Mercurial > repos > galaxyp > msconvert

diff test-data/small-threshold.mzML @ 15:6153e8ada1ee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
author galaxyp
date Mon, 30 Nov 2020 16:01:10 +0000
parents 9d5de24e6ef7
children
line wrap: on
line diff
--- a/test-data/small-threshold.mzML	Mon Nov 16 17:25:12 2020 +0000
+++ b/test-data/small-threshold.mzML	Mon Nov 30 16:01:10 2020 +0000
@@ -2,7 +2,7 @@
 <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="4.1.12" URI="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"/>
+      <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.1.41" 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>
@@ -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="d795eccea21733d1e5cc192bcf2e1c389ed59c20"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="8e3d422853cbd71cc5f2af6422e0893caf6447dc"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -30,17 +30,14 @@
         <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN06061F"/>
       </referenceableParamGroup>
     </referenceableParamGroupList>
-    <softwareList count="4">
+    <softwareList count="3">
       <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_3.0.19038" 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">
+      <software id="pwiz_3.0.20287" version="3.0.20287">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -85,11 +82,12 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.19038">
+        <processingMethod order="0" softwareRef="pwiz_3.0.20287">
           <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.19038">
+        <processingMethod order="1" softwareRef="pwiz_3.0.20287">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
+          <userParam name="CantWaiT (continuous wavelet transform) peak picker"/>
         </processingMethod>
       </dataProcessing>
     </dataProcessingList>
@@ -2719,59 +2717,59 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
-      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5698</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=2">10070</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=3">14461</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=4">20485</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26507</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=6">32496</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=7">38482</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=8">44503</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=9">48866</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=10">53225</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=11">59254</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=12">65279</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=13">71260</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=14">77249</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=15">83242</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=16">87618</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=17">92003</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=18">98035</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=19">104058</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=20">110037</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=21">116034</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=22">122033</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=23">126406</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=24">130744</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=25">136774</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=26">142803</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=27">148781</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=28">154772</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=29">160787</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=30">165158</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=31">169558</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=32">175583</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=33">181555</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=34">187540</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=35">193486</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=36">197863</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=37">202238</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=38">208268</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=39">214301</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=40">220286</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=41">226289</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=42">232266</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=43">236630</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=44">241026</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=45">247052</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=46">253068</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=47">259036</offset>
-      <offset idRef="controllerType=0 controllerNumber=1 scan=48">265014</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=1">5614</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=2">9986</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=3">14377</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=4">20401</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=5">26423</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=6">32412</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=7">38398</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=8">44419</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=9">48782</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=10">53141</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=11">59170</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=12">65195</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=13">71176</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=14">77165</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=15">83158</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=16">87534</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=17">91919</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=18">97951</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=19">103974</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=20">109953</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=21">115950</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=22">121949</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=23">126322</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=24">130660</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=25">136690</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=26">142719</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=27">148697</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=28">154688</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=29">160703</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=30">165074</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=31">169474</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=32">175499</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=33">181471</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=34">187456</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=35">193402</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=36">197779</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=37">202154</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=38">208184</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=39">214217</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=40">220202</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=41">226205</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=42">232182</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=43">236546</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=44">240942</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=45">246968</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=46">252984</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=47">258952</offset>
+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">264930</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">271077</offset>
+      <offset idRef="TIC">270993</offset>
     </index>
   </indexList>
-  <indexListOffset>273027</indexListOffset>
-  <fileChecksum>b1908e0016bbf6bf4fc21daa511924db77237312</fileChecksum>
+  <indexListOffset>272943</indexListOffset>
+  <fileChecksum>95a42b81dbc77e94be64a5f6577fe211616e6069</fileChecksum>
 </indexedmzML>