# HG changeset patch
# User galaxyp
# Date 1489524313 14400
# Node ID b00023193f6e874c82e6515929f6880d639b1e63
# Parent  5f8848c7d7b7afd7335c8adfeaeb0fd0658567cb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848

diff -r 5f8848c7d7b7 -r b00023193f6e msconvert_macros.xml
--- a/msconvert_macros.xml	Fri Apr 08 15:46:25 2016 -0400
+++ b/msconvert_macros.xml	Tue Mar 14 16:45:13 2017 -0400
@@ -1,34 +1,39 @@
 <macros>
   <xml name="generic_requirements">
     <requirements>
-      <requirement type="package" version="3.0.9016">proteowizard</requirement>
+      <requirement type="package" version="3.0.9992">proteowizard</requirement>
     </requirements>
   </xml>
-  <token name="@VERSION@">3.0</token>
+  <token name="@VERSION@">3.0.9992</token>
   
   <xml name="msconvertCommand">
     <command interpreter="python">
 <![CDATA[
     #import re
     #set $ext = $input.ext
+
+    ## sanitize display name for use as temp filename
+    #set basename = 'pwiz_in'
+    
+    #if hasattr($input, 'display_name')
+      ## explicit inclusion or exclusion ??
+      #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
+      ##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name)
+    #end if
+
     msconvert_wrapper.py
+
     #if $ext == 'wiff':
-      #set basename = 'absciex'
-      #if hasattr($input, 'display_name')
-        #set basename = $re.sub('\W','_',$input.display_name)
-      #end if
-      --input=${input.extra_files_path}/wiff
-      --input_name='${basename}.wiff
-      --implicit=${input.extra_files_path}/wiff_scan
-      --input=${input.extra_files_path}/wiff_scan
-      --input_name='${basename}.wiff.scan
+      --input='${input.extra_files_path}/wiff'
+      --input_name='${basename}.wiff'
+      --implicit='${input.extra_files_path}/wiff_scan'
+      --input='${input.extra_files_path}/wiff_scan'
+      --input_name='${basename}.wiff.scan'
     #else
-      --input=${input}
-      #if hasattr($input, 'display_name')
-      --input_name='${input.display_name}'
-      #end if
+      --input='${input}'
+      --input_name='$basename'
     #end if
-    --output=${output}
+    --output='${output}'
     ## BEGIN_VERSION_DEFAULT
     --fromextension=$ext
     ## END_VERSION_DEFAULT
@@ -36,15 +41,10 @@
 
     ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
       #if $data_processing.precursor_refinement.use_mzrefinement
-        #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name)
-        #if $data_processing.precursor_refinement.input_ident.ext == 'mzid':
-          #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name)
-        #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml':
-          #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
-        #end if
-      --ident=$data_processing.precursor_refinement.input_ident
-      --ident_name=$input_ident_name
-      --refinement=$output_refinement
+        #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
+      --ident='$data_processing.precursor_refinement.input_ident'
+      --ident_name='$input_ident_name'
+      --refinement='$output_refinement'
       --filter "mzRefiner $input_ident_name
         msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
         thresholdScore=$data_processing.precursor_refinement.thresholdScore
@@ -54,7 +54,7 @@
       #end if
 
       #if $data_processing.peak_picking.pick_peaks
-      --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
+        --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
       #end if
 
       #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
@@ -76,27 +76,27 @@
       #end if
 
       #for threshold_entry in $data_processing.thresholds
-      --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
+        --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
       #end for
 
       #if $data_processing.filter_mz_windows.do_mzwindow_filter
-      --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
+        --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
       #end if
 
       #if $data_processing.etd_filtering.do_etd_filtering
-      --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
-        $data_processing.etd_filtering.remove_charge_reduced
-        $data_processing.etd_filtering.remove_neutral_loss
-        $data_processing.etd_filtering.blanket_removal
-        $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
+        --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
+          $data_processing.etd_filtering.remove_charge_reduced
+          $data_processing.etd_filtering.remove_neutral_loss
+          $data_processing.etd_filtering.blanket_removal
+          $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
       #end if
 
       #if $data_processing.ms2denoise.denoise
-      --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
+        --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
       #end if
 
       #if str($data_processing.ms2deisotope) == "true"
-      --filter "MS2Deisotope"
+        --filter "MS2Deisotope"
       #end if
 
 
@@ -106,35 +106,35 @@
       #end if
 
       #if len($filtering.indices) > 0
-      --filter "index
-      #for $index in $filtering.indices
-      [${index.from},${index.to}]
-      #end for
-      "
+        --filter "index
+        #for $index in $filtering.indices
+          [${index.from},${index.to}]
+        #end for
+        "
       #end if
 
       #if len($filtering.scan_numbers) > 0
-      --filter "scanNumber
-      #for $scan_number in $filtering.scan_numbers
-      [${scan_number.from},${scan_number.to}]
-      #end for
-      "
+        --filter "scanNumber
+        #for $scan_number in $filtering.scan_numbers
+          [${scan_number.from},${scan_number.to}]
+        #end for
+        "
       #end if
 
       #if $filtering.strip_it.value
-      --filter "stripIT"
+         --filter "stripIT"
       #end if
 
       #if $filtering.filter_ms_levels.do_ms_level_filter
-      --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
+        --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
       #end if
 
       #if str($filtering.polarity) != "false"
-      --filter "polarity $filtering.polarity"
+        --filter "polarity $filtering.polarity"
       #end if
 
       #if str($filtering.analyzer) != "false"
-      --filter "analyzer $filtering.analyzer"
+        --filter "analyzer $filtering.analyzer"
       #end if
       
     ## OUTPUT ENCODING
@@ -154,21 +154,21 @@
 
       #set binary_compression = str($settings.binary_compression)
       #if $binary_compression == "zlib"
-      --zlib
+        --zlib
       #else if $binary_compression == "numpressLinearPic"
-      --numpressLinear --numpressPic
+        --numpressLinear --numpressPic
       #else if $binary_compression == "numpressLinearSlof"
-      --numpressLinear --numpressSlof
+        --numpressLinear --numpressSlof
       #else if $binary_compression == "numpressLinear"
-      --numpressLinear
+        --numpressLinear
       #else if $binary_compression == "numpressPic"
-      --numpressPic
+        --numpressPic
       #else if $binary_compression == "numpressSlof"
-      --numpressSlof
+        --numpressSlof
       #end if
 
       #if $settings.gzip_compression
-      --gzip
+        --gzip
       #end if
 
 ]]>
@@ -203,13 +203,23 @@
         </when>
       </conditional>
 
-      <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true">
+      <conditional name="precursor_refinement">
         <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
         <when value="false"></when>
         <when value="true">
           <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
-          <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" />
-          <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
+          <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
+            <sanitizer>
+              <valid initial="string.letters" />
+            </sanitizer>
+          </param>
+          <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10.">
+            <sanitizer>
+              <valid initial="string.letters,string.digits">
+                <add value="-" />
+              </valid>
+            </sanitizer>
+          </param>
           <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
           <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
           <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
@@ -322,14 +332,14 @@
         <option value="CID">CID</option>
         <option value="SA">SA</option>
         <option value="HCD">HCD</option>
-        <option>BIRD</option>
-        <option>ECD</option>
-        <option>IRMPD</option>
-        <option>PD</option>
-        <option>PSD</option>
-        <option>PQD</option>
-        <option>SID</option>
-        <option>SORI</option>
+        <option value="BIRD">BIRD</option>
+        <option value="ECD">ECD</option>
+        <option value="IRMPD">IRMPD</option>
+        <option value="PD">PD</option>
+        <option value="PSD">PSD</option>
+        <option value="PQD">PQD</option>
+        <option value="SID">SID</option>
+        <option value="SORI">SORI</option>
       </param>
 
       <repeat name="indices" title="Filter Scan Indices">
@@ -433,7 +443,7 @@
       <param name="output_type" value="mz5" />
       <param name="mz_encoding" value="64" />
       <param name="intensity_encoding" value="64" />
-      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
+      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
     </test>
     <test>
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
@@ -502,11 +512,11 @@
       <param name="output_type" value="mzML" />
       <param name="binary_compression" value="numpressLinearPic" />
       <param name="use_mzrefinement" value="true" />
-      <param name="input_ident" value="Rpal_01.pepXML.gz" />
+      <param name="input_ident" value="Rpal_01.pepXML" />
       <param name="thresholdScore" value="mvh" />
       <param name="thresholdValue" value="40-" />
       <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
-      <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
+      <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
     </test>
     
     <test>
diff -r 5f8848c7d7b7 -r b00023193f6e msconvert_wrapper.py
--- a/msconvert_wrapper.py	Fri Apr 08 15:46:25 2016 -0400
+++ b/msconvert_wrapper.py	Tue Mar 14 16:45:13 2017 -0400
@@ -7,6 +7,7 @@
 import subprocess
 import re
 import logging
+import shlex
 
 assert sys.version_info[:2] >= (2, 6)
 
@@ -40,7 +41,8 @@
     try:
         with open(tmp_stderr_name, 'wb') as tmp_stderr:
             with open(tmp_stdout_name, 'wb') as tmp_stdout:
-                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+                args = shlex.split(command) # handle proper splitting of quoted args
+                proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
                 returncode = proc.wait()
                 if returncode != 0:
                     raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-activation.mzML
--- a/test-data/small-activation.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-activation.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1272,7 +1272,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </spectrum>
-        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion">
+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
             </scan>
           </scanList>
           <binaryDataArrayList count="2">
-            <binaryDataArray encodedLength="3380">
+            <binaryDataArray encodedLength="3376">
               <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
               <cvParam cvRef="MS" accession="MS:1002312" name="MS-Numpress linear prediction compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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-  <fileChecksum>e18a3d758326d6d1adb2a8f00fa69cfb1dc5b83d</fileChecksum>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-analyzer-filter.mzML
--- a/test-data/small-analyzer-filter.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-analyzer-filter.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </cvList>
     <fileDescription>
@@ -20,7 +20,7 @@
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         </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="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1112,7 +1112,7 @@
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         </spectrum>
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+        <spectrum index="18" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1138,17 +1138,17 @@
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           </scanList>
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-  <fileChecksum>77c22cf716295527c57901738d27ed11ca93608e</fileChecksum>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-chargeStatePredictor.mzML
--- a/test-data/small-chargeStatePredictor.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-chargeStatePredictor.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
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@@ -20,7 +20,7 @@
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         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
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+      <software id="pwiz_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
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         </processingMethod>
-        <processingMethod order="1" softwareRef="pwiz_3.0.8990">
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
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@@ -1358,17 +1358,17 @@
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-  <fileChecksum>e34f2d83d57a605fa287b515b7432185e40b3806</fileChecksum>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-deisotope.mzML
--- a/test-data/small-deisotope.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-deisotope.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </cvList>
     <fileDescription>
@@ -20,7 +20,7 @@
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         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.8990" version="3.0.8990">
+      <software id="pwiz_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1272,7 +1272,7 @@
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         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
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           </scanList>
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-  <fileChecksum>4dc91f54798a123d6d0dd1c8901a443e67ab95c9</fileChecksum>
+  <indexListOffset>416380</indexListOffset>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-denoise.mzML
--- a/test-data/small-denoise.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-denoise.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1272,7 +1272,7 @@
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         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
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           </scanList>
           <binaryDataArrayList count="2">
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     <index name="chromatogram">
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   </indexList>
-  <indexListOffset>370581</indexListOffset>
-  <fileChecksum>d847e38185808668a5a4ac0f07bf22539e2dff96</fileChecksum>
+  <indexListOffset>370572</indexListOffset>
+  <fileChecksum>e792a4bdb6471008e8937217a2aed1bc8c3500df</fileChecksum>
 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-index-filter.mzML
--- a/test-data/small-index-filter.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-index-filter.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -496,18 +496,18 @@
   </mzML>
   <indexList count="2">
     <index name="spectrum">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">76395</offset>
+      <offset idRef="TIC">76394</offset>
     </index>
   </indexList>
-  <indexListOffset>78345</indexListOffset>
-  <fileChecksum>0d5bbd9cad4ad9471eba2e80d0ddea2cddcf3db9</fileChecksum>
+  <indexListOffset>78344</indexListOffset>
+  <fileChecksum>ee644abff7e27a2bdc852562fcd0258f31fb46eb</fileChecksum>
 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-ms-level-filter.mzML
--- a/test-data/small-ms-level-filter.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-ms-level-filter.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -2156,45 +2156,45 @@
   </mzML>
   <indexList count="2">
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     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">347713</offset>
+      <offset idRef="TIC">347712</offset>
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   </indexList>
-  <indexListOffset>349663</indexListOffset>
-  <fileChecksum>e47c8b99f8a38261a6a99445767638bda0d81200</fileChecksum>
+  <indexListOffset>349662</indexListOffset>
+  <fileChecksum>a9a8b2244bb3a277a399a710506652c0968ed670</fileChecksum>
 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-mzWindow.mzML
--- a/test-data/small-mzWindow.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-mzWindow.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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="3.79.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+      <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"/>
     </cvList>
     <fileDescription>
@@ -20,7 +20,7 @@
           <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="4efa13a2795731b5f2a1ff1c463daf0d24b9a9d9"/>
         </sourceFile>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-numpressL.mzML
--- a/test-data/small-numpressL.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-numpressL.mzML	Tue Mar 14 16:45:13 2017 -0400
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-numpressLP.mzML
--- a/test-data/small-numpressLP.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-numpressLP.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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@@ -37,7 +37,7 @@
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
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     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
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-        <processingMethod order="1" softwareRef="pwiz_3.0.8990">
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-  <fileChecksum>e18a3d758326d6d1adb2a8f00fa69cfb1dc5b83d</fileChecksum>
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-numpressLS.mzML
--- a/test-data/small-numpressLS.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-numpressLS.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
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         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
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         </processingMethod>
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+        <processingMethod order="1" softwareRef="pwiz_3.0.9987">
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@@ -1272,7 +1272,7 @@
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           </binaryDataArrayList>
         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
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           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
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               <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>
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     <index name="chromatogram">
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-  <fileChecksum>0cc3e1706b43b34a26e6ef49dee8aea5cea8c54e</fileChecksum>
+  <indexListOffset>502384</indexListOffset>
+  <fileChecksum>a652815af6f3486df23df7109340834f5922d5fa</fileChecksum>
 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-numpressP.mzML
--- a/test-data/small-numpressP.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-numpressP.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1272,7 +1272,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </spectrum>
-        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="701" dataProcessingRef="pwiz_Reader_conversion">
+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
             </scan>
           </scanList>
           <binaryDataArrayList count="2">
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+            <binaryDataArray encodedLength="7468">
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
               <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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-  <fileChecksum>f5217742062a1e5f6639fb825a243929c495b377</fileChecksum>
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 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-numpressS.mzML
--- a/test-data/small-numpressS.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-numpressS.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </cvList>
     <fileDescription>
@@ -20,7 +20,7 @@
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         </sourceFile>
         <sourceFile id="small-peakpicking-cwt-allMS.mzML" name="small-peakpicking-cwt-allMS.mzML" location="file:///">
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+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
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+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1272,7 +1272,7 @@
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           </binaryDataArrayList>
         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1298,17 +1298,17 @@
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           </scanList>
           <binaryDataArrayList count="2">
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+            <binaryDataArray encodedLength="7468">
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               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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-  <fileChecksum>2fde9311363a3eb86df6f28007d77e0fe528e033</fileChecksum>
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 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-peakpicking-cwt-allMS.mzML
--- a/test-data/small-peakpicking-cwt-allMS.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-peakpicking-cwt-allMS.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </cvList>
     <fileDescription>
@@ -34,7 +34,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -79,10 +79,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -1269,7 +1269,7 @@
             </binaryDataArray>
           </binaryDataArrayList>
         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
           <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>
           <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
           <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/>
@@ -1295,17 +1295,17 @@
             </scan>
           </scanList>
           <binaryDataArrayList count="2">
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+            <binaryDataArray encodedLength="4344">
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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-polarity-filter.mzML
--- a/test-data/small-polarity-filter.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-polarity-filter.mzML	Tue Mar 14 16:45:13 2017 -0400
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@@ -37,7 +37,7 @@
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@@ -82,10 +82,10 @@
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-  <fileChecksum>e18a3d758326d6d1adb2a8f00fa69cfb1dc5b83d</fileChecksum>
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 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-strip-it.mzML
--- a/test-data/small-strip-it.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-strip-it.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </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="8af1e376b6ed33679f7fcf965a5e7fd6b1bf77b7"/>
+          <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2d5cdd239d18de37386cf9409e30693767b16f82"/>
         </sourceFile>
       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
       <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_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
@@ -2436,52 +2436,52 @@
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-  <fileChecksum>f46f8578b4b1f75a5f2b12d15efeb29d29beb88a</fileChecksum>
+  <indexListOffset>411075</indexListOffset>
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 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-threshold.mzML
--- a/test-data/small-threshold.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-threshold.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
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     <fileDescription>
@@ -20,7 +20,7 @@
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         </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"/>
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     </fileDescription>
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.8990" version="3.0.8990">
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
           <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/>
         </processingMethod>
       </dataProcessing>
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     <index name="chromatogram">
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-  <fileChecksum>39712143d9caed5b0d1d0a476d57644357c23ec8</fileChecksum>
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 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-turbocharger.mzML
--- a/test-data/small-turbocharger.mzML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-turbocharger.mzML	Tue Mar 14 16:45:13 2017 -0400
@@ -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">
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+      <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"/>
     </cvList>
     <fileDescription>
@@ -20,7 +20,7 @@
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         </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="2d5cdd239d18de37386cf9409e30693767b16f82"/>
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       </sourceFileList>
     </fileDescription>
@@ -37,7 +37,7 @@
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         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
-      <software id="pwiz_3.0.8990" version="3.0.8990">
+      <software id="pwiz_3.0.9987" version="3.0.9987">
         <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>
       </software>
     </softwareList>
@@ -82,10 +82,10 @@
         </processingMethod>
       </dataProcessing>
       <dataProcessing id="pwiz_Reader_conversion">
-        <processingMethod order="0" softwareRef="pwiz_3.0.8990">
+        <processingMethod order="0" softwareRef="pwiz_3.0.9987">
           <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_3.0.9987">
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@@ -1290,7 +1290,7 @@
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         </spectrum>
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+        <spectrum index="22" id="controllerType=0 controllerNumber=1 scan=23" defaultArrayLength="700" dataProcessingRef="pwiz_Reader_conversion">
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@@ -1316,17 +1316,17 @@
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           </scanList>
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+            <binaryDataArray encodedLength="3376">
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+      <offset idRef="controllerType=0 controllerNumber=1 scan=48">474880</offset>
     </index>
     <index name="chromatogram">
-      <offset idRef="TIC">484164</offset>
+      <offset idRef="TIC">484155</offset>
     </index>
   </indexList>
-  <indexListOffset>486114</indexListOffset>
-  <fileChecksum>e7ec398af412704484453e19bd2bc7578529b5c0</fileChecksum>
+  <indexListOffset>486105</indexListOffset>
+  <fileChecksum>1dda3f0dfdbbd41618dd9aa7ac70fa871cbc4199</fileChecksum>
 </indexedmzML>
diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-zlib-32.mzXML
--- a/test-data/small-zlib-32.mzXML	Fri Apr 08 15:46:25 2016 -0400
+++ b/test-data/small-zlib-32.mzXML	Tue Mar 14 16:45:13 2017 -0400
@@ -27,9 +27,9 @@
       <processingOperation name="Conversion to mzML"/>
     </dataProcessing>
     <dataProcessing centroided="1">
-      <software type="conversion" name="ProteoWizard software" version="3.0.8990"/>
+      <software type="conversion" name="ProteoWizard software" version="3.0.9987"/>
       <processingOperation name="Conversion to mzML"/>
-      <software type="processing" name="ProteoWizard software" version="3.0.8990"/>
+      <software type="processing" name="ProteoWizard software" version="3.0.9987"/>
     </dataProcessing>
     <scan num="1"
           scanType="Full"
@@ -483,7 +483,7 @@
           scanType="Full"
           centroided="1"
           msLevel="1"
-          peaksCount="701"
+          peaksCount="700"
           polarity="+"
           retentionTime="PT13.0048S"
           lowMz="200.090909093618"
@@ -493,10 +493,10 @@
           totIonCurrent="1.5974105e06"
           msInstrumentID="2">
       <peaks compressionType="zlib"
-             compressedLen="4633"
+             compressedLen="4626"
              precision="32"
              byteOrder="network"
-             contentType="m/z-int">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diff -r 5f8848c7d7b7 -r b00023193f6e test-data/small-zlib-64.mz5
Binary file test-data/small-zlib-64.mz5 has changed
diff -r 5f8848c7d7b7 -r b00023193f6e tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 08 15:46:25 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
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-    <repository changeset_revision="fdc8eb732831" name="package_proteowizard_3_0_9016" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-</tool_dependency>