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Commit message:
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6 |
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modified:
README.md msconvert.xml msconvert_raw.xml msconvert_subset.xml msconvert_wrapper.py repository_dependencies.xml |
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added:
idconvert/idconvert.xml idconvert/msconvert_macros.xml idconvert/test-data/Rpal_01.mzid idconvert/test-data/Rpal_01.pepXML idconvert/tool_dependencies.xml msconvert_macros.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_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 test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 test-data/Rpal_01-mzRefinement.mzML test-data/Rpal_01.mz5 test-data/Rpal_01.mzid test-data/Rpal_01.pepXML 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-poisson.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 test-data/small.mzML |
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| diff -r d2c61663e33c -r dd4ba10d0c45 README.md --- a/README.md Fri Sep 26 14:44:54 2014 -0400 +++ b/README.md Wed Dec 07 16:43:07 2016 -0500 |
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| @@ -1,7 +1,7 @@ GalaxyP - ProteoWizard msconvert ================================ -* Home: <https://bitbucket.org/galaxyp/msconvert> +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> * Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/msconvert> * Tool ID: `msconvert` @@ -32,9 +32,9 @@ GalaxyP Community ----------------- -Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: -<https://bitbucket.org/galaxyp/galaxyp> +<https://github.com/galaxyproteomics> License @@ -52,7 +52,7 @@ Contributing ------------ -Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> Authors |
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| diff -r d2c61663e33c -r dd4ba10d0c45 idconvert/idconvert.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idconvert/idconvert.xml Wed Dec 07 16:43:07 2016 -0500 |
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| @@ -0,0 +1,123 @@ +<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 d2c61663e33c -r dd4ba10d0c45 idconvert/msconvert_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idconvert/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 |
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| b'@@ -0,0 +1,675 @@\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 d2c61663e33c -r dd4ba10d0c45 idconvert/test-data/Rpal_01.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idconvert/test-data/Rpal_01.mzid Wed Dec 07 16:43:07 2016 -0500 |
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| b'@@ -0,0 +1,78943 @@\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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searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA2576" accession="rev_RPA2576" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_RPA3081" accession="RPA3081" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA2589" accession="rev_RPA2589" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA0865" accession="rev_RPA0865" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_RPA1852" accession="RPA1852" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA0940" accession="rev_RPA0940" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA1045" accession="rev_RPA1045" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA4468" accession="rev_RPA4468" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_RPA2928" accession="RPA2928" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_rev_RPA1429" accession="rev_RPA1429" searchDatabase_ref="SDB"/>\n+ <DBSequence id="DBSeq_RPA2638" accession'..b'589" name="MyriMatch:MVH" value="16.589879512787"/>\n+ <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 d2c61663e33c -r dd4ba10d0c45 idconvert/test-data/Rpal_01.pepXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idconvert/test-data/Rpal_01.pepXML Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,49047 @@\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' |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 idconvert/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/idconvert/tool_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?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 d2c61663e33c -r dd4ba10d0c45 msconvert.xml --- a/msconvert.xml Fri Sep 26 14:44:54 2014 -0400 +++ b/msconvert.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| @@ -8,11 +8,24 @@ </requirements> --> <command interpreter="python"> + #import re #set $ext = $input.ext msconvert_wrapper.py - --input=${input} - #if hasattr($input, 'display_name') - --input_name='${input.display_name}' + #if $type.input_type == 'wiff': + #set basename = 'absciex' + #if hasattr($input, 'display_name') + #set basename = $re.sub('\W','_',$input.display_name) + #end if + --input=${input.extra_files_path}/wiff + --input_name='${basename}.wiff + --implicit=${input.extra_files_path}/wiff_scan + --input=${input.extra_files_path}/wiff_scan + --input_name='${basename}.wiff.scan + #else + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if #end if --output=${output} ## BEGIN_VERSION_DEFAULT @@ -122,6 +135,7 @@ <option value="mzxml">mzXML</option> <option value="mgf">mgf</option> <option value="ms2">ms2</option> + <option value="wiff">wiff</option> </param> <when value="mzml"> <param format="mzml" name="input" type="data" label="Input mzML"/> @@ -135,6 +149,9 @@ <when value="ms2"> <param format="ms2" name="input" type="data" label="Input ms2"/> </when> + <when value="wiff"> + <param format="wiff" name="input" type="data" label="Input wiff"/> + </when> </conditional> <!-- END_VERSION_DEFAULT --> <param name="output_type" type="select" label="Output Type"> @@ -347,7 +364,7 @@ </inputs> <outputs> - <data format="mzml" name="output"> + <data format="mzml" name="output" label="${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" /> |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,675 @@\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 d2c61663e33c -r dd4ba10d0c45 msconvert_nix/msconvert_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_nix/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,675 @@\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 d2c61663e33c -r dd4ba10d0c45 msconvert_nix/msconvert_nix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_nix/msconvert_nix.xml Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,28 @@ +<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 d2c61663e33c -r dd4ba10d0c45 msconvert_nix/msconvert_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_nix/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,298 @@\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 d2c61663e33c -r dd4ba10d0c45 msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_nix/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Wed Dec 07 16:43:07 2016 -0500 |
| b |
| b'@@ -0,0 +1,4759 @@\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" 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| @@ -0,0 +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 |
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<offset idRef="controllerType=0 controllerNumber=1 scan=21">1293376</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=22">1307015</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=23">1497624</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">1659981</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">1670735</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=26">1684796</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=27">1697470</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=28">1709201</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=29">1722596</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=30">1944787</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=31">2121562</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=32">2135647</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=33">2147075</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=34">2158976</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=35">2169802</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=36">2351595</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=37">2516517</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=38">2527211</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=39">2542485</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=40">2553894</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=41">2567377</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=42">2579754</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=43">2937502</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=44">3120057</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=45">3131111</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=46">3145852</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=47">3157836</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=48">3169358</offset>\n+ </index>\n+ <index name="chromatogram">\n+ <offset idRef="TIC">3180760</offset>\n+ </index>\n+ </indexList>\n+ <indexListOffset>3182770</indexListOffset>\n+ <fileChecksum>3a12c8cc54626511af9d128aab16b0ecb3357b1b</fileChecksum>\n+</indexedmzML>\n' |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_nix/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_nix/tool_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?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 d2c61663e33c -r dd4ba10d0c45 msconvert_raw.xml --- a/msconvert_raw.xml Fri Sep 26 14:44:54 2014 -0400 +++ b/msconvert_raw.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| @@ -366,7 +366,7 @@ </inputs> <outputs> - <data format="mzml" name="output"> + <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" > <change_format> <when input="output_type" value="mzXML" format="mzxml" /> <when input="output_type" value="unindexed_mzXML" format="mzxml" /> |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_subset.xml --- a/msconvert_subset.xml Fri Sep 26 14:44:54 2014 -0400 +++ b/msconvert_subset.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| @@ -91,7 +91,7 @@ </conditional> </inputs> <outputs> - <data format="mzml" name="output"> + <data format="mzml" name="output" label="${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" /> |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/README Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,15 @@ +**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 d2c61663e33c -r dd4ba10d0c45 msconvert_win/job_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/job_conf.xml.sample Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,88 @@ +<?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 d2c61663e33c -r dd4ba10d0c45 msconvert_win/msconvert_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/msconvert_macros.xml Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,675 @@\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 d2c61663e33c -r dd4ba10d0c45 msconvert_win/msconvert_win.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/msconvert_win.xml Wed Dec 07 16:43:07 2016 -0500 |
| b |
| @@ -0,0 +1,36 @@ +<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> |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/msconvert_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,298 @@\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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| Binary file msconvert_win/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5 has changed |
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| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/Rpal_01-mzRefinement.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/test-data/Rpal_01-mzRefinement.mzML Wed Dec 07 16:43:07 2016 -0500 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/Rpal_01.mz5 |
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| Binary file msconvert_win/test-data/Rpal_01.mz5 has changed |
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| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/Rpal_01.pepXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/test-data/Rpal_01.pepXML Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| b'@@ -0,0 +1,49047 @@\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: 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| @@ -0,0 +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 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/small-index-filter.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/test-data/small-index-filter.mzML Wed Dec 07 16:43:07 2016 -0500 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/small-zlib-32.mzXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/test-data/small-zlib-32.mzXML Wed Dec 07 16:43:07 2016 -0500 |
| b |
| b'@@ -0,0 +1,1067 @@\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="48" startTime="PT0.2961S" endTime="PT29.2342S">\n+ <parentFile fileName="file:///C:\\pwiz-src\\trunk\\pwiz\\example_data/small.RAW"\n+ fileType="RAWData"\n+ fileSha1="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>\n+ <msInstrument msInstrumentID="1">\n+ <msManufacturer category="msManufacturer" value="Thermo Scientific"/>\n+ <msModel category="msModel" value="LTQ FT"/>\n+ <msIonisation category="msIonisation" value="electrospray ionization"/>\n+ <msMassAnalyzer category="msMassAnalyzer" value="fourier transform ion cyclotron resonance mass spectrometer"/>\n+ <msDetector category="msDetector" value="inductive 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| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/small-zlib-64.mz5 |
| b |
| Binary file msconvert_win/test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/small.RAW |
| b |
| Binary file msconvert_win/test-data/small.RAW has changed |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 msconvert_win/test-data/small.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_win/test-data/small.mzML Wed Dec 07 16:43:07 2016 -0500 |
| b |
| b'@@ -0,0 +1,2757 @@\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 d2c61663e33c -r dd4ba10d0c45 msconvert_wrapper.py --- a/msconvert_wrapper.py Fri Sep 26 14:44:54 2014 -0400 +++ b/msconvert_wrapper.py Wed Dec 07 16:43:07 2016 -0500 |
| [ |
| @@ -88,7 +88,7 @@ #ENDTEMPLATE -to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2'] +to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'mz5', 'txt', 'ms2', 'cms2'] def str_to_bool(v): @@ -171,7 +171,7 @@ return filters_file_path -def _build_base_cmd(options): +def _build_base_cmd(options,args=None): to_extension = options.toextension if to_extension.startswith("unindexed_"): to_extension = to_extension[len("unindexed_"):] @@ -179,6 +179,8 @@ else: to_params = "" cmd = "msconvert --%s %s" % (to_extension, to_params) + if args: + cmd = "%s %s" % (cmd, ' '.join(args)) if str_to_bool(options.zlib): cmd = "%s %s" % (cmd, "--zlib") if options.binaryencoding: @@ -207,7 +209,11 @@ parser = optparse.OptionParser() parser.add_option('--input', dest='inputs', action='append', default=[]) parser.add_option('--input_name', dest='input_names', action='append', default=[]) + parser.add_option('--implicit', dest='implicits', action='append', default=[], help='input files that should NOT be on the msconvert command line.') + parser.add_option('--ident', dest='idents', action='append', default=[]) + parser.add_option('--ident_name', dest='ident_names', action='append', default=[]) parser.add_option('--output', dest='output') + parser.add_option('--refinement', dest='refinement') 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']) @@ -239,7 +245,7 @@ if not input_base: input_base = 'input%s' % i print("2- input_base: %s" % input_base) - if not input_base.lower().endswith(options.fromextension.lower()): + if not input_base.lower().endswith('.%s' % options.fromextension.lower()) and input not in options.implicits: input_file = '%s.%s' % (input_base, options.fromextension) print("3- input_base: %s" % input_base) print("3- input_file: %s" % input_file) @@ -249,9 +255,14 @@ print("4- input_file: %s" % input_file) input_file = input_file copy_to_working_directory(input, input_file) + if input in options.implicits: + continue input_files.append(input_file) + for i, ident in enumerate(options.idents): + ident_file = options.ident_names[i] + copy_to_working_directory(ident, ident_file) - cmd = _build_base_cmd(options) + cmd = _build_base_cmd(options,args=args) file_column = options.filter_table_file_column if not file_column: # Apply same filters to all files, just create a unviersal filter files @@ -272,7 +283,16 @@ cmd = "%s --merge" % cmd output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug) shutil.copy(output_file, options.output) + if options.refinement: + # .mzRefinement.tsv + files = os.listdir(os.getcwd()) + for fname in files: + if fname.endswith('.mzRefinement.tsv'): + shutil.copy(fname, options.refinement) + break +def __main__(): + run_script() if __name__ == '__main__': __main__() |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 repository_dependencies.xml --- a/repository_dependencies.xml Fri Sep 26 14:44:54 2014 -0400 +++ b/repository_dependencies.xml Wed Dec 07 16:43:07 2016 -0500 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Required proteomics dependencies."> - <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML Wed Dec 07 16:43:07 2016 -0500 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/Rpal_01.pepXML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Rpal_01.pepXML Wed Dec 07 16:43:07 2016 -0500 |
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| b'@@ -0,0 +1,49047 @@\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" 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| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/Rpal_01.pepXML.mzRefinement.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Rpal_01.pepXML.mzRefinement.tsv Wed Dec 07 16:43:07 2016 -0500 |
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| @@ -0,0 +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 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/small-activation.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small-activation.mzML Wed Dec 07 16:43:07 2016 -0500 |
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| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/small-zlib-64.mz5 |
| b |
| Binary file test-data/small-zlib-64.mz5 has changed |
| b |
| diff -r d2c61663e33c -r dd4ba10d0c45 test-data/small.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.mzML Wed Dec 07 16:43:07 2016 -0500 |
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