Mercurial > repos > galaxyp > thermo_raw_file_converter

changeset 10:b4fba9c32736 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
author galaxyp
date Sat, 10 Apr 2021 15:55:37 +0000
parents d160679217db
children 91f972c0f7b1
files 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
diffstat 5 files changed, 494 insertions(+), 290 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/really_small.indexed_mzML	Wed Feb 17 09:50:00 2021 +0000
+++ b/test-data/really_small.indexed_mzML	Sat Apr 10 15:55:37 2021 +0000
@@ -1,8 +1,8 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <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">
   <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">
     <cvList count="2">
-      <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" />
+      <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" />
       <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />
     </cvList>
     <fileDescription>
@@ -26,8 +26,8 @@
       </referenceableParamGroup>
     </referenceableParamGroupList>
     <softwareList count="1">
-      <software id="ThermoRawFileParser" version="1.3.2">
-        <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />
+      <software id="ThermoRawFileParser" version="1.3.3">
+        <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" />
       </software>
     </softwareList>
     <instrumentConfigurationList count="1">
@@ -2695,78 +2695,78 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=67">324901</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=100">371876</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=101">379207</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="BasePeak_0">385580</offset>
+      <offset idRef="BasePeak_0">385537</offset>
     </index>
   </indexList>
-  <indexListOffset>388584</indexListOffset>
-  <fileChecksum>8a5e1e41cfbb53217242d8cac4a2934375c76ca9</fileChecksum>
+  <indexListOffset>388541</indexListOffset>
+  <fileChecksum>d17fa5e67c8f89705eec985e7029ba040ec4ff8c</fileChecksum>
 </indexedmzML>
\ No newline at end of file
--- a/test-data/really_small.json	Wed Feb 17 09:50:00 2021 +0000
+++ b/test-data/really_small.json	Sat Apr 10 15:55:37 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
--- a/test-data/really_small.mzml	Wed Feb 17 09:50:00 2021 +0000
+++ b/test-data/really_small.mzml	Sat Apr 10 15:55:37 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <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">
   <cvList count="2">
-    <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" />
+    <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" />
     <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" />
   </cvList>
   <fileDescription>
@@ -25,8 +25,8 @@
     </referenceableParamGroup>
   </referenceableParamGroupList>
   <softwareList count="1">
-    <software id="ThermoRawFileParser" version="1.3.2">
-      <cvParam cvRef="MS" accession="MS:1000799" value="ThermoRawFileParser" name="custom unreleased software tool" />
+    <software id="ThermoRawFileParser" version="1.3.3">
+      <cvParam cvRef="MS" accession="MS:1003145" name="ThermoRawFileParser" />
     </software>
   </softwareList>
   <instrumentConfigurationList count="1">
@@ -1448,11 +1448,11 @@
           </scan>
         </scanList>
         <precursorList count="1">
-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=35">
+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=34">
             <isolationWindow>
               <cvParam cvRef="MS" accession="MS:1000827" value="675.248779296875" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
             </isolationWindow>
             <selectedIonList count="1">
               <selectedIon>
@@ -1546,11 +1546,11 @@
           </scan>
         </scanList>
         <precursorList count="1">
-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=37">
+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=35">
             <isolationWindow>
               <cvParam cvRef="MS" accession="MS:1000827" value="407.919311523438" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
             </isolationWindow>
             <selectedIonList count="1">
               <selectedIon>
@@ -1956,11 +1956,11 @@
           </scan>
         </scanList>
         <precursorList count="1">
-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=47">
+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=46">
             <isolationWindow>
               <cvParam cvRef="MS" accession="MS:1000827" value="436.341217041016" name="isolation window target m/z" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000828" value="0.699999988079071" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
-              <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000828" value="0.7" name="isolation window lower offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+              <cvParam cvRef="MS" accession="MS:1000829" value="0.7" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
             </isolationWindow>
             <selectedIonList count="1">
               <selectedIon>
@@ -2015,11 +2015,11 @@
           </scan>
         </scanList>
         <precursorList count="1">
-          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=47">
+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=46">
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--- a/test-data/really_small_ext.mzml	Wed Feb 17 09:50:00 2021 +0000
+++ b/test-data/really_small_ext.mzml	Sat Apr 10 15:55:37 2021 +0000
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@@ -2513,11 +2639,13 @@
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             <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />
+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />
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         </binaryDataArrayList>
@@ -2624,11 +2756,13 @@
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             <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />
+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />
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@@ -3323,11 +3481,11 @@
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+          <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=67">
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-              <cvParam cvRef="MS" accession="MS:1000829" value="0.699999988079071" name="isolation window upper offset" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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@@ -3345,11 +3503,13 @@
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+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />
             <binary>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</binary>
           </binaryDataArray>
           <binaryDataArray encodedLength="1080">
             <cvParam cvRef="MS" accession="MS:1000515" value="" name="intensity array" unitAccession="MS:1000131" unitName="number of counts" unitCvRef="MS" />
             <cvParam cvRef="MS" accession="MS:1000523" value="" name="64-bit float" />
+            <cvParam cvRef="MS" accession="MS:1000576" value="" name="no compression" />
             <binary>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</binary>
           </binaryDataArray>
         </binaryDataArrayList>
--- a/thermo_converter.xml	Wed Feb 17 09:50:00 2021 +0000
+++ b/thermo_converter.xml	Sat Apr 10 15:55:37 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>