changeset 4:60ee8c592b13 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit f1e1cd260ef2884d0ba12e2b614df3c72d0934dc
author galaxyp
date Sat, 04 Mar 2023 19:14:31 +0000
parents 71411ac28268
children
files maldi_macros.xml maldi_quant_preprocessing.xml test-data/Example_Processed.ibd test-data/Example_Processed.imzML test-data/annotations.tabular test-data/annotations_output3.tabular test-data/int3.tabular test-data/int4.tabular test-data/masspeaks3.tabular test-data/masspeaks4.tabular test-data/masspeaks5.tabular test-data/msidata_1.RData test-data/peak_detection2.ibd test-data/peak_detection2.imzml test-data/peak_detection2.imzml.txt test-data/peak_detection3.ibd test-data/peak_detection3.imzml test-data/peak_detection3.imzml.txt test-data/peak_detection3.imzml.txt.html test-data/peak_detection4.ibd test-data/peak_detection4.imzml test-data/peak_detection4.imzml.txt test-data/peak_detection5.ibd test-data/peak_detection5.imzml test-data/peak_detection5.imzml.txt test-data/peakdetection1_QC.pdf test-data/peakdetection2_QC.pdf test-data/peakdetection3_QC.pdf test-data/peakdetection4_QC.pdf test-data/peakdetection5_QC.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzML test-data/testfile_squares.rdata
diffstat 33 files changed, 2908 insertions(+), 2848 deletions(-) [+]
line wrap: on
line diff
--- a/maldi_macros.xml	Fri Feb 15 10:26:00 2019 -0500
+++ b/maldi_macros.xml	Sat Mar 04 19:14:31 2023 +0000
@@ -1,6 +1,5 @@
 <macros>
     <token name="@R_IMPORTS@"><![CDATA[
-        library (Cardinal)
         library (MALDIquantForeign)
         library (MALDIquant)
         library (ggplot2)
@@ -14,15 +13,14 @@
     ]]>
     </token>
 
-    <token name="@VERSION@">1.18.0</token>
+    <token name="@VERSION@">1.22.0</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.5.1">r-base</requirement>
-            <requirement type="package" version="1.12.1">bioconductor-cardinal</requirement>
-            <requirement type="package" version="0.11.5">r-maldiquantforeign</requirement>
-            <requirement type="package" version="1.18">r-maldiquant</requirement>
-            <requirement type="package" version="3.0">r-ggplot2</requirement>
+            <requirement type="package" version="4.2.2">r-base</requirement>
+            <requirement type="package" version="0.13">r-maldiquantforeign</requirement>
+            <requirement type="package" version="1.22">r-maldiquant</requirement>
+            <requirement type="package" version="3.4.1">r-ggplot2</requirement>
             <requirement type="package" version="2.3">r-gridextra</requirement>
         </requirements>
     </xml>
@@ -31,6 +29,7 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/bts447</citation>
         <citation type="doi">10.1007/978-3-319-45809-0_6</citation>
+        <citation type="doi">10.1093/gigascience/giz143</citation>
     </citations>
     </xml>
 </macros>
--- a/maldi_quant_preprocessing.xml	Fri Feb 15 10:26:00 2019 -0500
+++ b/maldi_quant_preprocessing.xml	Sat Mar 04 19:14:31 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.3">
+<tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="@VERSION@.0">
     <description>
         Preprocessing of mass-spectrometry imaging data
     </description>
@@ -19,8 +19,6 @@
             du infile.hdr &&
             du infile.img &&
             du -s -B1 infile.hdr &&
-        #else
-            ln -s $infile infile.RData &&
         #end if
         Rscript "${maldi_quant_preprocessing}" &&
 
@@ -59,22 +57,6 @@
         ## Import analyze7.5 file
         maldi_data = importAnalyze( 'infile.hdr' )
         coordinates_info = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))
-    #else
-        loadRData <- function(fileName){
-        ##loads an RData file, and returns it
-        load(fileName)
-        get(ls()[ls() != "fileName"])
-        }
-        msidata = loadRData('infile.RData')
-        ## save coordinates
-        cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])
-        ## save mz values
-        cardinal_mzs = Cardinal::mz(msidata)
-        ## create MALDIquant MassSpectrum object, order of pixels in iData is same as in coord(msidata):
-        maldi_data = list()
-        for(number_spectra in 1:ncol(msidata)){
-        maldi_data[[number_spectra]] = MALDIquant::createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])
-        }
     #end if
 
 #end if
@@ -344,10 +326,6 @@
             if (length(findEmptyMassObjects(maldi_data))>0)
 
                 {
-                    #if $infile.ext == 'rdata'
-                        cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(maldi_data),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
-                    #end if
-
                     maldi_data = removeEmptyMassObjects(maldi_data)
             }
         #end if
@@ -386,11 +364,7 @@
 
 ## export imzML file
 if (length(maldi_data)>0){
-    #if $infile.ext == 'rdata'
-        MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed, coordinates=cardinal_coordinates)
-    #else
         MALDIquantForeign::exportImzMl(maldi_data, file="out.imzMl", processed=$export_processed)
-    #end if
 
 }else{"All spectra are empty, outputfiles will be empty,too."}
 
@@ -398,7 +372,7 @@
         </configfile>
     </configfiles>
     <inputs>
-        <param name="infile" type="data" format="imzml,rdata,analyze75" label="MSI data" help="Input file as imzML (composite upload), or Cardinal MSImageSet saved as RData (regular upload). The file must be in profile mode, not centroided."/>
+        <param name="infile" type="data" format="imzml,analyze75" label="MSI data" help="Input file as imzML (composite upload). The file must be in profile mode, not centroided."/>
         <conditional name="restriction_conditional">
             <param name="restriction" type="select" label="Use only spectra of interest" help="This option only works for imzML files">
                 <option value="no_restriction" selected="True">No, calculate on entire file</option>
@@ -529,7 +503,7 @@
                     <param name="snr" type="integer" value="2" label="Signal-to-noise-ratio"/>
                     <param name="allow_nomatch" type="boolean" label="Allow no matches" help="Don't throw an error when less than 2 reference m/z were found in a spectrum" truevalue="TRUE" falsevalue="FALSE"/>
                     <param name="empty_nomatch" type="boolean" label="Empty no matches" help="If TRUE the intensity values of MassSpectrum or MassPeaks objects with missing (NA) warping functions are set to zero" truevalue="TRUE" falsevalue="FALSE"/>
-                    <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE" help="For Cardinal RData files this step can only be performed if pixel annotations were provided"/>
+                    <param name="remove_empty" type="boolean" label="Remove empty spectra" truevalue="TRUE" falsevalue="FALSE"/>
 
                     <conditional name="reference_for_alignment">
                         <param name="align_ref" type="select" label="Reference" help="If given, samples will be aligned to reference, use internal calibrants to perform m/z calibration">
@@ -579,33 +553,12 @@
                 <param name="baseline_method" value ="TopHat"/>
             </conditional>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing1.imzml.txt" lines_diff="4">
-                <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="6"/>
+                <extra_files type="file" file="outfile1.imzml" name="imzml" lines_diff="8"/>
                 <extra_files type="file" file="outfile1.ibd" name="ibd" compare="sim_size"/>
             </output>
             <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>
         </test>
         <test>
-            <param name="infile" value="msidata_1.RData" ftype="rdata"/>
-            <conditional name="methods_conditional">
-                <param name="method" value="Align"/>
-                <param name="warping_method" value="lowess"/>
-                <param name="halfWindowSize" value="5"/>
-                <param name="tolerance" value="0.001"/>
-                <param name="allow_nomatch" value="TRUE"/>
-                <param name="remove_empty" value="TRUE"/>
-                <param name="empty_nomatch" value="TRUE"/>
-                <conditional name="reference_for_alignment">
-                    <param name="align_ref" value="yes_reference"/>
-                    <param name="reference_file" value="inputpeptides.tabular" ftype="tabular"/>
-                </conditional>
-            </conditional>
-            <output name="outfile_imzml" ftype="imzml" file="preprocessing2.imzml.txt" lines_diff="4">
-                <extra_files type="file" file="outfile2.imzml" name="imzml" lines_diff="6"/>
-                <extra_files type="file" file="outfile2.ibd" name="ibd" compare="sim_size"/>
-            </output>
-            <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/>
-        </test>
-        <test>
             <param name="infile" value="" ftype="imzml">
                 <composite_data value="Example_Continuous.imzML"/>
                 <composite_data value="Example_Continuous.ibd"/>
@@ -615,7 +568,7 @@
                 <param name="calibrate_method" value="median"/>
             </conditional>
             <output name="outfile_imzml" ftype="imzml" file="preprocessing3.imzml.txt" lines_diff="4">
-                <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="6"/>
+                <extra_files type="file" file="outfile3.imzml" name="imzml" lines_diff="8"/>
                 <extra_files type="file" file="outfile3.ibd" name="ibd" compare="sim_size"/>
             </output>
             <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>
@@ -631,8 +584,7 @@
 
 - MSI data: 2 types of input data can be used:
 
-    - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
-    - Cardinal "MSImageSet" data saved as .RData
+    - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/imzml/>`_
 
 - Optional: Tabular file with pixel coordinates to restrict reading of imzML files to coordinates of interest. Tabular files with any header name or no header at all are supported. 
 
Binary file test-data/Example_Processed.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Example_Processed.imzML	Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,380 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<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" xmlns="http://psi.hupo.org/ms/mzml" version="1.1">
+  <cvList count="4">
+    <cv URI="http://ontologies.berkeleybop.org/pato.obo" fullName="Phenotype And Trait Ontology" id="PATO" version="releases/2017-07-10"/>
+    <cv URI="http://ontologies.berkeleybop.org/uo.obo" fullName="Units of Measurement Ontology" id="UO" version="releases/2017-09-25"/>
+    <cv URI="https://raw.githubusercontent.com/hupo-psi/psi-ms-cv/master/psi-ms.obo" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" id="MS" version="4.1.0"/>
+    <cv URI="https://raw.githubusercontent.com/imzML/imzML/master/imagingMS.obo" fullName="Mass Spectrometry Imaging Ontology" id="IMS" version="1.1.0"/>
+  </cvList>
+  <fileDescription>
+    <fileContent>
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
+      <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9d501bdc53444916b7e97e795b02c856"/>
+      <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7e8fdb93053915d3edb51b70aa0619ac209964df"/>
+      <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
+    </fileContent>
+    <sourceFileList count="1">
+      <sourceFile id="sf1" location="C:\Users\Thorsten Schramm\Documents\Promotion\imzML\Website\files\Beispiel-Dateien\Example images\" name="Example.raw">
+        <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format"/>
+        <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format"/>
+        <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>
+      </sourceFile>
+    </sourceFileList>
+    <contact>
+      <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>
+      <cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Institut für Anorganische und Analytische Chemie"/>
+      <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstraße 60, Haus 16, Gießen, Germany"/>
+      <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>
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+  </fileDescription>
+  <referenceableParamGroupList count="4">
+    <referenceableParamGroup id="mzArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="intensityArray">
+      <cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>
+      <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
+      <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>
+      <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="scan1">
+      <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan"/>
+      <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - p NSI Full ms [100,00-800,00]"/>
+    </referenceableParamGroup>
+    <referenceableParamGroup id="spectrum1">
+      <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
+      <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum"/>
+      <cvParam cvRef="MS" accession="MS:1000129" name="negative scan"/>
+    </referenceableParamGroup>
+  </referenceableParamGroupList>
+  <sampleList count="1">
+    <sample id="sample1" name="Sample1">
+      <cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1"/>
+    </sample>
+  </sampleList>
+  <softwareList count="2">
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+      <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur"/>
+    </software>
+    <software id="TMC" version="1.1 beta">
+      <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value=""/>
+    </software>
+  </softwareList>
+  <scanSettingsList count="1">
+    <scanSettings id="scansettings1">
+      <cvParam cvRef="IMS" accession="IMS:1000401" name="top down"/>
+      <cvParam cvRef="IMS" accession="IMS:1000413" name="flyback"/>
+      <cvParam cvRef="IMS" accession="IMS:1000480" name="horizontal line scan"/>
+      <cvParam cvRef="IMS" accession="IMS:1000491" name="linescan left right"/>
+      <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixels x" value="3"/>
+      <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixels y" value="3"/>
+      <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100.0" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
+    </scanSettings>
+  </scanSettingsList>
+  <instrumentConfigurationList count="1">
+    <instrumentConfiguration id="LTQFTUltra0">
+      <cvParam cvRef="MS" accession="MS:1000557" name="LTQ FT Ultra"/>
+      <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="none"/>
+      <componentList count="3">
+        <source order="1">
+          <cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization"/>
+          <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet"/>
+          <cvParam cvRef="MS" accession="MS:1000844" name="focus diameter x" value="10.0"/>
+          <cvParam cvRef="MS" accession="MS:1000845" name="focus diameter y" value="10.0"/>
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+          <cvParam cvRef="MS" accession="MS:1000850" name="gas laser"/>
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+          <cvParam cvRef="MS" accession="MS:1000835" name="matrix solution concentration" value="10.0"/>
+          <cvParam cvRef="MS" accession="MS:1000834" name="matrix solution" value="DHB"/>
+        </source>
+        <analyzer order="2">
+          <cvParam cvRef="MS" accession="MS:1000264" name="ion trap"/>
+          <cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0.0" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+        </analyzer>
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+          <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier"/>
+          <cvParam cvRef="MS" accession="MS:1000120" name="transient recorder"/>
+        </detector>
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+  <dataProcessingList count="2">
+    <dataProcessing id="XcaliburProcessing">
+      <processingMethod softwareRef="Xcalibur" order="1">
+        <cvParam cvRef="MS" accession="MS:1000594" name="low intensity data point removal"/>
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+    </dataProcessing>
+    <dataProcessing id="TMCConversion">
+      <processingMethod softwareRef="TMC" order="2">
+        <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML"/>
+      </processingMethod>
+    </dataProcessing>
+  </dataProcessingList>
+  <run defaultInstrumentConfigurationRef="LTQFTUltra0" defaultSourceFileRef="sf1" id="Experiment01" sampleRef="sample1" startTimeStamp="2009-08-11T15:59:44">
+    <spectrumList count="9" defaultDataProcessingRef="XcaliburProcessing">
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--- a/test-data/annotations_output3.tabular	Fri Feb 15 10:26:00 2019 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/int4.tabular	Sat Mar 04 19:14:31 2023 +0000
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--- a/test-data/masspeaks3.tabular	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/masspeaks3.tabular	Sat Mar 04 19:14:31 2023 +0000
@@ -1,298 +1,123 @@
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--- a/test-data/masspeaks4.tabular	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/masspeaks4.tabular	Sat Mar 04 19:14:31 2023 +0000
@@ -1,1862 +1,1083 @@
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Binary file test-data/msidata_1.RData has changed
Binary file test-data/peak_detection2.ibd has changed
--- a/test-data/peak_detection2.imzml	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection2.imzml	Sat Mar 04 19:14:31 2023 +0000
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--- a/test-data/peak_detection2.imzml.txt	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection2.imzml.txt	Sat Mar 04 19:14:31 2023 +0000
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 imzML file:
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--rw-r--r-- 1 meli meli 19244 Feb 14 18:44 imzml
+-rw-rw-r-- 1 meli meli   320 Mar  3 22:08 ibd
+-rw-rw-r-- 1 meli meli 19242 Mar  3 22:08 imzml
Binary file test-data/peak_detection3.ibd has changed
--- a/test-data/peak_detection3.imzml	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection3.imzml	Sat Mar 04 19:14:31 2023 +0000
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1184"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="10"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="80"/>
       <binary/>
      </binaryDataArray>
     </binaryDataArrayList>
    </spectrum>
-   <spectrum index="6" id="Spectrum=7" defaultArrayLength="38">
+   <spectrum index="6" id="Spectrum=7" defaultArrayLength="13">
     <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.595254080636" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="305" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="366.083343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
     <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
     <scanList count="1">
      <scan>
@@ -247,25 +247,25 @@
     <binaryDataArrayList count="2">
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="mzArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3184"/>
-      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1264"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="104"/>
       <binary/>
      </binaryDataArray>
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="intensityArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3488"/>
-      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="38"/>
-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="304"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1368"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="13"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="104"/>
       <binary/>
      </binaryDataArray>
     </binaryDataArrayList>
    </spectrum>
-   <spectrum index="7" id="Spectrum=8" defaultArrayLength="33">
+   <spectrum index="7" id="Spectrum=8" defaultArrayLength="17">
     <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="306.32292175293" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="370.523821149554" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304.666687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="393.583343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
     <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
     <scanList count="1">
      <scan>
@@ -276,25 +276,25 @@
     <binaryDataArrayList count="2">
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="mzArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3792"/>
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1472"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
       <binary/>
      </binaryDataArray>
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="intensityArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4056"/>
-      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="33"/>
-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="264"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1608"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="17"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="136"/>
       <binary/>
      </binaryDataArray>
     </binaryDataArrayList>
    </spectrum>
-   <spectrum index="8" id="Spectrum=9" defaultArrayLength="28">
+   <spectrum index="8" id="Spectrum=9" defaultArrayLength="14">
     <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="328.937515258789" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="396.916674804687" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="304" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="394.833343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
     <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>
     <scanList count="1">
      <scan>
@@ -305,16 +305,16 @@
     <binaryDataArrayList count="2">
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="mzArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4320"/>
-      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1744"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
       <binary/>
      </binaryDataArray>
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="intensityArray"/>
-      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4544"/>
-      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="28"/>
-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="224"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1856"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="14"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="112"/>
       <binary/>
      </binaryDataArray>
     </binaryDataArrayList>
--- a/test-data/peak_detection3.imzml.txt	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection3.imzml.txt	Sat Mar 04 19:14:31 2023 +0000
@@ -1,4 +1,4 @@
 imzML file:
-total 28
--rw-r--r-- 1 meli meli  4768 Feb 14 18:44 ibd
--rw-r--r-- 1 meli meli 19627 Feb 14 18:44 imzml
+total 24
+-rw-rw-r-- 1 meli meli  1968 Mar  3 23:22 ibd
+-rw-rw-r-- 1 meli meli 19536 Mar  3 23:22 imzml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection3.imzml.txt.html	Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,4 @@
+imzML file:
+total 24
+-rw-rw-r-- 1 meli meli   192 Mar  3 22:33 ibd
+-rw-rw-r-- 1 meli meli 19501 Mar  3 22:33 imzml
Binary file test-data/peak_detection4.ibd has changed
--- a/test-data/peak_detection4.imzml	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection4.imzml	Sat Mar 04 19:14:31 2023 +0000
@@ -8,14 +8,19 @@
  <fileDescription>
   <fileContent>
    <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>
-   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{a9ea11c4-975e-4f4a-a174-906e8cf0bb77}"/>
-   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7022792264dc3f66251f22bebb634de68cb6a9fc"/>
+   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{6c184702-d208-46d8-95e2-fafc3824c820}"/>
+   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="081e20966560412d72c8a619a33b621db427a318"/>
    <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>
    <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>
   </fileContent>
+  <sourceFileList count="1">
+   <sourceFile id="SF1" location="/tmp/tmp7arrd4fa/job_working_directory/000/15/working" name="infile.imzML">
+    <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="f882fe6dd21b5f206c5e7bdccd1e49d07ef3120a"/>
+   </sourceFile>
+  </sourceFileList>
  </fileDescription>
  <softwareList count="1">
-  <software id="MALDIquantForeign" version="0.11.5"/>
+  <software id="MALDIquantForeign" version="0.13"/>
  </softwareList>
  <referenceableParamGroupList count="2">
   <referenceableParamGroup id="mzArray">
@@ -33,9 +38,9 @@
  </referenceableParamGroupList>
  <scanSettingsList count="1">
   <scanSettings id="scansetting1">
-   <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="13"/>
+   <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3"/>
    <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>
-   <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="1300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
+   <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
    <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
    <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
    <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>
@@ -52,12 +57,12 @@
   </dataProcessing>
  </dataProcessingList>
  <run id="run0" defaultInstrumentConfigurationRef="IC0">
-  <spectrumList count="24" defaultDataProcessingRef="export">
-   <spectrum index="0" id="scan=0" defaultArrayLength="90">
-    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+  <spectrumList count="9" defaultDataProcessingRef="export">
+   <spectrum index="0" id="Scan=1" defaultArrayLength="78">
+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="900.470520019531" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="999.455810546875" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="107.972220526801" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="771.208343505859" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -69,24 +74,24 @@
      <binaryDataArray encodedLength="0">
       <referenceableParamGroupRef ref="mzArray"/>
       <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16"/>
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="720"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="78"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="624"/>
       <binary/>
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      <binaryDataArray encodedLength="0">
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="720"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="624"/>
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    </spectrum>
-   <spectrum index="1" id="scan=1" defaultArrayLength="70">
-    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+   <spectrum index="1" id="Scan=2" defaultArrayLength="133">
+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
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-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="999.267028808594" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="107.972220526801" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="799.666687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -97,25 +102,25 @@
     <binaryDataArrayList count="2">
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       <referenceableParamGroupRef ref="mzArray"/>
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="560"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1264"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="133"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1064"/>
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="560"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="2328"/>
+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="133"/>
+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1064"/>
       <binary/>
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    </spectrum>
-   <spectrum index="2" id="scan=2" defaultArrayLength="89">
-    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+   <spectrum index="2" id="Scan=3" defaultArrayLength="130">
+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="900.434692382812" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="999.418090820312" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.979166030884" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="794.750020345052" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -126,54 +131,25 @@
     <binaryDataArrayList count="2">
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="712"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="3392"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1040"/>
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-      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="712"/>
+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="4432"/>
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+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="1040"/>
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    </spectrum>
-   <spectrum index="3" id="scan=3" defaultArrayLength="89">
-    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>
+   <spectrum index="3" id="Scan=4" defaultArrayLength="130">
+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0"/>
     <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>
-    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="900.434692382812" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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-    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="999.342529296875" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="100.979166030884" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
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@@ -184,25 +160,25 @@
     <binaryDataArrayList count="2">
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--- a/test-data/peak_detection4.imzml.txt	Fri Feb 15 10:26:00 2019 -0500
+++ b/test-data/peak_detection4.imzml.txt	Sat Mar 04 19:14:31 2023 +0000
@@ -1,4 +1,4 @@
 imzML file:
-total 80
--rw-r--r-- 1 meli meli 29792 Feb 14 18:45 ibd
--rw-r--r-- 1 meli meli 45290 Feb 14 18:45 imzml
+total 40
+-rw-rw-r-- 1 meli meli 17328 Mar  3 23:28 ibd
+-rw-rw-r-- 1 meli meli 19635 Mar  3 23:28 imzml
Binary file test-data/peak_detection5.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection5.imzml	Sat Mar 04 19:14:31 2023 +0000
@@ -0,0 +1,150 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peak_detection5.imzml.txt	Sat Mar 04 19:14:31 2023 +0000
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+imzML file:
+total 16
+-rw-rw-r-- 1 meli meli 1744 Mar  4 18:10 ibd
+-rw-rw-r-- 1 meli meli 9244 Mar  4 18:10 imzml
Binary file test-data/peakdetection1_QC.pdf has changed
Binary file test-data/peakdetection2_QC.pdf has changed
Binary file test-data/peakdetection3_QC.pdf has changed
Binary file test-data/peakdetection4_QC.pdf has changed
Binary file test-data/peakdetection5_QC.pdf has changed
Binary file test-data/preprocessing_results3.ibd has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/preprocessing_results3.imzML	Sat Mar 04 19:14:31 2023 +0000
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+					<binaryDataArray encodedLength="0">
+						<referenceableParamGroupRef ref="intensityArray" />
+						<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="1312" />
+						<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />
+						<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />
+						<binary />
+					</binaryDataArray>
+				</binaryDataArrayList>
+			</spectrum>
+		</spectrumList>
+	</run>
+</mzML>
Binary file test-data/testfile_squares.rdata has changed