diff test-data/small-mzWindow.mzML @ 10:9d5de24e6ef7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:25:48 -0500
parents dd4ba10d0c45
children 6153e8ada1ee
line wrap: on
line diff
--- a/test-data/small-mzWindow.mzML	Wed Dec 07 16:43:07 2016 -0500
+++ b/test-data/small-mzWindow.mzML	Sat Feb 23 06:25:48 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="3.79.0" 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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <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_3.0.8990" version="3.0.8990">
+      <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_3.0.8990">
+        <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_3.0.8990">
+        <processingMethod order="1" softwareRef="pwiz_3.0.19038">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -2716,59 +2719,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5578</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=2">10683</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=3">15932</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=4">22747</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=5">30436</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=6">37948</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=7">45349</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=8">52665</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=9">57721</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=10">62818</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=11">69858</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=12">77514</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=13">84734</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=14">92162</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=15">99590</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=16">105128</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=17">110415</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=18">117450</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=19">125084</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=20">132294</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=21">139710</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=22">147220</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=23">152895</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=24">157870</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=25">164987</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=26">172691</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=27">180004</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=28">187246</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=29">194792</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=30">200481</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=31">205775</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=32">213371</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=33">220506</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=34">227942</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=35">235063</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=36">240414</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=37">245583</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=38">252620</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=39">260408</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=40">267584</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=41">275118</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=42">282378</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=43">288000</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=44">293258</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=45">300375</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=46">308050</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=47">315301</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=48">322658</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=2">10803</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=3">16052</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=4">22867</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=5">30556</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=6">38068</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=7">45469</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=8">52785</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=9">57841</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=10">62938</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=11">69978</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=12">77634</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=13">84854</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=14">92282</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=15">99710</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=16">105248</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=17">110535</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=18">117570</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=19">125204</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=20">132414</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=21">139830</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=22">147340</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=23">153015</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=24">157990</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=25">165107</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=26">172811</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=27">180124</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=28">187366</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=29">194912</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=30">200601</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=31">205895</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=32">213491</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=33">220626</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=34">228062</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=35">235183</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=36">240534</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=37">245703</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=38">252740</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=39">260528</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=40">267704</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=41">275238</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=42">282498</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=43">288120</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=44">293378</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=45">300495</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=46">308170</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=47">315421</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">322778</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">330016</offset>
+      <offset idRef="TIC">330136</offset>
     </index>
   </indexList>
-  <indexListOffset>331966</indexListOffset>
-  <fileChecksum>eb547bb98aaca512c02f4ad9f58e484f3f1b96da</fileChecksum>
+  <indexListOffset>332086</indexListOffset>
+  <fileChecksum>4c52055cc16e42e05ef5a8eae5df244ea6ead1ac</fileChecksum>
 </indexedmzML>