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Changeset 9:92ac8e086317 (2021-02-17)

Previous changeset 8:26c6706bfb07 (2020-07-25) Next changeset 10:b9b385097f13 (2021-04-10)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 9bb883e027809047684fd6c45e9a6f1f3bf69351"

modified:
test-data/really_small.mzml
thermo_converter.xml

added:
test-data/really_small.indexed_mzML
test-data/really_small.json
test-data/really_small.mgf
test-data/really_small_ext.mzml

removed:
test-data/really_small_2.raw
test-data/really_small_3.raw

diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small.indexed_mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/really_small.indexed_mzML Wed Feb 17 09:50:26 2021 +0000

b'@@ -0,0 +1,2772 @@\n+\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML 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" xmlns="http://psi.hupo.org/ms/mzml">\n+ <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" version="1.1.0" id="really_small">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Mass spectrometry ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" />\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000580" value="" name="MSn spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000810" value="" name="ion current chromatogram" />\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="really_small" location="file:///really_small.raw">\n+ <cvParam cvRef="MS" accession="MS:1000768" value="" name="Thermo nativeID format" />\n+ <cvParam cvRef="MS" accession="MS:1000563" value="" name="Thermo RAW format" />\n+ <cvParam cvRef="MS" accession="MS:1000569" value="a6c0d318207b271d5e2f31b3302239e040c66dbe" name="SHA-1" />\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="commonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1002416" value="" name="Orbitrap Fusion" />\n+ <cvParam cvRef="MS" accession="MS:1000529" value="FSN10188" name="instrument serial number" />\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="1">\n+ <software id="ThermoRawFileParser" version="1.3.2">\n+ <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="1">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="commonInstrumentParams" />\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" value="" name="nanoelectrospray" />\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000079" value="" name="fourier transform ion cyclotron resonance mass spectrometer" />\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" value="" name="inductive detector" />\n+ </detector>\n+ </componentList>\n+ </instrumentConfiguration>\n+ </instrumentConfigurationList>\n+ <dataProcessingList count="1">\n+ <dataProcessing id="ThermoRawFileParserProcessing">\n+ <processingMethod order="0" softwareRef="ThermoRawFileParser">\n+ <cvParam cvRef="MS" accession="MS:1000544" value="" name="Conversion to mzML" />\n+ </processingMethod>\n+ <processingMethod order="1" softwareRef="ThermoRawFileParser">\n+ <cvParam cvRef="MS" accession="MS:1000035" value="" name="peak picking" />\n+ </processingMethod>\n+ </dataProcessing>\n+ </dataProcessingList>\n+ <run id="really_small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2019-03-25T11:30:48.075Z" defaultSourceFileRef="RAW1">\n+ <spectrumList count="67" defaultDataProcessingRef="ThermoRawFileParserProcessing">\n+ <spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0" defaultArrayLength="136">\n+ <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />\n+ <cvPa'..b'ollerType=0 controllerNumber=1 scan=23">104772</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=24">108928</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=25">113903</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 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diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/really_small.json Wed Feb 17 09:50:26 2021 +0000

[

@@ -0,0 +1,1 @@
+{"FileProperties":[{"accession":"NCIT:C47922","cvLabel":"NCIT","name":"Pathname","value":"really_small.raw"},{"accession":"NCIT:C25714","cvLabel":"NCIT","name":"Version","value":"66"},{"accession":"NCIT:C69199","cvLabel":"NCIT","name":"Content Creation Date","value":"03/25/2019 11:30:48"},{"accession":"NCIT:C25365","cvLabel":"NCIT","name":"Description","value":""}],"InstrumentProperties":[{"accession":"MS:1000494","cvLabel":"MS","name":"Thermo Scientific instrument model","value":"Orbitrap Fusion"},{"accession":"MS:1000496","cvLabel":"MS","name":"instrument attribute","value":"Orbitrap Fusion"},{"accession":"MS:1000529","cvLabel":"MS","name":"instrument serial number","value":"FSN10188"}],"MsData":[{"accession":"PRIDE:0000481","cvLabel":"PRIDE","name":"Number of MS1 spectra","value":"67"},{"accession":"PRIDE:0000482","cvLabel":"PRIDE","name":"Number of MS2 spectra","value":"34"},{"accession":"PRIDE:0000472","cvLabel":"PRIDE","name":"MS min charge","value":"2"},{"accession":"PRIDE:0000473","cvLabel":"PRIDE","name":"MS max charge","value":"3"},{"accession":"PRIDE:0000474","cvLabel":"PRIDE","name":"MS min RT","value":"0.89012589865"},{"accession":"PRIDE:0000475","cvLabel":"PRIDE","name":"MS max RT","value":"1.5947900096"},{"accession":"PRIDE:0000476","cvLabel":"PRIDE","name":"MS min MZ","value":"407.919311523438"},{"accession":"PRIDE:0000477","cvLabel":"PRIDE","name":"MS max MZ","value":"1138.40502929688"}],"SampleData":[],"ScanSettings":[{"accession":"MS:1000016","cvLabel":"MS","name":"scan start time","value":"0.89012589865"},{"accession":"MS:1000011","cvLabel":"MS","name":"mass resolution","value":"0.5"},{"accession":"UO:0000002","cvLabel":"MS","name":"mass unit","value":"None"},{"accession":"PRIDE:0000478","cvLabel":"PRIDE","name":"Number of scans","value":"101"},{"accession":"PRIDE:0000479","cvLabel":"PRIDE","name":"MS scan range","value":"1:101"},{"accession":"PRIDE:0000484","cvLabel":"PRIDE","name":"Retention time range","value":"0.89012589865:1.5947900096"},{"accession":"PRIDE:0000485","cvLabel":"PRIDE","name":"Mz range","value":"120:2000"},{"accession":"MS:1000422","cvLabel":"MS","name":"beam-type collision-induced dissociation","value":"HCD"}]}
\ No newline at end of file

diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small.mgf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/really_small.mgf Wed Feb 17 09:50:26 2021 +0000

[

b'@@ -0,0 +1,4772 @@\n+BEGIN IONS\n+TITLE=controllerType=0 controllerNumber=1 scan=36 [PRECURSOR=controllerType=0 controllerNumber=1 scan=35]\n+SCANS=36\n+RTINSECONDS=73.863181104\n+PEPMASS=675.248779296875\n+CHARGE=2+\n+121.3116455 920.2367553711\n+121.3347778 946.6901855469\n+121.3463058 1461.1103515625\n+121.3569946 1011.2686157227\n+121.3639221 1393.5522460938\n+121.3678589 1715.3167724609\n+121.3758316 1333.3702392578\n+121.3811340 1140.8778076172\n+121.3862915 1413.1467285156\n+121.3897552 1080.8319091797\n+121.3988113 1171.1282958984\n+121.4128799 1142.3867187500\n+121.4206085 970.0669555664\n+121.4236221 1064.1722412109\n+121.4289703 1163.8079833984\n+121.4328461 1044.6525878906\n+121.4409103 1707.4576416016\n+121.4438019 1236.5410156250\n+121.4485321 1075.5264892578\n+121.4606476 2245.1250000000\n+121.4682999 1375.6916503906\n+121.4912186 1075.6673583984\n+121.4947281 859.3981933594\n+121.5146103 923.2062988281\n+121.5266953 1103.3685302734\n+121.5407639 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diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small.mzml
--- a/test-data/really_small.mzml Sat Jul 25 16:26:42 2020 -0400
+++ b/test-data/really_small.mzml Wed Feb 17 09:50:26 2021 +0000

b'@@ -1,16 +1,17 @@\n <?xml version="1.0" encoding="utf-8"?>\n-<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" version="1.1.0" id="input" xmlns="http://psi.hupo.org/ms/mzml">\n+<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" version="1.1.0" id="really_small" xmlns="http://psi.hupo.org/ms/mzml">\n <cvList count="2">\n- <cv id="MS" fullName="Mass spectrometry ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" />\n+ <cv id="MS" fullName="Mass spectrometry ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" />\n <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />\n </cvList>\n <fileDescription>\n <fileContent>\n <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />\n <cvParam cvRef="MS" accession="MS:1000580" value="" name="MSn spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000810" value="" name="ion current chromatogram" />\n </fileContent>\n <sourceFileList count="1">\n- <sourceFile id="RAW1" name="input" location="./raws_folder/input.raw">\n+ <sourceFile id="RAW1" name="really_small" location="file:///really_small.raw">\n <cvParam cvRef="MS" accession="MS:1000768" value="" name="Thermo nativeID format" />\n <cvParam cvRef="MS" accession="MS:1000563" value="" name="Thermo RAW format" />\n <cvParam cvRef="MS" accession="MS:1000569" value="a6c0d318207b271d5e2f31b3302239e040c66dbe" name="SHA-1" />\n@@ -24,7 +25,7 @@\n </referenceableParamGroup>\n </referenceableParamGroupList>\n <softwareList count="1">\n- <software id="ThermoRawFileParser" version="1.1.9">\n+ <software id="ThermoRawFileParser" version="1.3.2">\n <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />\n </software>\n </softwareList>\n@@ -49,9 +50,12 @@\n <processingMethod order="0" softwareRef="ThermoRawFileParser">\n <cvParam cvRef="MS" accession="MS:1000544" value="" name="Conversion to mzML" />\n </processingMethod>\n+ <processingMethod order="1" softwareRef="ThermoRawFileParser">\n+ <cvParam cvRef="MS" accession="MS:1000035" value="" name="peak picking" />\n+ </processingMethod>\n </dataProcessing>\n </dataProcessingList>\n- <run id="input" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2019-03-25T11:30:48.075Z" defaultSourceFileRef="RAW1">\n+ <run id="really_small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2019-03-25T11:30:48.075Z" defaultSourceFileRef="RAW1">\n <spectrumList count="101" defaultDataProcessingRef="ThermoRawFileParserProcessing">\n <spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0" defaultArrayLength="136">\n <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />\n@@ -1447,8 +1451,8 @@\n <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=35">\n <isolationWindow>\n <cvParam cvRef="MS" accession="MS:1000827" value="675.248779296875" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" uni'..b'rollerType=0 controllerNumber=1 scan=88">\n <isolationWindow>\n <cvParam cvRef="MS" accession="MS:1000827" value="960.893493652344" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n </isolationWindow>\n <selectedIonList count="1">\n <selectedIon>\n@@ -4466,8 +4470,8 @@\n <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=88">\n <isolationWindow>\n <cvParam cvRef="MS" accession="MS:1000827" value="824.7021484375" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n </isolationWindow>\n <selectedIonList count="1">\n <selectedIon>\n@@ -4525,8 +4529,8 @@\n <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=88">\n <isolationWindow>\n <cvParam cvRef="MS" accession="MS:1000827" value="1072.44873046875" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n- <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n </isolationWindow>\n <selectedIonList count="1">\n <selectedIon>\n@@ -4674,8 +4678,8 @@\n </spectrum>\n </spectrumList>\n <chromatogramList count="1" defaultDataProcessingRef="ThermoRawFileParserProcessing">\n- <chromatogram id="base_peak_0" index="0" defaultArrayLength="101">\n- <cvParam cvRef="MS" accession="MS:1000235" value="" name="total ion current chromatogram" />\n+ <chromatogram id="BasePeak_0" index="0" defaultArrayLength="101">\n+ <cvParam cvRef="MS" accession="MS:1000628" value="" name="basepeak chromatogram" />\n <binaryDataArrayList count="2">\n <binaryDataArray encodedLength="1092">\n <cvParam cvRef="MS" accession="MS:1000595" value="" name="time array" unitAccession="UO:0000031" unitName="minute" unitCvRef="UO" />\n'

diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small_2.raw

Binary file test-data/really_small_2.raw has changed

diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small_3.raw

Binary file test-data/really_small_3.raw has changed

diff -r 26c6706bfb07 -r 92ac8e086317 test-data/really_small_ext.mzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/really_small_ext.mzml Wed Feb 17 09:50:26 2021 +0000

b'@@ -0,0 +1,4493 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<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" version="1.1.0" id="really_small" xmlns="http://psi.hupo.org/ms/mzml">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Mass spectrometry ontology" version="4.1.41" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" />\n+ <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000580" value="" name="MSn spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000810" value="" name="ion current chromatogram" />\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="really_small" location="file:///really_small.raw">\n+ <cvParam cvRef="MS" accession="MS:1000768" value="" name="Thermo nativeID format" />\n+ <cvParam cvRef="MS" accession="MS:1000563" value="" name="Thermo RAW format" />\n+ <cvParam cvRef="MS" accession="MS:1000569" value="a6c0d318207b271d5e2f31b3302239e040c66dbe" name="SHA-1" />\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="commonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1002416" value="" name="Orbitrap Fusion" />\n+ <cvParam cvRef="MS" accession="MS:1000529" value="FSN10188" name="instrument serial number" />\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="1">\n+ <software id="ThermoRawFileParser" version="1.3.2">\n+ <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="1">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="commonInstrumentParams" />\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" value="" name="nanoelectrospray" />\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000079" value="" name="fourier transform ion cyclotron resonance mass spectrometer" />\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" value="" name="inductive detector" />\n+ </detector>\n+ </componentList>\n+ </instrumentConfiguration>\n+ </instrumentConfigurationList>\n+ <dataProcessingList count="1">\n+ <dataProcessing id="ThermoRawFileParserProcessing">\n+ <processingMethod order="0" softwareRef="ThermoRawFileParser">\n+ <cvParam cvRef="MS" accession="MS:1000544" value="" name="Conversion to mzML" />\n+ </processingMethod>\n+ </dataProcessing>\n+ </dataProcessingList>\n+ <run id="really_small" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2019-03-25T11:30:48.075Z" defaultSourceFileRef="RAW1">\n+ <spectrumList count="101" defaultDataProcessingRef="ThermoRawFileParserProcessing">\n+ <spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0" defaultArrayLength="136">\n+ <cvParam cvRef="MS" accession="MS:1000511" value="1" name="ms level" />\n+ <cvParam cvRef="MS" accession="MS:1000579" value="" name="MS1 spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000130" value="" name="positive scan" />\n+ <cvParam cvRef="MS" accession="MS:1000285" value="464386.25" name="total ion current" />\n+ <cvParam cvRef="MS" accession="MS:1000127" value="" name="centroid spectrum" />\n+ <cvParam cvRef="MS" accession="MS:1000504" value="536.163879394531" name="base peak m/z" unitAccession="MS:1000040" 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encodedLength="1080">\n+ <cvParam cvRef="MS" accession="MS:1000595" value="" name="time array" unitAccession="UO:0000031" unitName="minute" unitCvRef="UO" />\n+ <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />\n+ 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</binaryDataArray>\n+ <binaryDataArray encodedLength="1080">\n+ <cvParam cvRef="MS" accession="MS:1000515" value="" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS" />\n+ <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />\n+ <binary>AAAAIIcx8UAAAAAgskflQAAAAOCzq+FAAAAAoCqh80AAAACgybe8QAAAAOBZCNpAAAAAoAhk60AAAAAAhXPaQAAAAAAKEtNAAAAAYKYR7kAAAABAjfTzQAAAAEBtEuBAAAAAYDdz2kAAAAAA3ZTNQAAAAIAriuVAAAAAQHVg5UAAAAAAsnTtQAAAAECf9ONAAAAAYIyJ00AAAABAtmXiQAAAAODVScxAAAAAYAXUwkAAAADgIEHSQAAAAADxsPBAAAAAoCCH80AAAADgy1DXQAAAACC8RMFAAAAAAGkQ4kAAAACgZUjJQAAAAKCG/sdAAAAAoHSIzkAAAABA9j/dQAAAAMCPt9xAAAAAgCYp9kAAAABgqvXlQAAAAOAUachAAAAAYG7210AAAAAglcvCQAAAAGBHveJAAAAA4MZo70AAAAAA5QnuQAAAAADtp+dAAAAAwMR1s0AAAAAAtnLXQAAAAOAKF+RAAAAAYE7l9EAAAADgHQXjQAAAACCrIsdAAAAAwHLyxEAAAACANJ73QAAAAIAxQfJAAAAA4DrR40AAAAAg7q37QAAAAMAZkPRAAAAAYC4G20AAAAAA87YCQQAAACDqGP5AAAAAIAM780AAAAAAiYD0QAAAAGAANAxBAAAAoErDMEEAAABgwlDHQAAAAAAfJElBAAAAAMoVVUEAAABAFhhxQQAAAODoGnBBAAAAYNFKcUEAAACApAQvQQAAACANNghBAAAAAFMSEEEAAACgyA75QAAAACCLufNAAAAAIMc7+EAAAABAkV/nQAAAAOBb9eNAAAAAwClV9kAAAAAgVp3eQAAAAGCgxNlAAAAAIBfiYUEAAACA4KvsQAAAAGC8DOhAAAAAILJO0UAAAABA7OHbQAAAAGADVtRAAAAAIIyK0kAAAADAkE7ZQAAAAAA5usVAAAAAAP+1S0EAAADgdBXNQAAAAODWvNBAAAAAgLxuykAAAACgk87SQAAAAODq8M9AAAAAgIXn0EAAAADAg/zLQAAAAABzi89AAAAAoDeO0kAAAAAAJkC+QAAAAGC/FPRAAAAAoHLxA0EAAACA/qf0QA==</binary>\n+ </binaryDataArray>\n+ </binaryDataArrayList>\n+ </chromatogram>\n+ </chromatogramList>\n+ </run>\n+</mzML>\n\\ No newline at end of file\n'

diff -r 26c6706bfb07 -r 92ac8e086317 thermo_converter.xml
--- a/thermo_converter.xml Sat Jul 25 16:26:42 2020 -0400
+++ b/thermo_converter.xml Wed Feb 17 09:50:26 2021 +0000

[

b'@@ -1,145 +1,202 @@\n-<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3+galaxy0">\n+<tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy0" profile="20.05">\n <description>RAW file converter</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.3.2</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="1.2.3">thermorawfileparser</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">thermorawfileparser</requirement>\n </requirements>\n+ <stdio>\n+ <regex match="ERROR" source="both" level="fatal" description="Fatal error"/>\n+ </stdio>\n+ <version_command><![CDATA[ThermoRawFileParser.sh --version]]></version_command>\n <command>\n <![CDATA[\n #import re\n \n-mkdir ./raws_folder &&\n-mkdir ./output_folder &&\n-#for $input_raw in $input_files:\n- #set $input_name = re.sub(\'[^\\w\\-\\.]\', \'_\',$input_raw.element_identifier.split(\'/\')[-1].replace(".raw", "") + ".raw")\n- ln -s -f \'${input_raw}\' \'./raws_folder/${input_name}\' &&\n-#end for\n+#set $input_name = re.sub(\'[^\\w\\-\\.]\', \'_\', $input_file.element_identifier.replace(".raw", "") + ".raw")\n+ln -s -f \'$input_file\' \'$input_name\' &&\n \n ThermoRawFileParser.sh\n- -d=./raws_folder\n- -o=./output_folder\n- -f=$output_format\n+ --input=\'$input_name\'\n+ --output_file=\'$output\'\n+ -f=$format_cond.output_format\n #if $output_metadata_selector != "off":\n- --metadata="${output_metadata_selector}"\n+ --metadata="$output_metadata_selector"\n+ --metadata_output_file=\'$output_metadata\'\n+ #end if\n+ #if $format_cond.output_format == "0"\n+ $format_cond.mgfPrecursor\n #end if\n- $zlib_boolean\n- $peakpicking_boolean\n+ #if $format_cond.output_format in [\'1\', \'2\']\n+ $format_cond.zlib_boolean\n+ $format_cond.peakpicking_boolean\n+ #end if\n $ignore_instrument_errors_boolean\n-\n+ $allDetectors\n+ $includeExceptionData\n+ #if $msLevel != \'\'\n+ --msLevel="$msLevel"\n+ #end if\n ]]>\n </command>\n <inputs>\n- <param name="input_files" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"\n- optional="False" />\n-\n- <param name="output_format" type="select" label="Output format">\n- <option value="0">mgf</option>\n- <option value="1" selected="True">mzml</option>\n- <option value="2">Indexed mzml</option>\n- </param>\n-\n- <param name="zlib_boolean" type="boolean" truevalue="" falsevalue="-z" checked="true"\n- label="Use zlib compression for the m/z ratios and intensities" help="" />\n-\n- <param name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"\n- label="Use the peak picking provided by the native thermo library" help="" />\n-\n- <param name="ignore_instrument_errors_boolean" type="boolean" truevalue="-e" falsevalue="" checked="true"\n- label="Ignore missing instrument properties" help="If false, it stops the conversion if instrument properties are missing" />\n-\n- <param name="output_metadata_selector" type="select" label="Output metadata" >\n+ <param argument="--input" name="input_file" type="data" format="thermo.raw" label="Thermo RAW file" help="" optional="False"/>\n+ <conditional name="format_cond">\n+ <param argument="--format" name="output_format" type="select" label="Output format">\n+ <option value="0">mgf</option>\n+ <option value="1" selected="True">mzml</option>\n+ <option value="2">Indexed mzml</option>\n+ \n+ </param>\n+ <when value="0">\n+ <param argument="--mgfPrecursor" type="boolean" truevalue="--mgfPrecursor" falsevalue="" label="Include precursor scan number in MGF file" help=""/>\n+ </when>\n+ <when value="1">\n+ <para'..b'eakpicking_boolean" value="false"/>\n+ </conditional>\n+ <param name="output_metadata_selector" value="0"/>\n+ <output name="output" file="really_small_ext.mzml" ftype="mzml"/>\n+ <output name="output_metadata" value="really_small.json" ftype="json"/>\n+ <assert_command>\n+ <not_has_text text="--mgfPrecursor"></not_has_text>\n+ <has_text text="-z "></has_text>\n+ <has_text text="-p "></has_text>\n+ </assert_command>\n </test>\n \n- \n+ \n <test expect_num_outputs="2">\n- <param name="input_files" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>\n- <param name="output_format" value="0"/>\n- <param name="output_metadata_selector" value="0"/>\n- <output_collection name="output_mgf_collection" type="list" count="3"/>\n- <output_collection name="output_metadata_collection" type="list" count="3"/>\n+ <param name="input_file" value="really_small.raw" ftype="thermo.raw"/>\n+ <conditional name="format_cond">\n+ <param name="output_format" value="2"/>\n+ </conditional>\n+ <param name="output_metadata_selector" value="1"/>\n+ <param name="ignore_instrument_errors_boolean" value="true"/>\n+ <param name="allDetectors" value="true"/>\n+ <param name="includeExceptionData" value="--includeExceptionData"/>\n+ <param name="msLevel" value="1"/>\n+ <output name="output" value="really_small.indexed_mzML" ftype="mzml"/>\n+ <output name="output_metadata" ftype="txt">\n+ <assert_contents>\n+ <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>\n+ <has_text text="Instrument name=Orbitrap Fusion"/>\n+ <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>\n+ <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>\n+ <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>\n+ <has_text text="Number of scans=101"/>\n+ <has_text text="Scan range=1;101"/>\n+ <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>\n+ <has_text text="Time range=0.89;1.59"/>\n+ <has_text text="Mass range=120.0000;2000.0000"/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <not_has_text text="--mgfPrecursor"></not_has_text>\n+ <has_text text="-e "/>\n+ <has_text text="--allDetectors"/>\n+ <has_text text="--includeExceptionData"/>\n+ <has_text text="--msLevel="1""/>\n+ </assert_command>\n </test>\n+\n </tests>\n <help>\n <![CDATA[\n@@ -149,12 +206,6 @@\n ]]>\n </help>\n <citations>\n- <citation type="bibtex">@misc{Galaxy Proteomics Tools,\n- author = {Niels Hulstaert, et al.},\n- title = {Galaxy Proteomics Tools},\n- publisher = {GitHub},\n- journal = {GitHub repository},\n- year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}\n- </citation>\n+ <citation type="doi">10.1021/acs.jproteome.9b00328</citation>\n </citations>\n </tool>\n'