Repository 'cardinal_mz_images'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images

Changeset 5:4a05e47cd0ea (2019-12-13)
Previous changeset 4:56b3b7d5f2b5 (2019-03-22) Next changeset 6:25b83cbd596a (2020-03-25)
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a"
modified:
test-data/112_annotation_output.tabular
test-data/112_auto_combined.ibd
test-data/112_auto_combined.imzml
test-data/112_auto_combined.imzml.txt
test-data/112_auto_combined_QC.pdf
test-data/123_annotation_output.tabular
test-data/123_combined.RData
test-data/123_combined_QC.pdf
test-data/123_combined_auto.ibd
test-data/123_combined_auto.imzml
test-data/123_combined_auto.imzml.txt
test-data/123_combined_auto.pdf
test-data/12_annotation_output.tabular
test-data/12_combined_QC.pdf
test-data/2123_auto_combined_QC.pdf
added:
test-data/123_combine.rdata
test-data/123_combined.ibd
test-data/123_combined.imzml
test-data/123_combined.imzml.txt
test-data/123_combined_picked.rdata
test-data/123_combined_picked2.rdata
test-data/12_combined.ibd
test-data/12_combined.imzml
test-data/12_combined.imzml.txt
test-data/2123_auto_combined.ibd
test-data/2123_auto_combined.imzml
test-data/2123_auto_combined.imzml.txt
test-data/picked.ibd
test-data/picked.imzml
test-data/picked.imzml.txt
test-data/picked.tabular
test-data/picked_QC.pdf
test-data/xy_coordinates2.tabular
removed:
test-data/12_combined.RData
test-data/2123_auto_combined.RData
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/112_annotation_output.tabular
--- a/test-data/112_annotation_output.tabular Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/112_annotation_output.tabular Fri Dec 13 13:51:29 2019 -0500
b
@@ -1,16 +1,16 @@
-x y sample_name file_name column_name NA.x NA.y NA
-1 1 msidata_1.RData file_one col1 NA NA NA
-1 2 msidata_1.RData file_one col1 NA NA NA
-1 3 msidata_1.RData file_one col1 NA NA NA
-10 1 123_combined.RData file_two col3 NA NA NA
-10 2 123_combined.RData file_two col3 NA NA NA
-10 3 123_combined.RData file_two col3 NA NA NA
-15 1 123_combined.RData file_three col3 NA NA NA
-15 2 123_combined.RData file_three col3 NA NA NA
-15 3 123_combined.RData file_three col3 NA NA NA
-7 1 123_combined.RData file_one col1 NA NA NA
-7 2 123_combined.RData file_one col1 NA NA NA
-7 3 123_combined.RData file_one col1 NA NA NA
-9 1 123_combined.RData file_two col2 NA NA NA
-9 2 123_combined.RData file_two col2 NA NA NA
-9 3 123_combined.RData file_two col2 NA NA NA
+x y sample_name file_name column_name
+1 1 msidata_1.RData file_one col1
+1 2 msidata_1.RData file_one col1
+1 3 msidata_1.RData file_one col1
+7 1 123_combined.RData file_one col1
+7 2 123_combined.RData file_one col1
+7 3 123_combined.RData file_one col1
+9 1 123_combined.RData file_two col2
+10 1 123_combined.RData file_two col3
+9 2 123_combined.RData file_two col2
+10 2 123_combined.RData file_two col3
+9 3 123_combined.RData file_two col2
+10 3 123_combined.RData file_two col3
+15 1 123_combined.RData file_three col3
+15 2 123_combined.RData file_three col3
+15 3 123_combined.RData file_three col3
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/112_auto_combined.ibd
b
Binary file test-data/112_auto_combined.ibd has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/112_auto_combined.imzml
--- a/test-data/112_auto_combined.imzml Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/112_auto_combined.imzml Fri Dec 13 13:51:29 2019 -0500
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bcd78ace1e6441dc527501b5eb3994fcf15b894" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <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" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,18 +42,24 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.2.6">
  <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:1000042" name="max count of pixel x" value="15" />
+ <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="5" />
  <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="15" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/112_auto_combined.imzml.txt
--- a/test-data/112_auto_combined.imzml.txt Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/112_auto_combined.imzml.txt Fri Dec 13 13:51:29 2019 -0500
b
@@ -1,4 +1,4 @@
 imzML file:
 total 556
--rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd
--rw-r--r-- 1 meli meli  25466 Feb 12 12:25 imzml
+-rw-r--r-- 1 meli meli 537552 Dez 11 00:10 ibd
+-rw-r--r-- 1 meli meli  25811 Dez 11 00:10 imzml
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/112_auto_combined_QC.pdf
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Binary file test-data/112_auto_combined_QC.pdf has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_annotation_output.tabular
--- a/test-data/123_annotation_output.tabular Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/123_annotation_output.tabular Fri Dec 13 13:51:29 2019 -0500
b
@@ -1,13 +1,13 @@
-x y sample_name file_name column_name NA.x NA.y NA
-1 1 File1 file_one col1 NA NA NA
-1 2 File1 file_one col1 NA NA NA
-1 3 File1 file_one col1 NA NA NA
-3 1 File2 file_two col2 NA NA NA
-3 2 File2 file_two col2 NA NA NA
-3 3 File2 file_two col2 NA NA NA
-4 1 File2 file_two col3 NA NA NA
-4 2 File2 file_two col3 NA NA NA
-4 3 File2 file_two col3 NA NA NA
-9 1 File3 file_three col3 NA NA NA
-9 2 File3 file_three col3 NA NA NA
-9 3 File3 file_three col3 NA NA NA
+x y sample_name file_name column_name
+1 1 File1 file_one col1
+1 2 File1 file_one col1
+1 3 File1 file_one col1
+3 1 File2 file_two col2
+4 1 File2 file_two col3
+3 2 File2 file_two col2
+4 2 File2 file_two col3
+3 3 File2 file_two col2
+4 3 File2 file_two col3
+9 1 File3 file_three col3
+9 2 File3 file_three col3
+9 3 File3 file_three col3
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combine.rdata
b
Binary file test-data/123_combine.rdata has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined.RData
b
Binary file test-data/123_combined.RData has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined.ibd
b
Binary file test-data/123_combined.ibd has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined.imzml Fri Dec 13 13:51:29 2019 -0500
b
b'@@ -0,0 +1,399 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" 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_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8421b4d5-42be-4040-9d94-0398a40d6121" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d2cf2df8db9b95afd23834703bc933df1098bb6d" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="2.2.6">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="4" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="9" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n'..b'\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="335976" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=11" defaultArrayLength="0" index="11">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="369572" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=12" defaultArrayLength="0" index="12">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="9" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="403168" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/123_combined.imzml.txt Fri Dec 13 13:51:29 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 452
+-rw-r--r-- 1 meli meli 436764 Dez 11 00:02 ibd
+-rw-r--r-- 1 meli meli  21511 Dez 11 00:02 imzml
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_QC.pdf
b
Binary file test-data/123_combined_QC.pdf has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_auto.ibd
b
Binary file test-data/123_combined_auto.ibd has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_auto.imzml
--- a/test-data/123_combined_auto.imzml Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/123_combined_auto.imzml Fri Dec 13 13:51:29 2019 -0500
b
@@ -9,8 +9,8 @@
  <fileContent>
  <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />
  <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />
- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{7DC9B0BB-277B-4A92-8780-2879E0E6A8F2}" />
- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="6768CFB740661C3F0C560438B85A906EA05933D5" />
+ <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c12d4d26-5ff1-4c3c-99ea-95e0858faf36" />
+ <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="147d6aa7f71a366246c93d750fcc9240b84c748f" />
  <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />
  </fileContent>
  </fileDescription>
@@ -22,19 +22,18 @@
  </referenceableParamGroup>
  <referenceableParamGroup id="scan1">
  <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />
- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="mzArray">
  <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" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  <referenceableParamGroup id="intensityArray">
  <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />
  <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />
  <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />
- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" />
+ <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />
  </referenceableParamGroup>
  </referenceableParamGroupList>
  <sampleList count="1">
@@ -43,18 +42,24 @@
  </sample>
  </sampleList>
  <softwareList count="1">
- <software id="Cardinal" version="1.12.1">
+ <software id="Cardinal" version="2.2.6">
  <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:1000042" name="max count of pixel x" value="8" />
- <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="11" />
+ <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="6" />
+ <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="8" />
+ <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="11" />
+ <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />
+ <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />
  </scanSettings>
  </scanSettingsList>
  <instrumentConfigurationList count="1">
- <instrumentConfiguration id="IC1" />
+ <instrumentConfiguration id="IC1">
+ <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />
+ </instrumentConfiguration>
  </instrumentConfigurationList>
  <dataProcessingList count="1">
  <dataProcessing id="CardinalWriteImzML">
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_auto.imzml.txt
--- a/test-data/123_combined_auto.imzml.txt Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/123_combined_auto.imzml.txt Fri Dec 13 13:51:29 2019 -0500
b
@@ -1,4 +1,4 @@
 imzML file:
 total 452
--rw-r--r-- 1 meli meli 436764 Feb 12 00:51 ibd
--rw-r--r-- 1 meli meli  21166 Feb 12 00:51 imzml
+-rw-r--r-- 1 meli meli 436764 Dez 11 00:05 ibd
+-rw-r--r-- 1 meli meli  21514 Dez 11 00:05 imzml
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_auto.pdf
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Binary file test-data/123_combined_auto.pdf has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_picked.rdata
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Binary file test-data/123_combined_picked.rdata has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/123_combined_picked2.rdata
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Binary file test-data/123_combined_picked2.rdata has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_annotation_output.tabular
--- a/test-data/12_annotation_output.tabular Fri Mar 22 08:19:38 2019 -0400
+++ b/test-data/12_annotation_output.tabular Fri Dec 13 13:51:29 2019 -0500
b
@@ -1,10 +1,10 @@
-x y sample_name file_name column_name NA.x NA.y NA
-1 1 msidata_1.RData file_one col1 NA NA NA
-1 2 msidata_1.RData file_one col1 NA NA NA
-1 3 msidata_1.RData file_one col1 NA NA NA
-7 1 msidata_2.RData file_two col2 NA NA NA
-7 2 msidata_2.RData file_two col2 NA NA NA
-7 3 msidata_2.RData file_two col2 NA NA NA
-8 1 msidata_2.RData file_two col3 NA NA NA
-8 2 msidata_2.RData file_two col3 NA NA NA
-8 3 msidata_2.RData file_two col3 NA NA NA
+x y sample_name file_name column_name
+1 1 msidata_1.RData file_one col1
+1 2 msidata_1.RData file_one col1
+1 3 msidata_1.RData file_one col1
+7 1 msidata_2.RData file_two col2
+8 1 msidata_2.RData file_two col3
+7 2 msidata_2.RData file_two col2
+8 2 msidata_2.RData file_two col3
+7 3 msidata_2.RData file_two col2
+8 3 msidata_2.RData file_two col3
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_combined.RData
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Binary file test-data/12_combined.RData has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_combined.ibd
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Binary file test-data/12_combined.ibd has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_combined.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12_combined.imzml Fri Dec 13 13:51:29 2019 -0500
b
b'@@ -0,0 +1,318 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" 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_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e9aca5c3-32c8-416b-a9e9-e40ba239ce32" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c0c53177dc3a008c7a18ba10fe139ccaecc295a2" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="2.2.6">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n'..b'\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="235188" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=8" defaultArrayLength="0" index="8">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="7" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="268784" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=9" defaultArrayLength="0" index="9">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="302380" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/12_combined.imzml.txt Fri Dec 13 13:51:29 2019 -0500
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@@ -0,0 +1,4 @@
+imzML file:
+total 352
+-rw-r--r-- 1 meli meli 335976 Dez 11 00:07 ibd
+-rw-r--r-- 1 meli meli  17217 Dez 11 00:07 imzml
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/12_combined_QC.pdf
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/2123_auto_combined.RData
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Binary file test-data/2123_auto_combined.RData has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/2123_auto_combined.ibd
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/2123_auto_combined.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2123_auto_combined.imzml Fri Dec 13 13:51:29 2019 -0500
b
b'@@ -0,0 +1,561 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" 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_idx.xsd">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="89a84e82-79bf-466a-a1ce-e942e7cfe37d" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5d2027d8c0ad315ac09a1c7c4edf84d3d4facd90" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n+\t\t</fileContent>\n+\t</fileDescription>\n+\t<referenceableParamGroupList count="4">\n+\t\t<referenceableParamGroup id="spectrum1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="0" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="scan1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="mzArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t\t<referenceableParamGroup id="intensityArray">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" />\n+\t\t</referenceableParamGroup>\n+\t</referenceableParamGroupList>\n+\t<sampleList count="1">\n+\t\t<sample id="sample1" name="Sample1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000001" name="sample number" value="1" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="1">\n+\t\t<software id="Cardinal" version="2.2.6">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<scanSettingsList count="1">\n+\t\t<scanSettings id="scansettings1">\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="6" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="16" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" />\n+\t\t</scanSettings>\n+\t</scanSettingsList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="IC1">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">'..b'cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="537552" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=17" defaultArrayLength="0" index="17">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="571148" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t\t<spectrum id="Spectrum=18" defaultArrayLength="0" index="18">\n+\t\t\t\t<referenceableParamGroupRef ref="spectrum1" />\n+\t\t\t\t<scanList count="1">\n+\t\t\t\t\t<cvParam cvRef="MS" accession="MS:1000795" name="no combination" value="" />\n+\t\t\t\t\t<scan instrumentConfigurationRef="IC1">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="scan1" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" />\n+\t\t\t\t\t</scan>\n+\t\t\t\t</scanList>\n+\t\t\t\t<binaryDataArrayList count="2">\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t\t<binaryDataArray encodedLength="0">\n+\t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="604744" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8399" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="33596" />\n+\t\t\t\t\t\t<binary />\n+\t\t\t\t\t</binaryDataArray>\n+\t\t\t\t</binaryDataArrayList>\n+\t\t\t</spectrum>\n+\t\t</spectrumList>\n+\t</run>\n+</mzML>\n'
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/2123_auto_combined.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2123_auto_combined.imzml.txt Fri Dec 13 13:51:29 2019 -0500
b
@@ -0,0 +1,4 @@
+imzML file:
+total 656
+-rw-r--r-- 1 meli meli 638340 Dez 11 00:12 ibd
+-rw-r--r-- 1 meli meli  30107 Dez 11 00:12 imzml
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/2123_auto_combined_QC.pdf
b
Binary file test-data/2123_auto_combined_QC.pdf has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/picked.ibd
b
Binary file test-data/picked.ibd has changed
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/picked.imzml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.imzml Fri Dec 13 13:51:29 2019 -0500
b
b'@@ -0,0 +1,580 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<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="out" version="1.1.0">\n+ <cvList count="2">\n+  <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.44.0" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+  <cv id="UO" fullName="Unit Ontology" version="12:10:2012" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+  <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\n+ </cvList>\n+ <fileDescription>\n+  <fileContent>\n+   <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{3d75db19-25c6-4579-a1bc-fb0ee0bae869}"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="3fbb731b958a3ec73031a5894c29e3ef16586f39"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/>\n+   <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/>\n+  </fileContent>\n+ </fileDescription>\n+ <softwareList count="1">\n+  <software id="MALDIquantForeign" version="0.12"/>\n+ </softwareList>\n+ <referenceableParamGroupList count="2">\n+  <referenceableParamGroup id="mzArray">\n+   <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\n+   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>\n+   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\n+  </referenceableParamGroup>\n+  <referenceableParamGroup id="intensityArray">\n+   <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>\n+   <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\n+   <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>\n+   <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\n+  </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <scanSettingsList count="1">\n+  <scanSettings id="scansetting1">\n+   <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="17"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="1700" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="300" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>\n+   <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="100" unitCvRef="UO" unitAccession="UO:0000017" unitName="micrometer"/>\n+  </scanSettings>\n+ </scanSettingsList>\n+ <instrumentConfigurationList count="1">\n+  <instrumentConfiguration id="IC0"/>\n+ </instrumentConfigurationList>\n+ <dataProcessingList count="1">\n+  <dataProcessing id="export">\n+   <processingMethod order="1" softwareRef="MALDIquantForeign">\n+    <userParam name="MALDIquant object(s) exported to mzML" value=""/>\n+   </processingMethod>\n+  </dataProcessing>\n+ </dataProcessingList>\n+ <run id="run0" defaultInstrumentConfigurationRef="IC0">\n+  <spectrumList count="18" defaultDataProcessingRef="export">\n+   <spectrum index="0" id="scan=0" defaultArrayLength="1052">\n+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>\n+    <cvParam cvRef="MS" accession="MS:1000294" '..b'gth="0">\n+      <referenceableParamGroupRef ref="intensityArray"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156184"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="45"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="360"/>\n+      <binary/>\n+     </binaryDataArray>\n+    </binaryDataArrayList>\n+   </spectrum>\n+   <spectrum index="16" id="scan=16" defaultArrayLength="45">\n+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>\n+    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>\n+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="107.916664123535" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="789.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>\n+    <scanList count="1">\n+     <scan>\n+      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="17"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2"/>\n+     </scan>\n+    </scanList>\n+    <binaryDataArrayList count="2">\n+     <binaryDataArray encodedLength="0">\n+      <referenceableParamGroupRef ref="mzArray"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156544"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="45"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="360"/>\n+      <binary/>\n+     </binaryDataArray>\n+     <binaryDataArray encodedLength="0">\n+      <referenceableParamGroupRef ref="intensityArray"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156904"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="45"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="360"/>\n+      <binary/>\n+     </binaryDataArray>\n+    </binaryDataArrayList>\n+   </spectrum>\n+   <spectrum index="17" id="scan=17" defaultArrayLength="45">\n+    <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/>\n+    <cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum"/>\n+    <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="107.916664123535" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+    <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="789.916687011719" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\n+    <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum"/>\n+    <scanList count="1">\n+     <scan>\n+      <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="17"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3"/>\n+     </scan>\n+    </scanList>\n+    <binaryDataArrayList count="2">\n+     <binaryDataArray encodedLength="0">\n+      <referenceableParamGroupRef ref="mzArray"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="157264"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="45"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="360"/>\n+      <binary/>\n+     </binaryDataArray>\n+     <binaryDataArray encodedLength="0">\n+      <referenceableParamGroupRef ref="intensityArray"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="157624"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="45"/>\n+      <cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="360"/>\n+      <binary/>\n+     </binaryDataArray>\n+    </binaryDataArrayList>\n+   </spectrum>\n+  </spectrumList>\n+ </run>\n+</mzML>\n'
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/picked.imzml.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.imzml.txt Fri Dec 13 13:51:29 2019 -0500
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@@ -0,0 +1,4 @@
+imzML file:
+total 192
+-rw-r--r-- 1 meli meli 157984 Dez 11 00:03 ibd
+-rw-r--r-- 1 meli meli  35012 Dez 11 00:03 imzml
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/picked.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picked.tabular Fri Dec 13 13:51:29 2019 -0500
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@@ -0,0 +1,19 @@
+x y sample_name
+1 1 File1
+1 2 File1
+1 3 File1
+3 1 File1
+4 1 File1
+3 2 File1
+4 2 File1
+3 3 File1
+4 3 File1
+11 1 File2
+12 1 File2
+11 2 File2
+12 2 File2
+11 3 File2
+12 3 File2
+17 1 File2
+17 2 File2
+17 3 File2
b
diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/picked_QC.pdf
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Binary file test-data/picked_QC.pdf has changed
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diff -r 56b3b7d5f2b5 -r 4a05e47cd0ea test-data/xy_coordinates2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xy_coordinates2.tabular Fri Dec 13 13:51:29 2019 -0500
b
@@ -0,0 +1,2 @@
+0 0 File1
+8 0 File2