Repository 'thermo_raw_file_converter'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter

Changeset 10:b9b385097f13 (2021-04-10)
Previous changeset 9:92ac8e086317 (2021-02-17) Next changeset 11:19e45916daf9 (2021-04-21)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
modified:
test-data/really_small.indexed_mzML
test-data/really_small.json
test-data/really_small.mzml
test-data/really_small_ext.mzml
thermo_converter.xml
b
diff -r 92ac8e086317 -r b9b385097f13 test-data/really_small.indexed_mzML
--- a/test-data/really_small.indexed_mzML Wed Feb 17 09:50:26 2021 +0000
+++ b/test-data/really_small.indexed_mzML Sat Apr 10 15:56:48 2021 +0000
b
b'@@ -1,8 +1,8 @@\n-\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\n+<?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="MS" fullName="Mass spectrometry ontology" version="4.1.48" 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@@ -26,8 +26,8 @@\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 id="ThermoRawFileParser" version="1.3.3">\n+        <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" />\n       </software>\n     </softwareList>\n     <instrumentConfigurationList count="1">\n@@ -2695,78 +2695,78 @@\n   </mzML>\n   <indexList count="2">\n     <index name="spectrum">\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=1">3723</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=2">8681</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=3">13513</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=4">18208</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=5">23318</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=6">27279</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=7">31892</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=8">36768</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=9">41110</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=10">45420</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=11">50636</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=12">55790</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=13">60258</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=14">64661</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=15">68821</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=16">73547</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=17">78095</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=18">82897</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=19">87489</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=20">91850</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=21">96634</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=22">100711</offset>\n-      <offset idRef="controllerType=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 scan=26">119034</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=27">123347</offset>\n-      <offset idRef="controllerType=0 controllerNumber=1 scan=28">127385</offset>\n-      <offset idRef="controllerType=0 controllerNumber'..b'lerType=0 controllerNumber=1 scan=25">113860</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=26">118991</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=27">123304</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=28">127342</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=29">132138</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=30">136192</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=31">140294</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=32">144559</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=33">149090</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=34">153463</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=35">158870</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=37">163704</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=39">168004</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=40">172608</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=41">177642</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=42">182768</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=43">187467</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=44">191436</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=45">195870</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=46">200672</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=47">206011</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=50">210647</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=51">216058</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=52">221276</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=53">226017</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=54">231567</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=55">237114</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=56">241501</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=57">247221</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=58">252718</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=59">257835</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=60">263534</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=61">272252</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=63">281997</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=64">293023</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=65">304825</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=66">312583</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=67">324901</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=79">338860</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=88">354346</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=99">365556</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=100">371876</offset>\n+      <offset idRef="controllerType=0 controllerNumber=1 scan=101">379207</offset>\n     </index>\n     <index name="chromatogram">\n-      <offset idRef="BasePeak_0">385580</offset>\n+      <offset idRef="BasePeak_0">385537</offset>\n     </index>\n   </indexList>\n-  <indexListOffset>388584</indexListOffset>\n-  <fileChecksum>8a5e1e41cfbb53217242d8cac4a2934375c76ca9</fileChecksum>\n+  <indexListOffset>388541</indexListOffset>\n+  <fileChecksum>d17fa5e67c8f89705eec985e7029ba040ec4ff8c</fileChecksum>\n </indexedmzML>\n\\ No newline at end of file\n'
b
diff -r 92ac8e086317 -r b9b385097f13 test-data/really_small.json
--- a/test-data/really_small.json Wed Feb 17 09:50:26 2021 +0000
+++ b/test-data/really_small.json Sat Apr 10 15:56:48 2021 +0000
[
@@ -1,1 +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
+{"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"}],"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"},{"accession":"NCIT:C111093","cvLabel":"NCIT","name":"Software Version","value":"3.1.2412.17"}],"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"}],"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"}],"SampleData":[{"accession":"NCIT:C43378","cvLabel":"NCIT","name":"Row","value":"1"}]}
\ No newline at end of file
b
diff -r 92ac8e086317 -r b9b385097f13 test-data/really_small.mzml
--- a/test-data/really_small.mzml Wed Feb 17 09:50:26 2021 +0000
+++ b/test-data/really_small.mzml Sat Apr 10 15:56:48 2021 +0000
b
b'@@ -1,7 +1,7 @@\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="MS" fullName="Mass spectrometry ontology" version="4.1.48" 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@@ -25,8 +25,8 @@\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 id="ThermoRawFileParser" version="1.3.3">\n+      <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" />\n     </software>\n   </softwareList>\n   <instrumentConfigurationList count="1">\n@@ -1448,11 +1448,11 @@\n           </scan>\n         </scanList>\n         <precursorList count="1">\n-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=35">\n+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=34">\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="0.699999988079071" 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+              <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             </isolationWindow>\n             <selectedIonList count="1">\n               <selectedIon>\n@@ -1546,11 +1546,11 @@\n           </scan>\n         </scanList>\n         <precursorList count="1">\n-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=37">\n+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=35">\n             <isolationWindow>\n               <cvParam cvRef="MS" accession="MS:1000827" value="407.919311523438" name="isolation window target m/z" 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+              <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             </isolationWindow>\n             <selectedIonList count="1">\n               <selectedIon>\n@@ -1956,11 +1956,11 @@\n           </scan>\n         </scanList>\n         <precursorList count="1">\n-          <precursor spectrumRef="controllerTy'..b'me="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n             </isolationWindow>\n             <selectedIonList count="1">\n               <selectedIon>\n@@ -4408,11 +4408,11 @@\n           </scan>\n         </scanList>\n         <precursorList count="1">\n-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=88">\n+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=79">\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="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n-              <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079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b
diff -r 92ac8e086317 -r b9b385097f13 test-data/really_small_ext.mzml
--- a/test-data/really_small_ext.mzml Wed Feb 17 09:50:26 2021 +0000
+++ b/test-data/really_small_ext.mzml Sat Apr 10 15:56:48 2021 +0000
b
b'@@ -1,7 +1,7 @@\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="MS" fullName="Mass spectrometry ontology" version="4.1.48" 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@@ -25,8 +25,8 @@\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 id="ThermoRawFileParser" version="1.3.3">\n+      <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" />\n     </software>\n   </softwareList>\n   <instrumentConfigurationList count="1">\n@@ -82,11 +82,13 @@\n           <binaryDataArray encodedLength="1452">\n             <cvParam cvRef="MS" accession="MS:1000514" value="" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />\n             <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />\n+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />\n             <binary>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</binary>\n           </binaryDataArray>\n           <binaryDataArray encodedLength="1452">\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+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />\n             <binary>AAAAYKG0h0AAAAAgixyBQAAAACDS0YJAAAAAICjHj0AAAABApauIQAAAACBFlYNAAAAAIGfEgkAAAACg5tmKQAAAAODow4lAAAAAIKyrtkAAAACg6uuYQAAAAEAhHbdAAAAAoA9to0AAAAAAnGesQAAAAIA+i5VAAAAAwKyfg0AAAABAL1q2QAAAAKCeSqRAAAAAAB/pikAAAADgDd2VQAAAAEDzroNAAAAA4Hhph0AAAAAAgMfCQAAAACCVXqJAAAAAgJAfkEAAAABgXfqQQAAAACA4JuNAAAAAoIl9xEAAAADgpOCEQAAAAEDOB4lAAAAAIAaSu0AAAADgB1elQAAAAADTGIRAAAAAoFLOoUAAAADg1'..b'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</binary>\n           </binaryDataArray>\n         </binaryDataArrayList>\n@@ -4479,11 +4681,13 @@\n           <binaryDataArray 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+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />\n             <binary>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</binary>\n           </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+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />\n             <binary>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</binary>\n           </binaryDataArray>\n         </binaryDataArrayList>\n'
b
diff -r 92ac8e086317 -r b9b385097f13 thermo_converter.xml
--- a/thermo_converter.xml Wed Feb 17 09:50:26 2021 +0000
+++ b/thermo_converter.xml Sat Apr 10 15:56:48 2021 +0000
[
@@ -1,7 +1,7 @@
 <tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy0" profile="20.05">
     <description>RAW file converter</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.3.2</token>
+        <token name="@TOOL_VERSION@">1.3.3</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">thermorawfileparser</requirement>
@@ -173,12 +173,12 @@
                     <has_text text="Instrument name=Orbitrap Fusion"/>
                     <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>
                     <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>
-                    <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>
+                    <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.5]"/>
                     <has_text text="Number of scans=101"/>
                     <has_text text="Scan range=1;101"/>
-                    <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>
-                    <has_text text="Time range=0.89;1.59"/>
-                    <has_text text="Mass range=120.0000;2000.0000"/>
+                    <has_text text="Scan start time=0.89"/>
+                    <has_text text="Time range=0.89"/>
+                    <has_text text="Mass range=120;2000"/>
                 </assert_contents>
             </output>
             <assert_command>