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

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/BrukerBafTest.mzML	Sat Feb 23 06:25:48 2019 -0500
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="utf-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="BrukerBafTest" 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="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>
+        <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+      </fileContent>
+      <sourceFileList count="1">
+        <sourceFile id="BrukerBafTest.d_x005c_Analysis.baf" name="Analysis.baf" location="file:///">
+          <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF format" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="5e1b8f06983c2e671a4a96714721c327f1e67ee1"/>
+        </sourceFile>
+      </sourceFileList>
+    </fileDescription>
+    <referenceableParamGroupList count="1">
+      <referenceableParamGroup id="CommonInstrumentParams">
+        <cvParam cvRef="MS" accession="MS:1001556" name="Bruker Daltonics apex series" value=""/>
+      </referenceableParamGroup>
+    </referenceableParamGroupList>
+    <softwareList count="3">
+      <software id="BAF2SQL" version="2.7.300.20-112">
+        <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/>
+        <userParam name="software name" value="BAF2SQL"/>
+      </software>
+      <software id="apexControl" version="ApexControl 3.0.0.alpha.35 (development version, April 18, 2008)">
+        <cvParam cvRef="MS" accession="MS:1000706" name="apexControl" value=""/>
+      </software>
+      <software id="pwiz_Reader_Bruker" version="3.0.19044">
+        <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
+      </software>
+    </softwareList>
+    <instrumentConfigurationList count="1">
+      <instrumentConfiguration id="IC1">
+        <referenceableParamGroupRef ref="CommonInstrumentParams"/>
+        <componentList count="3">
+          <source order="1">
+            <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" value=""/>
+            <cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" value=""/>
+          </source>
+          <analyzer order="2">
+            <cvParam cvRef="MS" accession="MS:1000079" name="fourier transform ion cyclotron resonance mass spectrometer" value=""/>
+          </analyzer>
+          <detector order="3">
+            <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>
+          </detector>
+        </componentList>
+        <softwareRef ref="apexControl"/>
+      </instrumentConfiguration>
+    </instrumentConfigurationList>
+    <dataProcessingList count="1">
+      <dataProcessing id="pwiz_Reader_Bruker_conversion">
+        <processingMethod order="0" softwareRef="pwiz_Reader_Bruker">
+          <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/>
+        </processingMethod>
+        <processingMethod order="1" softwareRef="pwiz_Reader_Bruker">
+          <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
+          <userParam name="Bruker/Agilent/CompassXtract peak picking"/>
+        </processingMethod>
+      </dataProcessing>
+    </dataProcessingList>
+    <run id="BrukerBafTest" defaultInstrumentConfigurationRef="IC1" startTimeStamp="2008-11-04T10:55:29Z" defaultSourceFileRef="BrukerBafTest.d_x005c_Analysis.baf">
+      <spectrumList count="1" defaultDataProcessingRef="pwiz_Reader_Bruker_conversion">
+        <spectrum index="0" id="scan=1" defaultArrayLength="71">
+          <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+          <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
+          <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="7.81485056e08"/>
+          <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="5.704013312e09"/>
+          <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/>
+          <scanList count="1">
+            <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/>
+            <scan>
+              <scanWindowList count="1">
+                <scanWindow>
+                  <cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="347.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                  <cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+                </scanWindow>
+              </scanWindowList>
+            </scan>
+          </scanList>
+          <binaryDataArrayList count="2">
+            <binaryDataArray encodedLength="744">
+              <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+              <binary>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</binary>
+            </binaryDataArray>
+            <binaryDataArray encodedLength="396">
+              <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
+              <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+              <binary>eJwBHAHj/rDDDUyYqRlNHLfVSxCnz0tc0wNLIDP1SmBcI0wQODFMYEmGTYgzNkswU3FNYM99S4DvDEuAMXBNgDszTPB3ik3gYWBMcEOoS2DxQ0sgjjlLgEhLS6D3jUug3GJNUHMlToAmSkwAz7RLAKpPSwBFDkuAY2dLIGWbTID6CU0AvElLAB7zSmCQKkuAQKVLQIj0S+Bbk0wQUjpO4L3LS6C+kEvAXiNLwKgTS8DUMkxg5m5MoNNNTaD2gE3gcihLIA9ES2C5iUuAQARLQIwES4BHNEuA7qdLwMYuS4AHeEvAxgtLwKW6S8BuokvAQVpMQC09TEAwnUvAXlNNAHxfSyALAE2AYt5LgAduS8Ayvk2Ao1hLwAIsSwDi9EqAPGFLsyVy9w==</binary>
+            </binaryDataArray>
+          </binaryDataArrayList>
+        </spectrum>
+      </spectrumList>
+    </run>
+  </mzML>
+  <indexList count="2">
+    <index name="spectrum">
+      <offset idRef="scan=1">4166</offset>
+    </index>
+    <index name="chromatogram">
+    </index>
+  </indexList>
+  <indexListOffset>7590</indexListOffset>
+  <fileChecksum>e6b4d51fdbe306f0823fe1cb583e7ec52629303f</fileChecksum>
+</indexedmzML>