">\n- <SpectrumIdentificationItem id="SII_5750" rank="1" chargeState="2" peptide_ref="PEP_4739" experimentalMassToCharge="575.82" calculatedMassToCharge="574.64688646688" passThreshold="true">\n- <PeptideEvidenceRef peptideEvidence_ref="RPA0064_PEP_4739"/>\n- <cvParam cvRef="MS" accession="MS:1001121" name="number of matched peaks" value="10"/>\n- <cvParam cvRef="MS" accession="MS:1001362" name="number of unmatched peaks" value="6"/>\n- <cvParam cvRef="MS" accession="MS:1001589" name="MyriMatch:MVH" value="50.194524645805"/>\n- <cvParam cvRef="MS" accession="MS:1001590" name="MyriMatch:mzFidelity" value="86.851865019713"/>\n- <userParam name="number of matched peaks" value="10" type="xsd:float"/>\n- <userParam name="number of unmatched peaks" value="6" type="xsd:float"/>\n- <userParam name="xcorr" value="1.6098698580488562" type="xsd:float"/>\n- </SpectrumIdentificationItem>\n- <SpectrumIdentificationItem id="SII_5751" rank="2" chargeState="2" peptide_ref="PEP_4740" experimentalMassToCharge="575.82" calculatedMassToCharge="575.65482646688" passThreshold="true">\n- <PeptideEvidenceRef peptideEvidence_ref="RPA3576_PEP_4740"/>\n- <cvParam cvRef="MS" accession="MS:1001121" name="number of matched peaks" value="9"/>\n- <cvParam cvRef="MS" accession="MS:1001362" name="number of unmatched peaks" value="8"/>\n- <cvParam cvRef="MS" accession="MS:1001589" name="MyriMatch:MVH" value="42.459152936935"/>\n- <cvParam cvRef="MS" accession="MS:1001590" name="MyriMatch:mzFidelity" value="75.613555668398"/>\n- <userParam name="number of matched peaks" value="9" type="xsd:float"/>\n- <userParam name="number of unmatched peaks" value="8" type="xsd:float"/>\n- <userParam name="xcorr" value="1.9848502265699208" type="xsd:float"/>\n- </SpectrumIdentificationItem>\n- <SpectrumIdentificationItem id="SII_5752" rank="3" chargeState="2" peptide_ref="PEP_4741" experimentalMassToCharge="575.82" calculatedMassToCharge="577.11626646688" passThreshold="true">\n- <PeptideEvidenceRef peptideEvidence_ref="rev_RPA4459_PEP_4741"/>\n- <cvParam cvRef="MS" accession="MS:1001121" name="number of matched peaks" value="7"/>\n- <cvParam cvRef="MS" accession="MS:1001362" name="number of unmatched peaks" value="13"/>\n- <cvParam cvRef="MS" accession="MS:1001589" name="MyriMatch:MVH" value="29.204201936722"/>\n- <cvParam cvRef="MS" accession="MS:1001590" name="MyriMatch:mzFidelity" value="54.274397630421"/>\n- <userParam name="number of matched peaks" value="7" type="xsd:float"/>\n- <userParam name="number of unmatched peaks" value="13" type="xsd:float"/>\n- <userParam name="xcorr" value="1.0154997527897358" type="xsd:float"/>\n- </SpectrumIdentificationItem>\n- <userParam name="num_target_comparisons" value="871"/>\n- <userParam name="num_decoy_comparisons" value="890"/>\n- </SpectrumIdentificationResult>\n- </SpectrumIdentificationList>\n- </AnalysisData>\n- </DataCollection>\n-</MzIdentML>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 idconvert/test-data/Rpal_01.pepXML --- a/idconvert/test-data/Rpal_01.pepXML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,49047 +0,0 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\n-<msms_pipeline_analysis date="2011-10-31T11:08:11" summary_xml="Rpal_01.pepXML" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd">\n- <analysis_summary analysis="MyriMatch" version="2.1.101" time="2011-10-31T11:08:11"/>\n- <msms_run_summary base_name="Rpal_01" raw_data_type="" raw_data="">\n- <sample_enzyme name="Trypsin/P" independent="false" fidelity="specific">\n- <specificity sense="C" cut="KR" no_cut="" min_spacing="1"/>\n- </sample_enzyme>\n- <search_summary base_name="Rpal_01" search_engine="MyriMatch" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" out_data_type="" out_data="">\n- <search_database local_path="Mark12-Rpal-20050929-reverse.fasta" database_name="SDB" type="AA"/>\n- <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="100000" min_number_termini="2"/>\n- <parameter name="Config: AvgPrecursorMzTolerance" value="1.5mz"/>\n- <parameter name="Config: ClassSizeMultiplier" value="2"/>\n- <parameter name="Config: CleavageRules" value="trypsin/p"/>\n- <parameter name="Config: ComputeXCorr" value="1"/>\n- <parameter name="Config: DecoyPrefix" value="rev_"/>\n- <parameter name="Config: DynamicMods" value=""/>\n- <parameter name="Config: EstimateSearchTimeOnly" value="0"/>\n- <parameter name="Config: FragmentMzTolerance" value="30ppm"/>\n- <parameter name="Config: FragmentationAutoRule" value="1"/>\n- <parameter name="Config: FragmentationRule" value="cid"/>\n- <parameter name="Config: MaxDynamicMods" value="2"/>\n- <parameter name="Config: MaxFragmentChargeState" value="0"/>\n- <parameter name="Config: MaxMissedCleavages" value="100000"/>\n- <parameter name="Config: MaxPeakCount" value="300"/>\n- <parameter name="Config: MaxPeptideLength" value="75"/>\n- <parameter name="Config: MaxPeptideMass" value="10000"/>\n- <parameter name="Config: MaxPeptideVariants" value="1000000"/>\n- <parameter name="Config: MaxResultRank" value="2"/>\n- <parameter name="Config: MinPeptideLength" value="5"/>\n- <parameter name="Config: MinPeptideMass" value="0"/>\n- <parameter name="Config: MinResultScore" value="9.9999999999999995e-008"/>\n- <parameter name="Config: MinTerminiCleavages" value="2"/>\n- <parameter name="Config: MonoPrecursorMzTolerance" value="10ppm"/>\n- <parameter name="Config: MonoisotopeAdjustmentSet" value="[-1,2] "/>\n- <parameter name="Config: NumBatches" value="50"/>\n- <parameter name="Config: NumChargeStates" value="3"/>\n- <parameter name="Config: NumIntensityClasses" value="3"/>\n- <parameter name="Config: NumMzFidelityClasses" value="3"/>\n- <parameter name="Config: OutputFormat" value="pepXML"/>\n- <parameter name="Config: OutputSuffix" value=""/>\n- <parameter name="Config: PrecursorMzToleranceRule" value="auto"/>\n- <parameter name="Config: PreferIntenseComplements" value="1"/>\n- <parameter name="Config: ProteinDatabase" value="Mark12-Rpal-20050929-reverse.fasta"/>\n- <parameter name="Config: ProteinListFilters" value=""/>\n- <parameter name="Config: ProteinSamplingTime" value="15"/>\n- <parameter name="Config: ResultsPerBatch" value="200000"/>\n- <parameter name="Config: SpectrumListFilters" value="peakPicking true 2-"/>\n- <parameter name="Config: StaticMods" value=""/>\n- <parameter name="Config: StatusUpdateFrequency" value="5"/>\n- <parameter name="Config: TicCutoffPercentage" value="0.97999999999999998"/>\n- <parameter name="Config: UseMultipleProcessors" value="1"/>\n- <parameter name="Config: UseSmartPlusThreeModel" value="1"/>\n- <parameter name="Config: WorkingDirectory" value="C:\\test\\rpal-orbi-orbi\\raw"/>\n- <parameter name="PeakCounts: 1stQuartile: Fil'..b'<search_score name="number of matched peaks" value="8"/>\n- <search_score name="number of unmatched peaks" value="10"/>\n- <search_score name="mvh" value="38.772735834122"/>\n- <search_score name="mzFidelity" value="65.054646326801"/>\n- <search_score name="xcorr" value="1.6667071547922678"/>\n- </search_hit>\n- <search_hit hit_rank="2" peptide="NPALRREVK" peptide_prev_aa="K" peptide_next_aa="L" protein="RPA2977" num_tot_proteins="1" calc_neutral_pep_mass="1081.63562584" massdiff="-0.00118841374" num_tol_term="2" num_missed_cleavages="2" num_matched_ions="4" tot_num_ions="16">\n- <search_score name="number of matched peaks" value="4"/>\n- <search_score name="number of unmatched peaks" value="12"/>\n- <search_score name="mvh" value="17.102844238281"/>\n- <search_score name="mzFidelity" value="30.837907609603"/>\n- <search_score name="xcorr" value="0.44266026132227854"/>\n- </search_hit>\n- <search_hit hit_rank="3" peptide="AVFVGTLAFR" peptide_prev_aa="K" peptide_next_aa="S" protein="rev_RPA4668" num_tot_proteins="1" calc_neutral_pep_mass="1079.6127651329" massdiff="-0.00671928964" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="4" tot_num_ions="18">\n- <search_score name="number of matched peaks" value="4"/>\n- <search_score name="number of unmatched peaks" value="14"/>\n- <search_score name="mvh" value="16.589879512787"/>\n- <search_score name="mzFidelity" value="29.849243245154"/>\n- <search_score name="xcorr" value="0.67468716832110653"/>\n- </search_hit>\n- </search_result>\n- </spectrum_query>\n- <spectrum_query spectrum="Rpal_01.2436.2436.2" spectrumNativeID="controllerType=0 controllerNumber=1 scan=2436" start_scan="2436" end_scan="2436" precursor_neutral_mass="1149.62544706624" assumed_charge="2" index="4043">\n- <search_result num_target_comparisons="871" num_decoy_comparisons="890">\n- <search_hit hit_rank="1" peptide="NPWEVFVEK" peptide_prev_aa="R" peptide_next_aa="H" protein="RPA0064" num_tot_proteins="1" calc_neutral_pep_mass="1147.27922" massdiff="-2.34622706624" num_tol_term="2" num_missed_cleavages="0" num_matched_ions="10" tot_num_ions="16">\n- <search_score name="number of matched peaks" value="10"/>\n- <search_score name="number of unmatched peaks" value="6"/>\n- <search_score name="mvh" value="50.194524645805"/>\n- <search_score name="mzFidelity" value="86.851865019713"/>\n- <search_score name="xcorr" value="1.6098698580488562"/>\n- </search_hit>\n- <search_hit hit_rank="2" peptide="AWLDFVAEKA" peptide_prev_aa="R" peptide_next_aa="-" protein="RPA3576" num_tot_proteins="1" calc_neutral_pep_mass="1149.2951" massdiff="-0.33034706624" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="9" tot_num_ions="17">\n- <search_score name="number of matched peaks" value="9"/>\n- <search_score name="number of unmatched peaks" value="8"/>\n- <search_score name="mvh" value="42.459152936935"/>\n- <search_score name="mzFidelity" value="75.613555668398"/>\n- <search_score name="xcorr" value="1.9848502265699208"/>\n- </search_hit>\n- <search_hit hit_rank="3" peptide="DYGLRAGGSTR" peptide_prev_aa="R" peptide_next_aa="V" protein="rev_RPA4459" num_tot_proteins="1" calc_neutral_pep_mass="1152.21798" massdiff="2.59253293376" num_tol_term="2" num_missed_cleavages="1" num_matched_ions="7" tot_num_ions="20">\n- <search_score name="number of matched peaks" value="7"/>\n- <search_score name="number of unmatched peaks" value="13"/>\n- <search_score name="mvh" value="29.204201936722"/>\n- <search_score name="mzFidelity" value="54.274397630421"/>\n- <search_score name="xcorr" value="1.0154997527897358"/>\n- </search_hit>\n- </search_result>\n- </spectrum_query>\n- </msms_run_summary>\n-</msms_pipeline_analysis>\n' |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 idconvert/tool_dependencies.xml --- a/idconvert/tool_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 +++ /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> |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert.xml --- a/msconvert.xml Wed Dec 07 16:43:07 2016 -0500 +++ b/msconvert.xml Sat Feb 23 06:25:48 2019 -0500 |
| [ |
| b'@@ -1,394 +1,22 @@\n-<tool id="msconvert" name="msconvert" version="0.3.0">\n- <!-- BEGIN_VERSION_DEFAULT -->\n- <description>Convert and filter a mass spec peak list</description>\n- <!-- END_VERSION_DEFAULT -->\n- <!--\n+<tool id="msconvert" name="msconvert" version="@VERSION@.0">\n+ <description>Convert and/or filter mass spectrometry files</description>\n+ <macros>\n+ <import>msconvert_macros.xml</import>\n+ </macros>\n <requirements>\n- <requirement type="package" version="3_0_4388">proteowizard</requirement>\n+ <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>\n </requirements>\n--->\n- <command interpreter="python">\n- #import re\n- #set $ext = $input.ext\n- msconvert_wrapper.py\n- #if $type.input_type == \'wiff\':\n- #set basename = \'absciex\'\n- #if hasattr($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=\'${basename}.wiff.scan\n- #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n-\n-\n- --toextension=${output_type}\n-\n- #if $settings.settingsType == "full"\n- --binaryencoding=${settings.binary_encoding}\n- --mzencoding=${settings.mz_encoding}\n- --intensityencoding=${settings.intensity_encoding}\n- --zlib=${settings.zlib}\n- #end if\n-\n- #if $filtering.filtering_use\n-\n- #if $filtering.precursor_recalculation.value\n- --filter "precursorRecalculation"\n- #end if\n-\n- #if $filtering.peak_picking.pick_peaks\n- --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n- #end if\n-\n- #if str($filtering.activation) != "false"\n- --filter "activation $filtering.activation"\n- #end if\n-\n- #if len($filtering.indices) > 0\n- --filter "index\n- #for $index in $filtering.indices\n- [${index.from},${index.to}]\n- #end for\n- "\n- #end if\n-\n- #if len($filtering.scan_numbers) > 0\n- --filter "scanNumber\n- #for $scan_number in $filtering.scan_numbers\n- [${scan_number.from},${scan_number.to}]\n- #end for\n- "\n- #end if\n-\n- #for threshold_entry in $filtering.threshold_repeat\n- --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n- #end for\n-\n-\n- #if $filtering.strip_it.value\n- --filter "stripIT"\n- #end if\n-\n- #if $filtering.filter_mz_windows.do_filter\n- --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n- #end if\n-\n-\n- #if $filtering.filter_ms_levels.do_filter\n- --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n- #end if\n-\n- #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n- --filter "ETDFilter"\n- #end if\n-\n- #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n- --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"\n- #end if\n-\n- ## BEGIN_VERSION_3\n-\n- #if $filtering.precursor_refine.value\n- --filter "precursorRefine"\n- #end if\n-\n- #if $filtering.ms2denoise.denoise\n- --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"\n- #end if\n-\n- #if str($filtering.ms2deisotope) '..b'l="De-noise: Number of peaks in window" value="6" type="integer" />\n- <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />\n- <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />\n- </when>\n- <when value="false" />\n- </conditional>\n- <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />\n-\n- <param name="polarity" type="select" label="Filter by Polarity">\n- <option value="false" selected="true">no</option>\n- <option value="positive">positive</option>\n- <option value="negative">negative</option>\n- </param>\n-\n- <param name="analyzer" type="select" label="Filter by Analyzer">\n- <option value="false" selected="true">no</option>\n- <option value="quad">quad</option>\n- <option value="orbi">orbi</option>\n- <option value="FT">FT</option>\n- <option value="IT">IT</option>\n- <option value="TOF">TOF</option>\n- </param>\n- <!-- END_VERSION_3 -->\n- </when>\n- </conditional>\n-\n- <conditional name="settings">\n- <param name="settingsType" type="select" label="Advanced Settings" help="">\n- <option value="default">Use Defaults</option>\n- <option value="full">Full Parameter List</option>\n- </param>\n- <when value="default" />\n- <when value="full">\n- <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n- <option value="64" selected="true">64</option>\n- <option value="32">32</option>\n- </param>\n- <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n- <option value="64" selected="true">64</option>\n- <option value="32">32</option>\n- </param>\n- <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n- <option value="64">64</option>\n- <option value="32" selected="true">32</option>\n- </param>\n- <param type="boolean" name="zlib" label="Use zlib">\n- </param>\n- </when>\n- </conditional>\n-\n-\n+ <expand macro="msconvertCommand" />\n+ <inputs> \n+ <param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />\n+ <expand macro="msconvertInputParameters" />\n </inputs>\n- <outputs>\n- <data format="mzml" name="output" label="${type.input.name.rsplit(\'.\',1)[0]}.${output_type}" >\n- <change_format>\n- <when input="output_type" value="mzXML" format="mzxml" />\n- <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n- <when input="output_type" value="ms2" format="ms2" />\n- <when input="output_type" value="mgf" format="mgf" />\n- </change_format>\n- </data>\n- </outputs>\n+ <expand macro="msconvertOutput" />\n+ <tests>\n+ <expand macro="msconvert_tests" />\n+ </tests>\n <help>\n-**What it does**\n-\n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n-\n-------\n-\n-**Citation**\n-\n-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`\n-\n-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert\n-\n+ <expand macro="msconvert_help" />\n </help>\n+ <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_macros.xml --- a/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 +++ b/msconvert_macros.xml Sat Feb 23 06:25:48 2019 -0500 |
| [ |
| b'@@ -1,60 +1,91 @@\n <macros>\n- <xml name="generic_requirements">\n- <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n- </requirements>\n- </xml>\n- <token name="@VERSION@">3.0</token>\n+ <token name="@VERSION@">3.0.19052</token>\n+ <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n \n <xml name="msconvertCommand">\n- <command interpreter="python">\n+ <command detect_errors="exit_code">\n <![CDATA[\n #import re\n #set $ext = $input.ext\n- msconvert_wrapper.py\n+\n+ ## sanitize display name for use as temp filename\n+ #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.element_identifier)\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+ ln -s \'${input.extra_files_path}/wiff\' \'${basename}.wiff\' &&\n+ ln -s \'${input.extra_files_path}/wiff_scan\' \'${basename}.wiff.scan\' &&\n+ #elif $ext.endswith(\'tar\'):\n+ ln -s \'$input\' \'${basename}\' &&\n+ tar xf \'${basename}\' &&\n+ #set basename = $os.path.splitext($basename)[0]\n+ #else\n+ ln -s \'$input\' \'${basename}\' &&\n+ #end if\n+ \n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))\n+ #set output_refinement_name = os.path.splitext($basename)[0] + \'.mzRefinement.tsv\'\n+ ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n+ #end if\n+\n+ uid=`id -u` &&\n+ gid=`id -g` &&\n+\n+ wine64_anyuser msconvert \'${basename}\'\n+ --outdir outputs\n+ --${output_type}\n+\n+ #if $general_options.combineIonMobilitySpectra:\n+ --combineIonMobilitySpectra\n+ #end if\n+\n+ #if $general_options.simAsSpectra:\n+ --simAsSpectra\n+ #end if\n+\n+ #if $general_options.srmAsSpectra:\n+ --srmAsSpectra\n+ #end if\n+\n+ #if $general_options.acceptZeroLengthSpectra:\n+ --acceptZeroLengthSpectra\n+ #end if\n+\n+ #if $general_options.ignoreUnknownInstrumentError:\n+ --ignoreUnknownInstrumentError\n+ #end if\n+\n+ #if $general_options.scan_summing.do_scan_summing:\n+ --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n+ #end if\n+\n+ #if $general_options.multi_run_output.do_multi_run_output:\n+ #if len($general_options.multi_run_output.run_index_set) > 0\n+ --runIndexSet "\n+ #for $index in $general_options.multi_run_output.run_index_set\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n #end if\n- --input=${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 #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n+ --runIndexSet $general_options.multi_run_output.runIndexSet\n #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n- --toextension=${output_type}\n+\n+ ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests\n+ --stripLocationFromSourceFiles\n \n ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\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+ #end if\n+\n #if $data_processing.precursor_refinement.use_mzrefinement\n- #set $input_ident_name = $re.sub(\'\\W\',\'_\',$data_processing.precursor_refinement.input_ident.displa'..b'>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="indices_0|from" value="2" />\n <param name="indices_0|to" value="4" />\n@@ -603,40 +802,45 @@\n <param name="indices_2|from" value="13" />\n <param name="indices_2|to" value="15" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="strip_it" value="true" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" />\n+ <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="do_ms_level_filter" value="true" />\n <param name="ms_level_from" value="2" />\n <param name="ms_level_to" value="2" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" />\n+ <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="polarity" value="positive" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" />\n+ <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="analyzer" value="IT" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" />\n+ <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n </test>\n <test>\n <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n <param name="output_type" value="mzML" />\n <param name="scan_numbers_0|from" value="3" />\n <param name="scan_numbers_0|to" value="5" />\n@@ -645,7 +849,7 @@\n <param name="scan_numbers_2|from" value="14" />\n <param name="scan_numbers_2|to" value="16" />\n <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->\n+ <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n </test>\n <!--<test>\n <param name="input" value="small.mzML" />\n@@ -657,7 +861,7 @@\n <xml name="msconvert_help">\n **What it does**\n \n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n+Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.\n \n You can view the original documentation here_.\n \n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_macros.xml.orig Sat Feb 23 06:25:48 2019 -0500 |
| [ |
| b'@@ -0,0 +1,897 @@\n+<macros>\n+ <token name="@VERSION@">3.0.19052</token>\n+ <token name="@FULL_VERSION@">@VERSION@-089e81090</token>\n+ \n+ <xml name="msconvertCommand">\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+ #import re\n+ #set $ext = $input.ext\n+\n+ ## sanitize display name for use as temp filename\n+ #set basename = $re.sub(r\'[^\\w\\.\\-\\+]\',\'_\',$input.element_identifier)\n+\n+ #if $ext == \'wiff\':\n+ ln -s \'${input.extra_files_path}/wiff\' \'${basename}.wiff\' &&\n+ ln -s \'${input.extra_files_path}/wiff_scan\' \'${basename}.wiff.scan\' &&\n+ #elif $ext.endswith(\'tar\'):\n+ ln -s \'$input\' \'${basename}\' &&\n+ tar xf \'${basename}\' &&\n+ #set basename = $os.path.splitext($basename)[0]\n+ #else\n+ ln -s \'$input\' \'${basename}\' &&\n+ #end if\n+ \n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))\n+ #set output_refinement_name = os.path.splitext($basename)[0] + \'.mzRefinement.tsv\'\n+ ln -s \'$data_processing.precursor_refinement.input_ident\' \'$input_ident_name\' &&\n+ #end if\n+\n+ uid=`id -u` &&\n+ gid=`id -g` &&\n+\n+ wine64_anyuser msconvert \'${basename}\'\n+ --outdir outputs\n+ --${output_type}\n+\n+ #if $general_options.combineIonMobilitySpectra:\n+ --combineIonMobilitySpectra\n+ #end if\n+\n+ #if $general_options.simAsSpectra:\n+ --simAsSpectra\n+ #end if\n+\n+ #if $general_options.srmAsSpectra:\n+ --srmAsSpectra\n+ #end if\n+\n+ #if $general_options.acceptZeroLengthSpectra:\n+ --acceptZeroLengthSpectra\n+ #end if\n+\n+ #if $general_options.ignoreUnknownInstrumentError:\n+ --ignoreUnknownInstrumentError\n+ #end if\n+\n+ #if $general_options.scan_summing.do_scan_summing:\n+ --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"\n+ #end if\n+\n+ #if $general_options.multi_run_output.do_multi_run_output:\n+ #if len($general_options.multi_run_output.run_index_set) > 0\n+ --runIndexSet "\n+ #for $index in $general_options.multi_run_output.run_index_set\n+ [${index.from},${index.to}]\n+ #end for\n+ "\n+ #end if\n+ #else\n+ --runIndexSet $general_options.multi_run_output.runIndexSet\n+ #end if\n+\n+ ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests\n+ --stripLocationFromSourceFiles\n+\n+ ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)\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+ #end if\n+\n+ #if $data_processing.precursor_refinement.use_mzrefinement\n+ --filter "mzRefiner $input_ident_name\n+ msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n+ thresholdScore=$data_processing.precursor_refinement.thresholdScore\n+ thresholdValue=$data_processing.precursor_refinement.thresholdValue\n+ thresholdStep=$data_processing.precursor_refinement.thresholdStep\n+ maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"\n+ #end if\n+\n+ #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n+ --filter "chargeStatePredictor\n+ overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n+ minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n+ maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n+ singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n+ maxKnownCharge='..b'param name="indices_1|to" value="10" />\n+ <param name="indices_2|from" value="13" />\n+ <param name="indices_2|to" value="15" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="32" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="strip_it" value="true" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-strip-it.mzML" lines_diff="100" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="do_ms_level_filter" value="true" />\n+ <param name="ms_level_from" value="2" />\n+ <param name="ms_level_to" value="2" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="polarity" value="positive" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="analyzer" value="IT" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />\n+ </test>\n+ <test>\n+ <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n+ <param name="license_agreement" value="true" />\n+ <param name="output_type" value="mzml" />\n+ <param name="scan_numbers_0|from" value="3" />\n+ <param name="scan_numbers_0|to" value="5" />\n+ <param name="scan_numbers_1|from" value="11" />\n+ <param name="scan_numbers_1|to" value="11" />\n+ <param name="scan_numbers_2|from" value="14" />\n+ <param name="scan_numbers_2|to" value="16" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->\n+ </test>\n+ <!--<test>\n+ <param name="input" value="small.mzML" />\n+ <param name="output_type" value="mzml" />\n+ <param name="binary_compression" value="numpressLinearPic" />\n+ <output name="output" file="small-deisotope-poisson.mzML" />\n+ </test>-->\n+ </xml>\n+ <xml name="msconvert_help">\n+**What it does**\n+\n+Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.\n+\n+You can view the original documentation here_.\n+\n+.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btn323</citation>\n+ <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n+ year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n+ </citations>\n+ </xml>\n+\n+</macros>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/msconvert_macros.xml --- a/msconvert_nix/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,675 +0,0 @@\n-<macros>\n- <xml name="generic_requirements">\n- <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n- </requirements>\n- </xml>\n- <token name="@VERSION@">3.0</token>\n- \n- <xml name="msconvertCommand">\n- <command interpreter="python">\n-<![CDATA[\n- #import re\n- #set $ext = $input.ext\n- msconvert_wrapper.py\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=\'${basename}.wiff.scan\n- #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n- --toextension=${output_type}\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- --filter "mzRefiner $input_ident_name\n- msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n- thresholdScore=$data_processing.precursor_refinement.thresholdScore\n- thresholdValue=$data_processing.precursor_refinement.thresholdValue\n- thresholdStep=$data_processing.precursor_refinement.thresholdStep\n- maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"\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- #end if\n-\n- #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n- --filter "chargeStatePredictor\n- overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n- minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n- maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n- singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n- maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"\n- #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"\n- --filter "turbocharger\n- minCharge=$data_processing.charge_state_calculation.minCharge\n- maxCharge=$data_processing.charge_state_calculation.maxCharge\n- precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore\n- precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter\n- halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth\n- defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge\n- defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"\n- #end if\n-\n- #for threshold_entry in $data_processing.thresholds\n- --filter "threshold $threshold_entry.threshold_type $thres'..b'e="mzML" />\n- <param name="activation" value="CID" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-activation.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="indices_0|from" value="2" />\n- <param name="indices_0|to" value="4" />\n- <param name="indices_1|from" value="10" />\n- <param name="indices_1|to" value="10" />\n- <param name="indices_2|from" value="13" />\n- <param name="indices_2|to" value="15" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->\n- </test>\n- <!--<test>\n- <param name="input" value="small.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-deisotope-poisson.mzML" />\n- </test>-->\n- </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btn323</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n- year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n- </citations>\n- </xml>\n-\n-</macros>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/msconvert_nix.xml --- a/msconvert_nix/msconvert_nix.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -<tool id="msconvert_nix" name="msconvert" version="@VERSION@.0"> - <description>Convert and/or filter mass spectrometry files</description> - - <macros> - <import>msconvert_macros.xml</import> - </macros> - - <expand macro="generic_requirements" /> - - <expand macro="msconvertCommand" /> - - <inputs> - <param format="mzml,mzxml,mz5,mgf,ms2" name="input" type="data" label="Input unrefined MS data" /> - - <expand macro="msconvertInputParameters" /> - </inputs> - - <expand macro="msconvertOutput" /> - - <tests> - <expand macro="msconvert_tests" /> - - </tests> - <help> - <expand macro="msconvert_help" /> - </help> - <expand macro="citations" /> -</tool> |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/msconvert_wrapper.py --- a/msconvert_nix/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,298 +0,0 @@\n-#!/usr/bin/env python\n-import optparse\n-import os\n-import sys\n-import tempfile\n-import shutil\n-import subprocess\n-import re\n-import logging\n-\n-assert sys.version_info[:2] >= (2, 6)\n-\n-log = logging.getLogger(__name__)\n-working_directory = os.getcwd()\n-tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n-tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n-\n-\n-def stop_err(msg):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit()\n-\n-\n-def read_stderr():\n- stderr = \'\'\n- if(os.path.exists(tmp_stderr_name)):\n- with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read(buffsize)\n- if not stderr or len(stderr) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- return stderr\n-\n-\n-def execute(command, stdin=None):\n- try:\n- with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n- with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n- proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n- returncode = proc.wait()\n- if returncode != 0:\n- raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n- finally:\n- print(( open(tmp_stderr_name, "r").read() ))\n- print(( open(tmp_stdout_name, "r").read() ))\n-\n-\n-def delete_file(path):\n- if os.path.exists(path):\n- try:\n- os.remove(path)\n- except:\n- pass\n-\n-\n-def delete_directory(directory):\n- if os.path.exists(directory):\n- try:\n- shutil.rmtree(directory)\n- except:\n- pass\n-\n-\n-def symlink(source, link_name):\n- import platform\n- if platform.system() == \'Windows\':\n- try:\n- import win32file\n- win32file.CreateSymbolicLink(source, link_name, 1)\n- except:\n- shutil.copy(source, link_name)\n- else:\n- os.symlink(source, link_name)\n-\n-\n-def copy_to_working_directory(data_file, relative_path):\n- if os.path.abspath(data_file) != os.path.abspath(relative_path):\n- symlink(data_file, relative_path)\n- return relative_path\n-\n-\n-def __main__():\n- run_script()\n-\n-#ENDTEMPLATE\n-\n-to_extensions = [\'mzML\', \'mzXML\', \'unindexed_mzML\', \'unindexed_mzXML\', \'mgf\', \'mz5\', \'txt\', \'ms2\', \'cms2\']\n-\n-\n-def str_to_bool(v):\n- """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """\n- return v.lower() in ["yes", "true", "t", "1"]\n-\n-\n-def _add_filter(filters_file, contents):\n- filters_file.write("filter=%s\\n" % contents)\n-\n-\n-def _skip_line(options, file_num, line_parts):\n- file_num_column = options.filter_table_file_column\n- if not file_num_column:\n- return False\n- else:\n- target_file_num_val = str(file_num).strip()\n- query_file_num_val = line_parts[int(file_num_column) - 1].strip()\n- #print "target %s, query %s" % (target_file_num_val, query_file_num_val)\n- return target_file_num_val != query_file_num_val\n-\n-\n-def _read_table_numbers(path, options, file_num=None):\n- unique_numbers = set([])\n- column_num = options.filter_table_column\n- input = open(path, "r")\n- first_line = True\n- for line in input:\n- if not line:\n- continue\n- line = line.strip()\n- if line.startswith("#"):\n- first_line = False\n- continue\n- if column_num == None:\n- column = line\n- else:\n- line_parts = line.split("\\t")\n- if _skip_line(options, file_num, line_parts):\n- continue\n- column = line_parts[int(column_num) - 1]\n- match = re.match("\\d+", column)\n- '..b' parser.add_option(\'--binaryencoding\', dest=\'binaryencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--mzencoding\', dest=\'mzencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--intensityencoding\', dest=\'intensityencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--zlib\', dest=\'zlib\', default="false")\n- parser.add_option(\'--filter\', dest=\'filter\', action=\'append\', default=[])\n- parser.add_option(\'--filters_file\', dest=\'filters_file\', default=None)\n- parser.add_option(\'--filter_table\', default=None)\n- parser.add_option(\'--filter_table_type\', default=\'index\', choices=[\'index\', \'number\'])\n- parser.add_option(\'--filter_table_column\', default=None)\n- parser.add_option(\'--filter_table_file_column\', default=None)\n- parser.add_option(\'--debug\', dest=\'debug\', action=\'store_true\', default=False)\n-\n- (options, args) = parser.parse_args()\n- if len(options.inputs) < 1:\n- stop_err("No input files to msconvert specified")\n- if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):\n- stop_err("Number(s) of supplied input names and input files do not match")\n- if not options.output:\n- stop_err("Must specify output location")\n- input_files = []\n- for i, input in enumerate(options.inputs):\n- input_base = None\n- if len(options.input_names) > i:\n- input_base = options.input_names[i]\n- input_base = input_base.replace("\'", "").replace("\\"", "")\n- print("1- input_base: %s" % input_base)\n- if not input_base:\n- input_base = \'input%s\' % i\n- print("2- input_base: %s" % input_base)\n- if not input_base.lower().endswith(\'.%s\' % options.fromextension.lower()) and input not in options.implicits:\n- input_file = \'%s.%s\' % (input_base, options.fromextension)\n- print("3- input_base: %s" % input_base)\n- print("3- input_file: %s" % input_file)\n- else:\n- input_file = input_base\n- print("4- input_base: %s" % input_base)\n- print("4- input_file: %s" % input_file)\n- input_file = input_file\n- copy_to_working_directory(input, input_file)\n- if input in options.implicits:\n- continue\n- input_files.append(input_file)\n- for i, ident in enumerate(options.idents):\n- ident_file = options.ident_names[i]\n- copy_to_working_directory(ident, ident_file)\n-\n- cmd = _build_base_cmd(options,args=args)\n- file_column = options.filter_table_file_column\n- if not file_column:\n- # Apply same filters to all files, just create a unviersal filter files\n- # and run msconvert once.\n- filters_file_path = _create_filters_file(options, debug=options.debug)\n- cmd = "%s -c %s" % (cmd, filters_file_path)\n- else:\n- # Dispatching on a column to filter different files differently, need to filter\n- # each input once with msconvert and then merge once.\n- filtered_files = []\n- for index, input_file in enumerate(input_files):\n- filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)\n- filter_cmd = "%s -c %s" % (cmd, filters_file_path)\n- filtered_output_file = _run(filter_cmd, output_dir=\'output%d\' % index, inputs=[input_file], debug=options.debug)\n- filtered_files.append(filtered_output_file)\n- input_files = filtered_files\n- if len(input_files) > 1:\n- cmd = "%s --merge" % cmd\n- output_file = _run(cmd, output_dir=\'output\', inputs=input_files, debug=options.debug)\n- shutil.copy(output_file, options.output)\n- if options.refinement:\n- # .mzRefinement.tsv\n- files = os.listdir(os.getcwd())\n- for fname in files:\n- if fname.endswith(\'.mzRefinement.tsv\'):\n- shutil.copy(fname, options.refinement)\n- break\n-\n-def __main__():\n- run_script()\n-\n-if __name__ == \'__main__\':\n- __main__()\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- a/msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 |
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| Binary file msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 has changed |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/test-data/Rpal_01-mzRefinement.mzML --- a/msconvert_nix/test-data/Rpal_01-mzRefinement.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/test-data/small-zlib-64.mz5 |
| b |
| Binary file msconvert_nix/test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/test-data/small.mzML --- a/msconvert_nix/test-data/small.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2757 +0,0 @@\n-<?xml version="1.0" encoding="utf-8"?>\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="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- <fileContent>\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" 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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_nix/tool_dependencies.xml --- a/msconvert_nix/tool_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 +++ /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> |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_raw.xml --- a/msconvert_raw.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,396 +0,0 @@\n-<tool id="msconvert_raw" name="msconvert RAW" version="0.3.0">\n- <!-- BEGIN_VERSION_RAW -->\n- <description>Convert and filter a Thermo Finnigan RAW file</description>\n- <!-- END_VERSION_RAW -->\n- <requirements>\n-<!--\n- <requirement type="package" version="3_0_4388">proteowizard</requirement>\n--->\n- <!-- BEGIN_VERSION_RAW -->\n- <requirement type="platform">windows</requirement>\n- <!-- END_VERSION_RAW -->\n- </requirements>\n- <command interpreter="python">\n- #set $ext = $input.ext\n- msconvert_wrapper.py\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- --output=${output}\n-\n- ## BEGIN_VERSION_RAW\n- --fromextension=RAW\n- ## END_VERSION_RAW\n-\n- --toextension=${output_type}\n-\n- #if $settings.settingsType == "full"\n- --binaryencoding=${settings.binary_encoding}\n- --mzencoding=${settings.mz_encoding}\n- --intensityencoding=${settings.intensity_encoding}\n- --zlib=${settings.zlib}\n- #end if\n-\n- #if $filtering.filtering_use\n-\n- #if $filtering.precursor_recalculation.value\n- --filter "precursorRecalculation"\n- #end if\n-\n- #if $filtering.peak_picking.pick_peaks\n- --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"\n- #end if\n-\n- #if str($filtering.activation) != "false"\n- --filter "activation $filtering.activation"\n- #end if\n-\n- #if len($filtering.indices) > 0\n- --filter "index\n- #for $index in $filtering.indices\n- [${index.from},${index.to}]\n- #end for\n- "\n- #end if\n-\n- #if len($filtering.scan_numbers) > 0\n- --filter "scanNumber\n- #for $scan_number in $filtering.scan_numbers\n- [${scan_number.from},${scan_number.to}]\n- #end for\n- "\n- #end if\n-\n- #for threshold_entry in $filtering.threshold_repeat\n- --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"\n- #end for\n-\n- $filtering.strip_it\n- $filtering.metadataFixer\n- $filtering.sortByScanTime\n-\n- #if $filtering.filter_mz_windows.do_filter\n- --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"\n- #end if\n-\n- #if $filtering.filter_chargeStatePredictor.do_filter\n- --filter "chargeStatePredictor $filtering.filter_chargeStatePredictor.overrideExistingCharge $filtering.filter_chargeStatePredictor.maxMultipleCharge $filtering.filter_chargeStatePredictor.minMultipleCharge $filtering.filter_chargeStatePredictor.singleChargeFractionTIC $filtering.filter_chargeStatePredictor.algorithmMakeMS2"\n- #end if\n-\n-\n- #if $filtering.filter_ms_levels.do_filter\n- --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"\n- #end if\n-\n- #if str($filtering.etd_filtering.do_etd_filtering) == "default"\n- --filter "ETDFilter"\n- #end if\n-\n- #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"\n- --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"\n- #end if\n-\n- ## BEGIN_VERSION_3\n-\n- #if $filtering.precursor_refine.value\n- --filter "precursorRefine"\n- #end if\n-\n- #if $filtering.ms2denoise.denoise\n- --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"\n- #end if\n-\n- #if str($filtering.ms2deisotope) == "true"\n- --filter "MS2Deisotope"\n- #end if\n-\n- #if str($filtering.polarity) != "false"\n- --filter "polarity $filtering.polarity"\n- #end if\n-\n- #if str($filtering.analyzer) != "false"\n- --filter "analyzer $filtering.analyzer"\n- #en'..b' </param>\n- <param name="blanket_removal" type="select" label="ETD Blanket Removal">\n- <option value="true" selected="true">yes</option>\n- <option value="false">no</option>\n- </param>\n- </when>\n- </conditional>\n-\n-\n- <!-- BEGIN_VERSION_3 -->\n- <conditional name="ms2denoise">\n- <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />\n- <when value="true">\n- <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />\n- <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />\n- <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />\n- </when>\n- <when value="false" />\n- </conditional>\n- <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />\n-\n- <param name="polarity" type="select" label="Filter by Polarity">\n- <option value="false" selected="true">no</option>\n- <option value="positive">positive</option>\n- <option value="negative">negative</option>\n- </param>\n-\n- <param name="analyzer" type="select" label="Filter by Analyzer">\n- <option value="false" selected="true">no</option>\n- <option value="quad">quad</option>\n- <option value="orbi">orbi</option>\n- <option value="FT">FT</option>\n- <option value="IT">IT</option>\n- <option value="TOF">TOF</option>\n- </param>\n- <!-- END_VERSION_3 -->\n- </when>\n- </conditional>\n-\n- <conditional name="settings">\n- <param name="settingsType" type="select" label="Advanced Settings" help="">\n- <option value="default">Use Defaults</option>\n- <option value="full">Full Parameter List</option>\n- </param>\n- <when value="default" />\n- <when value="full">\n- <param type="select" name="binary_encoding" label="Binary Encoding Precision">\n- <option value="64" selected="true">64</option>\n- <option value="32">32</option>\n- </param>\n- <param type="select" name="mz_encoding" label="m/z Encoding Precision">\n- <option value="64" selected="true">64</option>\n- <option value="32">32</option>\n- </param>\n- <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">\n- <option value="64">64</option>\n- <option value="32" selected="true">32</option>\n- </param>\n- <param type="boolean" name="zlib" label="Use zlib">\n- </param>\n- </when>\n- </conditional>\n-\n-\n- </inputs>\n- <outputs>\n- <data format="mzml" name="output" label="${input.name.rsplit(\'.\',1)[0]}.${output_type}" >\n- <change_format>\n- <when input="output_type" value="mzXML" format="mzxml" />\n- <when input="output_type" value="unindexed_mzXML" format="mzxml" />\n- <when input="output_type" value="ms2" format="ms2" />\n- <when input="output_type" value="mgf" format="mgf" />\n- </change_format>\n- </data>\n- </outputs>\n- <help>\n-**What it does**\n-\n-Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n-\n-------\n-\n-**Citation**\n-\n-For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`\n-\n-If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert\n-\n- </help>\n-</tool>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_raw_wrapper.py --- a/msconvert_raw_wrapper.py Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,124 +0,0 @@ -#!/usr/bin/env python -import optparse -import os -import sys -import tempfile -import shutil -import subprocess -import re -from os.path import basename -import logging - -assert sys.version_info[:2] >= ( 2, 6 ) - -log = logging.getLogger(__name__) -working_directory = os.getcwd() -tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name -tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def read_stderr(): - stderr = '' - if(os.path.exists(tmp_stderr_name)): - with open(tmp_stderr_name, 'rb') as tmp_stderr: - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read(buffsize) - if not stderr or len(stderr) % buffsize != 0: - break - except OverflowError: - pass - return stderr - -def execute(command, stdin=None): - 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) - returncode = proc.wait() - if returncode != 0: - raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) - -def delete_file(path): - if os.path.exists(path): - try: - os.remove(path) - except: - pass - -def delete_directory(directory): - if os.path.exists(directory): - try: - shutil.rmtree(directory) - except: - pass - -def symlink(source, link_name): - import platform - if platform.system() == 'Windows': - import win32file - win32file.CreateSymbolicLink(source, link_name, 1) - else: - os.symlink(source, link_name) - - -def copy_to_working_directory(data_file, relative_path): - if os.path.abspath(data_file) != os.path.abspath(relative_path): - shutil.copy(data_file, relative_path) - return relative_path - -def __main__(): - run_script() - -#ENDTEMPLATE - -to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2'] - -def str_to_bool(v): - """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """ - return v.lower() in ["yes", "true", "t", "1"] - - -def run_script(): - parser = optparse.OptionParser() - parser.add_option('--input', dest='input') - parser.add_option('--output', dest='output') - parser.add_option('--fromextension', dest='fromextension') - parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) - parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) - parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64']) - parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64']) - parser.add_option('--noindex', dest='noindex') - parser.add_option('--zlib', dest='zlib') - parser.add_option('--filter', dest='filter', action='append', default=[]) - - (options, args) = parser.parse_args() - - filter_commands = '' - for filter in options.filter: - filter_commands = "%s --filter \"%s\"" % (filter_commands, filter) - - input_file = 'input.%s' % options.fromextension - copy_to_working_directory(options.input, input_file) - os.mkdir('output') - cmd = "msconvert --%s -o output" % (options.toextension) - if str_to_bool(options.noindex): - cmd = "%s %s" % (cmd, "--noindex") - if str_to_bool(options.zlib): - cmd = "%s %s" % (cmd, "--zlib") - cmd = "%s --%s" % (cmd, options.binaryencoding) - cmd = "%s --mz%s" % (cmd, options.mzencoding) - cmd = "%s --inten%s" % (cmd, options.intensityencoding) - cmd = "%s %s" % (cmd, input_file) - cmd = "%s %s" % (cmd, filter_commands) - print(cmd) - execute(cmd) - output_files = os.listdir('output') - assert len(output_files) == 1 - output_file = output_files[0] - shutil.copy(os.path.join('output', output_file), options.output) - -if __name__ == '__main__': __main__() |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_subset.xml --- a/msconvert_subset.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,105 +0,0 @@ -<tool id="msconvert_subset" name="msconvert Subset Peak List" version="0.3.0"> - <description>against list of scan numbers or indices.</description> - <!-- - <requirements> - <requirement type="package" version="3_0_4388">proteowizard</requirement> - </requirements> ---> - <command interpreter="python"> - msconvert_wrapper.py - --input=${input} - --output=${output} - --fromextension=${input.ext} - --toextension=${output_type} - #if $settings.settingsType == "full" - --binaryencoding=${settings.binary_encoding} - --mzencoding=${settings.mz_encoding} - --intensityencoding=${settings.intensity_encoding} - --zlib=${settings.zlib} - #end if - --filter_table="$filter.filterList" - #if $filter.filterType == "scan_number" - --filter_table_type="number" - #else - --filter_table_type="index" - #end if - </command> - - <inputs> - <conditional name="type"> - <param name="input_type" type="select" label="Input Type"> - <option value="mzml">mzML</option> - <option value="mzxml">mzXML</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <when value="mzml"> - <param format="mzml" name="input" type="data" label="Input mzML"/> - </when> - <when value="mzxml"> - <param format="mzxml" name="input" type="data" label="Input mzXML"/> - </when> - <when value="mgf"> - <param format="mgf" name="input" type="data" label="Input mgf"/> - </when> - <when value="ms2"> - <param format="ms2" name="input" type="data" label="Input ms2"/> - </when> - </conditional> - <param name="output_type" type="select" label="Output Type"> - <option value="mzML">mzML (indexed)</option> - <option value="unindexed_mzML">mzML (unindexed)</option> - <option value="mzXML">mzXML (indexed)</option> - <option value="unindexed_mzXML">mzXML (unindexed)</option> - <option value="mgf">mgf</option> - <option value="ms2">ms2</option> - </param> - <conditional name="filter"> - <param name="filterType" type="select" label="Filter by" help=""> - <option value="scan_number" selected="true">Scan Number</option> - <option value="scan_index">Scan Index</option> - </param> - <when value="scan_number"> - <param format="text" name="filterList" type="data" label="Scan Numbers"/> - </when> - <when value="scan_index"> - <param format="text" name="filterList" type="data" label="Scan Indices"/> - </when> - </conditional> - <conditional name="settings"> - <param name="settingsType" type="select" label="Advanced msconvert Settings" help=""> - <option value="default">Use Defaults</option> - <option value="full">Full Parameter List</option> - </param> - <when value="default" /> - <when value="full"> - <param type="select" name="binary_encoding" label="Binary Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="mz_encoding" label="m/z Encoding Precision"> - <option value="64" selected="true">64</option> - <option value="32">32</option> - </param> - <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> - <option value="64">64</option> - <option value="32" selected="true">32</option> - </param> - <param type="boolean" name="zlib" label="Use zlib"> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > - <change_format> - <when input="output_type" value="mzXML" format="mzxml" /> - <when input="output_type" value="unindexed_mzXML" format="mzxml" /> - <when input="output_type" value="ms2" format="ms2" /> - <when input="output_type" value="mgf" format="mgf" /> - </change_format> - </data> - </outputs> - <help> - </help> -</tool> |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/README --- a/msconvert_win/README Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -**NOTE** -This tool must be run on a Windows Operating System. - -Your system administrator will need to: - - - install proteowizard on a windows server - http://proteowizard.sourceforge.net/downloads.shtml - - - install the galaxy pulsar rest server on the windows server - http://pulsar.readthedocs.org/en/latest/ - - - setup the galaxy job_conf.xml to send msconvert jobs to the windows server via pulsar - https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster - https://wiki.galaxyproject.org/Admin/Config/Jobs - http://pulsar.readthedocs.org/en/latest/job_managers.html |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/job_conf.xml.sample --- a/msconvert_win/job_conf.xml.sample Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,88 +0,0 @@ -<?xml version="1.0"?> -<job_conf> - <plugins workers="4"> - <!-- "workers" is the number of threads for the runner's work queue. - The default from <plugins> is used if not defined for a <plugin>. - --> - <plugin id="plugin_local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> - <plugin id="plugin_pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner"> - <!-- Allow optimized HTTP calls with libcurl (defaults to urllib) --> - <!-- <param id="transport">curl</param> --> - <!-- *Experimental Caching*: Next parameter enables caching. - Likely will not work with newer features such as MQ support. - If this is enabled be sure to specify a `file_cache_dir` in - the remote Pulsar's servers main configuration file. - --> - <!-- <param id="cache">True</param> --> - </plugin> - </plugins> - - <destinations default="destination_local"> - <destination id="destination_local" runner="plugin_local"/> - - <destination id="destination_winserver_pulsar_rest" runner="plugin_pulsar_rest"> - <param id="manager">_default_</param> - <param id="url">http://winserver.myu.edu:8900/</param> - <!-- If set, private_token must match token in remote Pulsar's - configuration. --> - <param id="private_token">your_ultra-secret_magic_token_here</param> - <!-- Uncomment the following statement to disable file staging (e.g. - if there is a shared file system between Galaxy and the Pulsar - server). Alternatively action can be set to 'copy' - to replace - http transfers with file system copies, 'remote_transfer' to cause - the Pulsar to initiate HTTP transfers instead of Galaxy, or - 'remote_copy' to cause Pulsar to initiate file system copies. - If setting this to 'remote_transfer' be sure to specify a - 'galaxy_url' attribute on the runner plugin above. - --> - <!-- <param id="default_file_action">none</param> --> - <!-- The above option is just the default, the transfer behavior - none|copy|http can be configured on a per path basis via the - following file. See Pulsar documentation for more details and - examples. - --> - <!-- <param id="file_action_config">file_actions.yaml</param> --> - <!-- The non-legacy Pulsar runners will attempt to resolve Galaxy - dependencies remotely - to enable this set a tool_dependency_dir - in Pulsar's configuration (can work with all the same dependency - resolutions mechanisms as Galaxy - tool Shed installs, Galaxy - packages, etc...). To disable this behavior, set the follow parameter - to none. To generate the dependency resolution command locally - set the following parameter local. - --> - <!-- <param id="dependency_resolution">none</params> --> - <!-- Uncomment following option to enable setting metadata on remote - Pulsar server. The 'use_remote_datatypes' option is available for - determining whether to use remotely configured datatypes or local - ones (both alternatives are a little brittle). - --> - <!-- <param id="remote_metadata">true</param> --> - <!-- <param id="use_remote_datatypes">false</param> --> - <!-- <param id="remote_property_galaxy_home">/path/to/remote/galaxy-central</param> --> - <!-- If remote Pulsar server is configured to run jobs as the real user, - uncomment the following line to pass the current Galaxy user - along. - --> - <!-- <param id="submit_user">$__user_name__</param> --> - <!-- Various other submission parameters can be passed along to the Pulsar - whose use will depend on the remote Pulsar's configured job manager. - For instance: - --> - <!-- <param id="submit_native_specification">-P bignodes -R y -pe threads 8</param> --> - <!-- Disable parameter rewriting and rewrite generated commands - instead. This may be required if remote host is Windows machine - but probably not otherwise. - --> - <!-- <param id="rewrite_parameters">false</params> --> - </destination> - - </destinations> - - <tools> - <tool id="msconvert_win" destination="destination_winserver_pulsar_rest"/> - </tools> - -</job_conf> - - - |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/msconvert_macros.xml --- a/msconvert_win/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,675 +0,0 @@\n-<macros>\n- <xml name="generic_requirements">\n- <requirements>\n- <requirement type="package" version="3.0.9016">proteowizard</requirement>\n- </requirements>\n- </xml>\n- <token name="@VERSION@">3.0</token>\n- \n- <xml name="msconvertCommand">\n- <command interpreter="python">\n-<![CDATA[\n- #import re\n- #set $ext = $input.ext\n- msconvert_wrapper.py\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=\'${basename}.wiff.scan\n- #else\n- --input=${input}\n- #if hasattr($input, \'display_name\')\n- --input_name=\'${input.display_name}\'\n- #end if\n- #end if\n- --output=${output}\n- ## BEGIN_VERSION_DEFAULT\n- --fromextension=$ext\n- ## END_VERSION_DEFAULT\n- --toextension=${output_type}\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- --filter "mzRefiner $input_ident_name\n- msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels\n- thresholdScore=$data_processing.precursor_refinement.thresholdScore\n- thresholdValue=$data_processing.precursor_refinement.thresholdValue\n- thresholdStep=$data_processing.precursor_refinement.thresholdStep\n- maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"\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- #end if\n-\n- #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"\n- --filter "chargeStatePredictor\n- overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge\n- minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge\n- maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge\n- singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC\n- maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"\n- #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"\n- --filter "turbocharger\n- minCharge=$data_processing.charge_state_calculation.minCharge\n- maxCharge=$data_processing.charge_state_calculation.maxCharge\n- precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore\n- precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter\n- halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth\n- defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge\n- defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"\n- #end if\n-\n- #for threshold_entry in $data_processing.thresholds\n- --filter "threshold $threshold_entry.threshold_type $thres'..b'e="mzML" />\n- <param name="activation" value="CID" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-activation.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="indices_0|from" value="2" />\n- <param name="indices_0|to" value="4" />\n- <param name="indices_1|from" value="10" />\n- <param name="indices_1|to" value="10" />\n- <param name="indices_2|from" value="13" />\n- <param name="indices_2|to" value="15" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="strip_it" value="true" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-strip-it.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="do_ms_level_filter" value="true" />\n- <param name="ms_level_from" value="2" />\n- <param name="ms_level_to" value="2" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-ms-level-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="polarity" value="positive" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-polarity-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="analyzer" value="IT" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-analyzer-filter.mzML" />\n- </test>\n- <test>\n- <param name="input" value="small-peakpicking-cwt-allMS.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="scan_numbers_0|from" value="3" />\n- <param name="scan_numbers_0|to" value="5" />\n- <param name="scan_numbers_1|from" value="11" />\n- <param name="scan_numbers_1|to" value="11" />\n- <param name="scan_numbers_2|from" value="14" />\n- <param name="scan_numbers_2|to" value="16" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->\n- </test>\n- <!--<test>\n- <param name="input" value="small.mzML" />\n- <param name="output_type" value="mzML" />\n- <param name="binary_compression" value="numpressLinearPic" />\n- <output name="output" file="small-deisotope-poisson.mzML" />\n- </test>-->\n- </xml>\n- <xml name="msconvert_help">\n-**What it does**\n-\n-Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.\n-\n-You can view the original documentation here_.\n-\n-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btn323</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n- year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->\n- </citations>\n- </xml>\n-\n-</macros>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/msconvert_win.xml --- a/msconvert_win/msconvert_win.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,36 +0,0 @@ -<tool id="msconvert_win" name="msconvert (vendor support)" version="@VERSION@.0"> - <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description> - - <macros> - <import>msconvert_macros.xml</import> - </macros> - - <expand macro="msconvertCommand" /> - - <inputs> - <!-- TODO: add Bruker, Waters, Agilent types --> - <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" /> - - <expand macro="msconvertInputParameters" /> - </inputs> - - <expand macro="msconvertOutput" /> - - <tests> - <expand macro="msconvert_tests" /> - - <test> - <param name="input" value="small.raw" /> - <param name="output_type" value="mgf" /> - <param name="pick_peaks" value="true" /> - <param name="pick_peaks_algorithm" value="vendor" /> - <param name="pick_peaks_ms_levels" value="1" /> - <output name="output" file="small-peakpicking-vendor-ms1.mgf" /> - </test> - - </tests> - <help> - <expand macro="msconvert_help" /> - </help> - <expand macro="citations" /> -</tool> |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/msconvert_wrapper.py --- a/msconvert_win/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,298 +0,0 @@\n-#!/usr/bin/env python\n-import optparse\n-import os\n-import sys\n-import tempfile\n-import shutil\n-import subprocess\n-import re\n-import logging\n-\n-assert sys.version_info[:2] >= (2, 6)\n-\n-log = logging.getLogger(__name__)\n-working_directory = os.getcwd()\n-tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n-tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n-\n-\n-def stop_err(msg):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit()\n-\n-\n-def read_stderr():\n- stderr = \'\'\n- if(os.path.exists(tmp_stderr_name)):\n- with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read(buffsize)\n- if not stderr or len(stderr) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- return stderr\n-\n-\n-def execute(command, stdin=None):\n- try:\n- with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n- with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n- proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n- returncode = proc.wait()\n- if returncode != 0:\n- raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n- finally:\n- print(( open(tmp_stderr_name, "r").read() ))\n- print(( open(tmp_stdout_name, "r").read() ))\n-\n-\n-def delete_file(path):\n- if os.path.exists(path):\n- try:\n- os.remove(path)\n- except:\n- pass\n-\n-\n-def delete_directory(directory):\n- if os.path.exists(directory):\n- try:\n- shutil.rmtree(directory)\n- except:\n- pass\n-\n-\n-def symlink(source, link_name):\n- import platform\n- if platform.system() == \'Windows\':\n- try:\n- import win32file\n- win32file.CreateSymbolicLink(source, link_name, 1)\n- except:\n- shutil.copy(source, link_name)\n- else:\n- os.symlink(source, link_name)\n-\n-\n-def copy_to_working_directory(data_file, relative_path):\n- if os.path.abspath(data_file) != os.path.abspath(relative_path):\n- symlink(data_file, relative_path)\n- return relative_path\n-\n-\n-def __main__():\n- run_script()\n-\n-#ENDTEMPLATE\n-\n-to_extensions = [\'mzML\', \'mzXML\', \'unindexed_mzML\', \'unindexed_mzXML\', \'mgf\', \'mz5\', \'txt\', \'ms2\', \'cms2\']\n-\n-\n-def str_to_bool(v):\n- """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """\n- return v.lower() in ["yes", "true", "t", "1"]\n-\n-\n-def _add_filter(filters_file, contents):\n- filters_file.write("filter=%s\\n" % contents)\n-\n-\n-def _skip_line(options, file_num, line_parts):\n- file_num_column = options.filter_table_file_column\n- if not file_num_column:\n- return False\n- else:\n- target_file_num_val = str(file_num).strip()\n- query_file_num_val = line_parts[int(file_num_column) - 1].strip()\n- #print "target %s, query %s" % (target_file_num_val, query_file_num_val)\n- return target_file_num_val != query_file_num_val\n-\n-\n-def _read_table_numbers(path, options, file_num=None):\n- unique_numbers = set([])\n- column_num = options.filter_table_column\n- input = open(path, "r")\n- first_line = True\n- for line in input:\n- if not line:\n- continue\n- line = line.strip()\n- if line.startswith("#"):\n- first_line = False\n- continue\n- if column_num == None:\n- column = line\n- else:\n- line_parts = line.split("\\t")\n- if _skip_line(options, file_num, line_parts):\n- continue\n- column = line_parts[int(column_num) - 1]\n- match = re.match("\\d+", column)\n- '..b' parser.add_option(\'--binaryencoding\', dest=\'binaryencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--mzencoding\', dest=\'mzencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--intensityencoding\', dest=\'intensityencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--zlib\', dest=\'zlib\', default="false")\n- parser.add_option(\'--filter\', dest=\'filter\', action=\'append\', default=[])\n- parser.add_option(\'--filters_file\', dest=\'filters_file\', default=None)\n- parser.add_option(\'--filter_table\', default=None)\n- parser.add_option(\'--filter_table_type\', default=\'index\', choices=[\'index\', \'number\'])\n- parser.add_option(\'--filter_table_column\', default=None)\n- parser.add_option(\'--filter_table_file_column\', default=None)\n- parser.add_option(\'--debug\', dest=\'debug\', action=\'store_true\', default=False)\n-\n- (options, args) = parser.parse_args()\n- if len(options.inputs) < 1:\n- stop_err("No input files to msconvert specified")\n- if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):\n- stop_err("Number(s) of supplied input names and input files do not match")\n- if not options.output:\n- stop_err("Must specify output location")\n- input_files = []\n- for i, input in enumerate(options.inputs):\n- input_base = None\n- if len(options.input_names) > i:\n- input_base = options.input_names[i]\n- input_base = input_base.replace("\'", "").replace("\\"", "")\n- print("1- input_base: %s" % input_base)\n- if not input_base:\n- input_base = \'input%s\' % i\n- print("2- input_base: %s" % input_base)\n- if not input_base.lower().endswith(\'.%s\' % options.fromextension.lower()) and input not in options.implicits:\n- input_file = \'%s.%s\' % (input_base, options.fromextension)\n- print("3- input_base: %s" % input_base)\n- print("3- input_file: %s" % input_file)\n- else:\n- input_file = input_base\n- print("4- input_base: %s" % input_base)\n- print("4- input_file: %s" % input_file)\n- input_file = input_file\n- copy_to_working_directory(input, input_file)\n- if input in options.implicits:\n- continue\n- input_files.append(input_file)\n- for i, ident in enumerate(options.idents):\n- ident_file = options.ident_names[i]\n- copy_to_working_directory(ident, ident_file)\n-\n- cmd = _build_base_cmd(options,args=args)\n- file_column = options.filter_table_file_column\n- if not file_column:\n- # Apply same filters to all files, just create a unviersal filter files\n- # and run msconvert once.\n- filters_file_path = _create_filters_file(options, debug=options.debug)\n- cmd = "%s -c %s" % (cmd, filters_file_path)\n- else:\n- # Dispatching on a column to filter different files differently, need to filter\n- # each input once with msconvert and then merge once.\n- filtered_files = []\n- for index, input_file in enumerate(input_files):\n- filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)\n- filter_cmd = "%s -c %s" % (cmd, filters_file_path)\n- filtered_output_file = _run(filter_cmd, output_dir=\'output%d\' % index, inputs=[input_file], debug=options.debug)\n- filtered_files.append(filtered_output_file)\n- input_files = filtered_files\n- if len(input_files) > 1:\n- cmd = "%s --merge" % cmd\n- output_file = _run(cmd, output_dir=\'output\', inputs=input_files, debug=options.debug)\n- shutil.copy(output_file, options.output)\n- if options.refinement:\n- # .mzRefinement.tsv\n- files = os.listdir(os.getcwd())\n- for fname in files:\n- if fname.endswith(\'.mzRefinement.tsv\'):\n- shutil.copy(fname, options.refinement)\n- break\n-\n-def __main__():\n- run_script()\n-\n-if __name__ == \'__main__\':\n- __main__()\n' |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- a/msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,4759 +0,0 @@\n-<?xml version="1.0" encoding="utf-8"?>\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="D100930_yeast_SCX10S_rak_ft8E_pc_01" version="1.1.0">\n- <cvList count="2">\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.74.0" 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- <fileContent>\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n- <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n- </fileContent>\n- <sourceFileList count="1">\n- <sourceFile id="RAW1" name="D100930_yeast_SCX10S_rak_ft8E_pc_01.RAW" location="file:///D:\\test\\iPRG_2011">\n- <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n- <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="5291a8af1478f3ff0295ec296cd7f4766383f1b3"/>\n- </sourceFile>\n- </sourceFileList>\n- </fileDescription>\n- <referenceableParamGroupList count="1">\n- <referenceableParamGroup id="CommonInstrumentParams">\n- <cvParam cvRef="MS" accession="MS:1000556" name="LTQ Orbitrap XL" value=""/>\n- <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN01272B"/>\n- </referenceableParamGroup>\n- </referenceableParamGroupList>\n- <softwareList 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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 |
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| Binary file msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 has changed |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/test-data/Rpal_01-mzRefinement.mzML --- a/msconvert_win/test-data/Rpal_01-mzRefinement.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_win/test-data/small-ms-level-filter.mzML --- a/msconvert_win/test-data/small-ms-level-filter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 msconvert_wrapper.py --- a/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,298 +0,0 @@\n-#!/usr/bin/env python\n-import optparse\n-import os\n-import sys\n-import tempfile\n-import shutil\n-import subprocess\n-import re\n-import logging\n-\n-assert sys.version_info[:2] >= (2, 6)\n-\n-log = logging.getLogger(__name__)\n-working_directory = os.getcwd()\n-tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n-tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n-\n-\n-def stop_err(msg):\n- sys.stderr.write("%s\\n" % msg)\n- sys.exit()\n-\n-\n-def read_stderr():\n- stderr = \'\'\n- if(os.path.exists(tmp_stderr_name)):\n- with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n- buffsize = 1048576\n- try:\n- while True:\n- stderr += tmp_stderr.read(buffsize)\n- if not stderr or len(stderr) % buffsize != 0:\n- break\n- except OverflowError:\n- pass\n- return stderr\n-\n-\n-def execute(command, stdin=None):\n- try:\n- with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n- with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n- proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n- returncode = proc.wait()\n- if returncode != 0:\n- raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n- finally:\n- print(( open(tmp_stderr_name, "r").read() ))\n- print(( open(tmp_stdout_name, "r").read() ))\n-\n-\n-def delete_file(path):\n- if os.path.exists(path):\n- try:\n- os.remove(path)\n- except:\n- pass\n-\n-\n-def delete_directory(directory):\n- if os.path.exists(directory):\n- try:\n- shutil.rmtree(directory)\n- except:\n- pass\n-\n-\n-def symlink(source, link_name):\n- import platform\n- if platform.system() == \'Windows\':\n- try:\n- import win32file\n- win32file.CreateSymbolicLink(source, link_name, 1)\n- except:\n- shutil.copy(source, link_name)\n- else:\n- os.symlink(source, link_name)\n-\n-\n-def copy_to_working_directory(data_file, relative_path):\n- if os.path.abspath(data_file) != os.path.abspath(relative_path):\n- symlink(data_file, relative_path)\n- return relative_path\n-\n-\n-def __main__():\n- run_script()\n-\n-#ENDTEMPLATE\n-\n-to_extensions = [\'mzML\', \'mzXML\', \'unindexed_mzML\', \'unindexed_mzXML\', \'mgf\', \'mz5\', \'txt\', \'ms2\', \'cms2\']\n-\n-\n-def str_to_bool(v):\n- """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """\n- return v.lower() in ["yes", "true", "t", "1"]\n-\n-\n-def _add_filter(filters_file, contents):\n- filters_file.write("filter=%s\\n" % contents)\n-\n-\n-def _skip_line(options, file_num, line_parts):\n- file_num_column = options.filter_table_file_column\n- if not file_num_column:\n- return False\n- else:\n- target_file_num_val = str(file_num).strip()\n- query_file_num_val = line_parts[int(file_num_column) - 1].strip()\n- #print "target %s, query %s" % (target_file_num_val, query_file_num_val)\n- return target_file_num_val != query_file_num_val\n-\n-\n-def _read_table_numbers(path, options, file_num=None):\n- unique_numbers = set([])\n- column_num = options.filter_table_column\n- input = open(path, "r")\n- first_line = True\n- for line in input:\n- if not line:\n- continue\n- line = line.strip()\n- if line.startswith("#"):\n- first_line = False\n- continue\n- if column_num == None:\n- column = line\n- else:\n- line_parts = line.split("\\t")\n- if _skip_line(options, file_num, line_parts):\n- continue\n- column = line_parts[int(column_num) - 1]\n- match = re.match("\\d+", column)\n- '..b' parser.add_option(\'--binaryencoding\', dest=\'binaryencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--mzencoding\', dest=\'mzencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--intensityencoding\', dest=\'intensityencoding\', choices=[\'32\', \'64\'])\n- parser.add_option(\'--zlib\', dest=\'zlib\', default="false")\n- parser.add_option(\'--filter\', dest=\'filter\', action=\'append\', default=[])\n- parser.add_option(\'--filters_file\', dest=\'filters_file\', default=None)\n- parser.add_option(\'--filter_table\', default=None)\n- parser.add_option(\'--filter_table_type\', default=\'index\', choices=[\'index\', \'number\'])\n- parser.add_option(\'--filter_table_column\', default=None)\n- parser.add_option(\'--filter_table_file_column\', default=None)\n- parser.add_option(\'--debug\', dest=\'debug\', action=\'store_true\', default=False)\n-\n- (options, args) = parser.parse_args()\n- if len(options.inputs) < 1:\n- stop_err("No input files to msconvert specified")\n- if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs):\n- stop_err("Number(s) of supplied input names and input files do not match")\n- if not options.output:\n- stop_err("Must specify output location")\n- input_files = []\n- for i, input in enumerate(options.inputs):\n- input_base = None\n- if len(options.input_names) > i:\n- input_base = options.input_names[i]\n- input_base = input_base.replace("\'", "").replace("\\"", "")\n- print("1- input_base: %s" % input_base)\n- if not input_base:\n- input_base = \'input%s\' % i\n- print("2- input_base: %s" % input_base)\n- if not input_base.lower().endswith(\'.%s\' % options.fromextension.lower()) and input not in options.implicits:\n- input_file = \'%s.%s\' % (input_base, options.fromextension)\n- print("3- input_base: %s" % input_base)\n- print("3- input_file: %s" % input_file)\n- else:\n- input_file = input_base\n- print("4- input_base: %s" % input_base)\n- print("4- input_file: %s" % input_file)\n- input_file = input_file\n- copy_to_working_directory(input, input_file)\n- if input in options.implicits:\n- continue\n- input_files.append(input_file)\n- for i, ident in enumerate(options.idents):\n- ident_file = options.ident_names[i]\n- copy_to_working_directory(ident, ident_file)\n-\n- cmd = _build_base_cmd(options,args=args)\n- file_column = options.filter_table_file_column\n- if not file_column:\n- # Apply same filters to all files, just create a unviersal filter files\n- # and run msconvert once.\n- filters_file_path = _create_filters_file(options, debug=options.debug)\n- cmd = "%s -c %s" % (cmd, filters_file_path)\n- else:\n- # Dispatching on a column to filter different files differently, need to filter\n- # each input once with msconvert and then merge once.\n- filtered_files = []\n- for index, input_file in enumerate(input_files):\n- filters_file_path = _create_filters_file(options, index + 1, debug=options.debug)\n- filter_cmd = "%s -c %s" % (cmd, filters_file_path)\n- filtered_output_file = _run(filter_cmd, output_dir=\'output%d\' % index, inputs=[input_file], debug=options.debug)\n- filtered_files.append(filtered_output_file)\n- input_files = filtered_files\n- if len(input_files) > 1:\n- cmd = "%s --merge" % cmd\n- output_file = _run(cmd, output_dir=\'output\', inputs=input_files, debug=options.debug)\n- shutil.copy(output_file, options.output)\n- if options.refinement:\n- # .mzRefinement.tsv\n- files = os.listdir(os.getcwd())\n- for fname in files:\n- if fname.endswith(\'.mzRefinement.tsv\'):\n- shutil.copy(fname, options.refinement)\n- break\n-\n-def __main__():\n- run_script()\n-\n-if __name__ == \'__main__\':\n- __main__()\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 repository_dependencies.xml --- a/repository_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Required proteomics dependencies."> - <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories> |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/AgilentMassHunterTest.d.tar |
| b |
| Binary file test-data/AgilentMassHunterTest.d.tar has changed |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/AgilentMassHunterTest.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AgilentMassHunterTest.mzXML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -0,0 +1,4263 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<mzXML xmlns="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n+ <msRun scanCount="212" startTime="PT0.668S" endTime="PT209.708S">\n+ <msInstrument msInstrumentID="1">\n+ <msManufacturer category="msManufacturer" value="instrument model"/>\n+ <msModel category="msModel" value="Agilent instrument model"/>\n+ <msIonisation category="msIonisation" value="microelectrospray"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="time-of-flight"/>\n+ <msDetector category="msDetector" value="microchannel plate detector"/>\n+ <software type="acquisition" name="MassHunter Data Acquisition" version="8.0"/>\n+ </msInstrument>\n+ <dataProcessing>\n+ <software type="conversion" name="ProteoWizard software" 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| @@ -1,2 +1,2 @@ -ThresholdScore ThresholdValue Excluded (score) Excluded (mass error) MS1 Included MS1 Shift method MS1 Final stDev MS1 Tolerance for 99% MS1 Final MAD MS1 MAD Tolerance for 99% MS2 Included MS2 Shift method MS2 Final stDev MS2 Tolerance for 99% MS2 Final MAD MS2 MAD Tolerance for 99% -MyriMatch:MVH 40 <= MME <= 1.7976931348623157e+308 4390 175 1024 m/z 3.37955 10.1387 0.519682 2.31144 0 m/z 3.37955 10.1387 0.519682 2.31144 +ThresholdScore ThresholdValue Excluded (score) Excluded (mass error) MS1 Included MS1 Shift method MS1 Final stDev MS1 Tolerance for 99% MS1 Final MAD MS1 MAD Tolerance for 99% MS2 Included MS2 Shift method MS2 Final stDev MS2 Tolerance for 99% MS2 Final MAD MS2 MAD Tolerance for 99% +MyriMatch:MVH 40 <= MME <= 1.7976931348623157e+308 4390 175 1024 m/z 3.37955 10.1387 0.519682 2.31144 0 m/z 3.37955 10.1387 0.519682 2.31144 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/SciexTest-HPINalone-NE.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SciexTest-HPINalone-NE.mzML Sat Feb 23 06:25:48 2019 -0500 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/SciexTest-HPINalone-srmAsSpectra.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SciexTest-HPINalone-srmAsSpectra.mzXML Sat Feb 23 06:25:48 2019 -0500 |
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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-analyzer-filter.mzML --- a/test-data/small-analyzer-filter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-analyzer-filter.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-chargeStatePredictor.mzML --- a/test-data/small-chargeStatePredictor.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-chargeStatePredictor.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-deisotope.mzML --- a/test-data/small-deisotope.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-deisotope.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-denoise.mzML --- a/test-data/small-denoise.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-denoise.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-index-filter.mzML --- a/test-data/small-index-filter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-index-filter.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| @@ -2,8 +2,8 @@ <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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/> + <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/> </cvList> <fileDescription> <fileContent> @@ -11,7 +11,7 @@ <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> </fileContent> <sourceFileList count="3"> - 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<softwareList count="3"> + <softwareList count="4"> <software id="Xcalibur" version="1.1 Beta 7"> <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/> </software> <software id="pwiz" version="3.0.8981"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> - <software id="pwiz_3.0.8990" version="3.0.8990"> + <software id="pwiz_3.0.19038" version="3.0.19038"> + <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> + </software> + <software id="pwiz_3.0.19044" version="3.0.19044"> <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/> </software> </softwareList> @@ -82,10 +85,10 @@ </processingMethod> </dataProcessing> <dataProcessing id="pwiz_Reader_conversion"> - <processingMethod order="0" softwareRef="pwiz_3.0.8990"> + <processingMethod order="0" softwareRef="pwiz_3.0.19038"> <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> </processingMethod> - 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-ms-level-filter.mzML --- a/test-data/small-ms-level-filter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-ms-level-filter.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-mzWindow.mzML --- a/test-data/small-mzWindow.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-mzWindow.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-numpressL.mzML --- a/test-data/small-numpressL.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-numpressL.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-numpressLP.mzML --- a/test-data/small-numpressLP.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-numpressLP.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-numpressLS.mzML --- a/test-data/small-numpressLS.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-numpressLS.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-numpressP.mzML --- a/test-data/small-numpressP.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-numpressP.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-numpressS.mzML --- a/test-data/small-numpressS.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-numpressS.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-peakpicking-cwt-allMS.mzML --- a/test-data/small-peakpicking-cwt-allMS.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-peakpicking-cwt-allMS.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-peakpicking-vendor-allMS.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small-peakpicking-vendor-allMS.mzML Sat Feb 23 06:25:48 2019 -0500 |
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| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-polarity-filter.mzML --- a/test-data/small-polarity-filter.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-polarity-filter.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-strip-it.mzML --- a/test-data/small-strip-it.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-strip-it.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n@@ -20,7 +20,7 @@\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>\n 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| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-threshold.mzML --- a/test-data/small-threshold.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-threshold.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\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="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,14 +30,17 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="3">\n+ <softwareList count="4">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.19038" version="3.0.19038">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ <software id="pwiz_3.0.19044" version="3.0.19044">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +85,10 @@\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_3.0.19038">\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_3.0.19038">\n <cvParam cvRef="MS" accession'..b'Number=1 scan=5">26507</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">32496</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">38482</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">44503</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=9">48866</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">53225</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">59254</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">65279</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">71260</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">77249</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=15">83242</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">87618</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">92003</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">98035</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">104058</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">110037</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">116034</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">122033</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">126406</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">130744</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">136774</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">142803</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">148781</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">154772</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">160787</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">165158</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">169558</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">175583</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">181555</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">187540</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">193486</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">197863</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">202238</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">208268</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">214301</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">220286</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">226289</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">232266</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">236630</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">241026</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">247052</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">253068</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">259036</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">265014</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">270957</offset>\n+ <offset idRef="TIC">271077</offset>\n </index>\n </indexList>\n- <indexListOffset>272907</indexListOffset>\n- <fileChecksum>39712143d9caed5b0d1d0a476d57644357c23ec8</fileChecksum>\n+ <indexListOffset>273027</indexListOffset>\n+ <fileChecksum>b1908e0016bbf6bf4fc21daa511924db77237312</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-turbocharger.mzML --- a/test-data/small-turbocharger.mzML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-turbocharger.mzML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -2,8 +2,8 @@\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="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>\n </cvList>\n <fileDescription>\n <fileContent>\n@@ -11,7 +11,7 @@\n <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>\n </fileContent>\n <sourceFileList count="3">\n- <sourceFile id="RAW1" name="small.RAW" location="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data">\n+ <sourceFile id="RAW1" name="small.RAW" location="file:///">\n <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\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="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>\n </sourceFile>\n </sourceFileList>\n </fileDescription>\n@@ -30,14 +30,17 @@\n <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>\n </referenceableParamGroup>\n </referenceableParamGroupList>\n- <softwareList count="3">\n+ <softwareList count="4">\n <software id="Xcalibur" version="1.1 Beta 7">\n <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n </software>\n <software id="pwiz" version="3.0.8981">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n- <software id="pwiz_3.0.8990" version="3.0.8990">\n+ <software id="pwiz_3.0.19038" version="3.0.19038">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ <software id="pwiz_3.0.19044" version="3.0.19044">\n <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n </software>\n </softwareList>\n@@ -82,10 +85,10 @@\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_3.0.19038">\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_3.0.19038">\n <cvParam cvRef="MS" accession'..b' scan=5">46335</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=6">56897</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=7">66312</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=8">76888</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=9">83977</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=10">95755</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=11">104825</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=12">116343</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=13">125673</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=14">135991</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=15">145521</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=16">153303</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=17">164335</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=18">173596</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=19">184932</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=20">194449</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=21">204031</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">214935</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">222850</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">231506</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">240769</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">252299</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">262494</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">272110</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">282906</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">291219</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">301581</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">313067</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">322485</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">332195</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">341108</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">348679</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">357696</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">366914</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">379245</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">388663</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">399499</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">409506</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">423045</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">434388</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">443818</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">455724</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">465549</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">475001</offset>\n </index>\n <index name="chromatogram">\n- <offset idRef="TIC">484164</offset>\n+ <offset idRef="TIC">484276</offset>\n </index>\n </indexList>\n- <indexListOffset>486114</indexListOffset>\n- <fileChecksum>e7ec398af412704484453e19bd2bc7578529b5c0</fileChecksum>\n+ <indexListOffset>486226</indexListOffset>\n+ <fileChecksum>d828d0af4d60fcecdcdd35f94c1dbd53dd6064c6</fileChecksum>\n </indexedmzML>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-zlib-32.mzXML --- a/test-data/small-zlib-32.mzXML Wed Dec 07 16:43:07 2016 -0500 +++ b/test-data/small-zlib-32.mzXML Sat Feb 23 06:25:48 2019 -0500 |
| b |
| b'@@ -3,7 +3,7 @@\n xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/mzXML_3.2 http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_idx_3.2.xsd">\n <msRun scanCount="48" startTime="PT0.2961S" endTime="PT29.2342S">\n- <parentFile fileName="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data/small.RAW"\n+ <parentFile fileName="file:////small.RAW"\n fileType="RAWData"\n fileSha1="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n <msInstrument msInstrumentID="1">\n@@ -26,10 +26,13 @@\n <software type="conversion" name="ProteoWizard software" version="3.0.8981"/>\n <processingOperation name="Conversion to mzML"/>\n </dataProcessing>\n+ <dataProcessing>\n+ <software type="conversion" name="ProteoWizard software" version="3.0.19038"/>\n+ <processingOperation name="Conversion to mzML"/>\n+ </dataProcessing>\n <dataProcessing centroided="1">\n- <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>\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="3.0.19038"/>\n+ <processingOperation name="peak picking"/>\n </dataProcessing>\n <scan num="1"\n scanType="Full"\n@@ -483,7 +486,7 @@\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 +496,10 @@\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'jzzDl3IlWJ7owpfbVXSUcxJf+mtwW9UM35Z30lxjVXzb0IRLm3zwjd4Qp1owvu1tRKTSJkxtu0iiUkcxpduGILFOTNnJo/TpCXyftZg2J73G93AFkvo9hO9XytC8zQPfSy/RbP7O/wEteZ5t</peaks>\n </scan>\n <scan num="43"\n scanType="Full"\n@@ -1013,55 +1016,55 @@\n </scan>\n </msRun>\n <index name="scan">\n- <offset id="1">2080</offset>\n- <offset id="2">9665</offset>\n- <offset id="3">19144</offset>\n- <offset id="4">24664</offset>\n- <offset id="5">35242</offset>\n- <offset id="6">44241</offset>\n- <offset id="7">51421</offset>\n- <offset id="8">59677</offset>\n- <offset id="9">64681</offset>\n- <offset id="10">75596</offset>\n- <offset id="11">81775</offset>\n- <offset id="12">91690</offset>\n- <offset id="13">98725</offset>\n- <offset id="14">107278</offset>\n- <offset id="15">114645</offset>\n- <offset id="16">120539</offset>\n- <offset id="17">130155</offset>\n- <offset id="18">136600</offset>\n- <offset id="19">146297</offset>\n- <offset id="20">153675</offset>\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="1">2139</offset>\n+ <offset id="2">9724</offset>\n+ <offset id="3">19203</offset>\n+ <offset id="4">24723</offset>\n+ <offset id="5">35301</offset>\n+ <offset id="6">44300</offset>\n+ <offset id="7">51480</offset>\n+ <offset id="8">59736</offset>\n+ <offset id="9">64740</offset>\n+ <offset id="10">75655</offset>\n+ <offset id="11">81834</offset>\n+ <offset id="12">91749</offset>\n+ <offset id="13">98784</offset>\n+ <offset id="14">107337</offset>\n+ <offset id="15">114704</offset>\n+ <offset id="16">120598</offset>\n+ <offset id="17">130214</offset>\n+ <offset id="18">136659</offset>\n+ <offset id="19">146356</offset>\n+ <offset id="20">153734</offset>\n+ <offset id="21">161154</offset>\n+ <offset id="22">170676</offset>\n+ <offset id="23">176788</offset>\n+ <offset id="24">183537</offset>\n+ <offset id="25">189982</offset>\n+ <offset id="26">199882</offset>\n+ <offset id="27">208429</offset>\n+ <offset id="28">215983</offset>\n+ <offset id="29">225257</offset>\n+ <offset id="30">231917</offset>\n+ <offset id="31">240628</offset>\n+ <offset id="32">250540</offset>\n+ <offset id="33">257754</offset>\n+ <offset id="34">265462</offset>\n+ <offset id="35">272045</offset>\n+ <offset id="36">277669</offset>\n+ <offset id="37">284751</offset>\n+ <offset id="38">291122</offset>\n+ <offset id="39">302259</offset>\n+ <offset id="40">309479</offset>\n+ <offset id="41">318838</offset>\n+ <offset id="42">327039</offset>\n+ <offset id="43">340377</offset>\n+ <offset id="44">350377</offset>\n+ <offset id="45">357129</offset>\n+ <offset id="46">367740</offset>\n+ <offset id="47">375513</offset>\n+ <offset id="48">382804</offset>\n </index>\n- <indexOffset>389817</indexOffset>\n- <sha1>352d6c47e7a76389270f5e063a125ae498ad9f9c</sha1>\n+ <indexOffset>389864</indexOffset>\n+ <sha1>22755d784c31491eb1a1f5f2dd9db13dd5e52277</sha1>\n </mzXML>\n' |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small-zlib-64.mz5 |
| b |
| Binary file test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r dd4ba10d0c45 -r 9d5de24e6ef7 test-data/small.RAW |
| b |
| Binary file test-data/small.RAW has changed |