Mercurial > repos > galaxyp > msconvert

diff test-data/small-ms-level-filter.mzML @ 7:e638f7fad66a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:21:27 -0500
parents 6b6bba73eadb
children 052798dd73dd
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--- a/test-data/small-ms-level-filter.mzML	Tue Mar 14 16:52:39 2017 -0400
+++ b/test-data/small-ms-level-filter.mzML	Sat Feb 23 06:21:27 2019 -0500
@@ -2,8 +2,8 @@
 <indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">
   <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="small" version="1.1.0">
     <cvList count="2">
-      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
-      <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="UO" fullName="Unit Ontology" version="09:04:2014" URI="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo"/>
     </cvList>
     <fileDescription>
       <fileContent>
@@ -11,7 +11,7 @@
         <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/>
       </fileContent>
       <sourceFileList count="3">
-        <sourceFile id="RAW1" name="small.RAW" location="file:///C:\pwiz-src\trunk\pwiz\example_data">
+        <sourceFile id="RAW1" name="small.RAW" location="file:///">
           <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>
           <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>
           <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="b43e9286b40e8b5dbc0dfa2e428495769ca96a96"/>
@@ -20,7 +20,7 @@
           <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
-          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -30,14 +30,17 @@
         <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
       </referenceableParamGroup>
     </referenceableParamGroupList>
-    <softwareList count="3">
+    <softwareList count="4">
       <software id="Xcalibur" version="1.1 Beta 7">
         <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>
       </software>
       <software id="pwiz" version="3.0.8981">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.9987" version="3.0.9987">
+      <software id="pwiz_3.0.19038" version="3.0.19038">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
+      </software>
+      <software id="pwiz_3.0.19044" version="3.0.19044">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +85,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
+        <processingMethod order="0" softwareRef="pwiz_3.0.19038">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.9987">
+        <processingMethod order="1" softwareRef="pwiz_3.0.19038">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -2156,45 +2159,45 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=3">5698</offset>
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">338603</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">347712</offset>
+      <offset idRef="TIC">347833</offset>
     </index>
   </indexList>
-  <indexListOffset>349662</indexListOffset>
-  <fileChecksum>a9a8b2244bb3a277a399a710506652c0968ed670</fileChecksum>
+  <indexListOffset>349783</indexListOffset>
+  <fileChecksum>b37853cea35a8233460f48bc42abefd34f982729</fileChecksum>
 </indexedmzML>