| Previous changeset 5:4a05e47cd0ea (2019-12-13) Next changeset 7:5e6f8fb2df07 (2020-04-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" |
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modified:
macros.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/analyze75_filtered2.pdf test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf test-data/preprocessing_results4.ibd test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/preprocessing_results5.pdf test-data/rdata_notfiltered.pdf |
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added:
test-data/imzml_filtered8.pdf test-data/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/preprocessing_results5.ibd test-data/preprocessing_results5.imzml test-data/preprocessing_results5.imzml.txt |
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removed:
test-data/preprocessing_results5.RData |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a macros.xml --- a/macros.xml Fri Dec 13 13:51:29 2019 -0500 +++ b/macros.xml Wed Mar 25 05:31:15 2020 -0400 |
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| b'@@ -1,316 +1,322 @@\n-<macros>\r\n- <token name="@VERSION@">1.12.1</token>\r\n-\r\n- <xml name="requirements">\r\n- <requirements>\r\n- <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement>\r\n- <requirement type="package" version="3.5.1">r-base</requirement>\r\n- <yield/>\r\n- </requirements>\r\n- </xml>\r\n-\r\n- <xml name="print_version">\r\n- <version_command><![CDATA[\r\n-echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\\$otherPkgs\\$Cardinal\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\r\n- ]]></version_command>\r\n- </xml>\r\n-\r\n- <token name="@INPUT_LINKING@"><![CDATA[\r\n- #if $infile.ext == \'imzml\'\r\n- ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\r\n- ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\r\n- #elif $infile.ext == \'analyze75\'\r\n- ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\r\n- ln -s \'${infile.extra_files_path}/img\' infile.img &&\r\n- ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\r\n- #else\r\n- ln -s $infile infile.RData &&\r\n- #end if\r\n- ]]></token>\r\n-\r\n-\r\n- <token name="@READING_MSIDATA@"><![CDATA[\r\n- ## importing MSI data files\r\n-\r\n- ## function to read RData files independent of filename\r\n- loadRData <- function(fileName){\r\n- load(fileName)\r\n- get(ls()[ls() != "fileName"])\r\n- }\r\n-\r\n- #if $infile.ext == \'imzml\'\r\n- #if str($processed_cond.processed_file) == "processed":\r\n- msidata <- readImzML(\'infile\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)\r\n- centroided(msidata) = $centroids\r\n- #else\r\n- msidata <- readImzML(\'infile\', attach.only=TRUE)\r\n- centroided(msidata) = $centroids\r\n- #end if\r\n- #elif $infile.ext == \'analyze75\'\r\n- msidata = readAnalyze(\'infile\', attach.only=TRUE)\r\n- centroided(msidata) = $centroids\r\n- #else\r\n- msidata = loadRData(\'infile.RData\')\r\n- #end if\r\n-\r\n- ]]></token>\r\n-\r\n- <token name="@DATA_PROPERTIES@"><![CDATA[\r\n- ## Number of features (mz)\r\n- maxfeatures = length(features(msidata))\r\n- ## Range mz\r\n- minmz = round(min(mz(msidata)), digits=2)\r\n- maxmz = round(max(mz(msidata)), digits=2)\r\n- ## Number of spectra (pixels)\r\n- pixelcount = length(pixels(msidata))\r\n- ## Range x coordinates\r\n- minimumx = min(coord(msidata)[,1])\r\n- maximumx = max(coord(msidata)[,1])\r\n- ## Range y coordinates\r\n- minimumy = min(coord(msidata)[,2])\r\n- maximumy = max(coord(msidata)[,2])\r\n-\r\n-\r\n- properties = c("Number of m/z features",\r\n- "Range of m/z values",\r\n- "Number of pixels", \r\n- "Range of x coordinates", \r\n- "Range of y coordinates")\r\n-\r\n- values = c(paste0(maxfeatures), \r\n- paste0(minmz, " - ", maxmz), \r\n- paste0(pixelcount), \r\n- paste0(minimumx, " - ", maximumx),\r\n- paste0(minimumy, " - ", maximumy))\r\n-\r\n- property_df = data.frame(properties, values)\r\n- ]]></token>\r\n-\r\n- <token name="@READING_MSIDATA_INRAM@"><![CDATA[\r\n- ## importing MSI data files\r\n-\r\n- ## function to read RData files independent of filename\r\n- loadRData <- function(fileName){\r\n- load(fileName)\r\n- get(ls()[ls() != "fileName"])\r\n- }\r\n-\r\n- #if $infile.ext == \'imzml\'\r\n- #if str($processed_cond.processed_file) == "processed":\r\n- msidata <- readImzML(\'infile\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")\r\n- centroi'..b'"radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">\n+ <option value="mz" >mz</option>\n+ <option value="ppm" selected="True" >ppm</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="pdf_filename">\n+ <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_"/>\n+ <add value=" "/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </xml>\n+\n+ <xml name="sanitizer_multiple_digits">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.digits">\n+ <add value=":" />\n+ <add value="," />\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+\n+ <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features">\n+ <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/>\n+ <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/>\n+ <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="reading_2_column_mz_tabular" token_optional="false">\n+ <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular"\n+ label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/>\n+ <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/>\n+ <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/>\n+ <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="reading_pixel_annotations">\n+ <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation"\n+ help="Tabular file with three columns: x values, y values and pixel annotations"/>\n+ <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>\n+ <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>\n+ <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>\n+ <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ </citations>\n+ </xml>\n+ <xml name="infile_analyze75">\n+ <param name="infile" value="" ftype="analyze75">\n+ <composite_data value="Analyze75.hdr"/>\n+ <composite_data value="Analyze75.img"/>\n+ <composite_data value="Analyze75.t2m"/>\n+ </param>\n+ </xml>\n+ <xml name="infile_imzml">\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Continuous.imzML"/>\n+ <composite_data value="Example_Continuous.ibd"/>\n+ </param>\n+ </xml>\n+ <xml name="processed_infile_imzml">\n+ <param name="infile" value="" ftype="imzml">\n+ <composite_data value="Example_Processed.imzML"/>\n+ <composite_data value="Example_Processed.ibd"/>\n+ </param>\n+ </xml>\n+</macros>\n' |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/analyze75_filtered2.pdf |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/imzml_filtered8.pdf |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.ibd |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.imzml --- a/test-data/out3.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out3.imzml Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -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="{AEDF2DEE-A321-4DAF-B971-943AE2AF79A6}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8311A159EC925605745E409F14BB6C570FF59ACA" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" /> <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="2.4.0"> <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="3" /> - <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="1" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="Inf" /> </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"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out3.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd --rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml +-rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd +-rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.ibd |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.imzml --- a/test-data/out4.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -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="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="b0dec95e-b66f-4c3f-86df-166d942f42c3" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" /> <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="2.4.0"> <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="3" /> + <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="2" /> <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="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="2.000000" /> + <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"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out4.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: total 44 --rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd --rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml +-rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd +-rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out5.imzml --- a/test-data/out5.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out5.imzml Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -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="{CC0B2B92-FB40-42C8-822F-834AA528954C}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" /> <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="2.4.0"> <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="3" /> - <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <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"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -208,6 +223,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out5.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 20 --rw-r--r-- 1 meli meli 380 Feb 12 00:50 ibd --rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml +-rw-r--r-- 1 meli meli 380 Mär 24 19:24 ibd +-rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.ibd |
| b |
| Binary file test-data/out6.ibd has changed |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.imzml --- a/test-data/out6.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out6.imzml Wed Mar 25 05:31:15 2020 -0400 |
| 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="{24BF18EC-E1DE-4B67-BC12-C3EB475CFC0A}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA0417F6AA4EDD71F808B6EA0D7A0706737464EB" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8b625a26-987e-4e32-b7d4-729efe840814" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" /> <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"> @@ -43,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> @@ -51,10 +50,16 @@ <scanSettings id="scansettings1"> <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="3" /> + <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"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -208,6 +223,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -235,6 +252,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -262,6 +281,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -289,6 +310,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out6.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 164 --rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd --rw-r--r-- 1 meli meli 16868 Feb 12 00:51 imzml +-rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd +-rw-r--r-- 1 meli meli 18221 Mär 24 19:25 imzml |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.ibd |
| b |
| Binary file test-data/out7.ibd has changed |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.imzml --- a/test-data/out7.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out7.imzml Wed Mar 25 05:31:15 2020 -0400 |
| 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="{B095BB77-684D-4BFF-82D3-B76D0EB1C0CD}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="628A551B81DCF301B65E3A5AB1182F0BF319533C" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" /> <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"> @@ -43,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> @@ -51,10 +50,16 @@ <scanSettings id="scansettings1"> <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="3" /> + <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"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -208,6 +223,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -235,6 +252,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -262,6 +281,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -289,6 +310,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/out7.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 116 --rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd --rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml +-rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd +-rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.ibd |
| b |
| Binary file test-data/out8.ibd has changed |
| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml Wed Mar 25 05:31:15 2020 -0400 |
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| b'@@ -0,0 +1,224 @@\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 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| b |
| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/out8.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 348 +-rw-r--r-- 1 meli meli 335976 Mär 24 19:27 ibd +-rw-r--r-- 1 meli meli 12402 Mär 24 19:27 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.ibd |
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| Binary file test-data/preprocessing_results1.ibd has changed |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results1.imzml Wed Mar 25 05:31:15 2020 -0400 |
| b |
| b'@@ -9,8 +9,8 @@\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:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{728FBFFE-E6FC-4283-8068-393A66F6BD5C}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="375094460F3B80674CB2F541DCD9928B3D61B2FF" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="722d404b-4188-40b4-a3b2-3764ebbdecad" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c5aded0bab57fd7317901ff7709f2395fc91152e" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" 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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 96 Feb 24 14:11 ibd --rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml +-rw-r--r-- 1 meli meli 216 Mär 24 10:39 ibd +-rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results1.pdf |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.ibd |
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| Binary file test-data/preprocessing_results2.ibd has changed |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results2.imzml Wed Mar 25 05:31:15 2020 -0400 |
| b |
| b'@@ -9,8 +9,8 @@\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:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{40F230A1-1893-4A8C-BAE2-A8BBEF24DB20}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="417ADF38FBC4D0304A9B75B4C85799137846DD2F" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="e536d1e2-427b-4c5b-9743-8210ae52a564" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="7cea783e9d345946b874fc1f25d40ce90bffd2f9" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\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\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" 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="32-bit float" />\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" 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name="position y" value="2" />\n+\t\t\t\t\t\t<userParam name="3DPositionX" value="9.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="2.000000" />\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="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\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="46304" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="31652" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -370,21 +397,23 @@\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\t<userParam name="3DPositionX" value="9.000000" />\n+\t\t\t\t\t\t<userParam name="3DPositionY" value="3.000000" />\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="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\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="50512" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="1052" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="4208" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="34528" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="719" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="2876" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n' |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results2.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: -total 80 --rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml +total 64 +-rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd +-rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results2.pdf |
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| Binary file test-data/preprocessing_results2.pdf has changed |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.ibd |
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| Binary file test-data/preprocessing_results3.ibd has changed |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results3.imzml Wed Mar 25 05:31:15 2020 -0400 |
| b |
| b'@@ -9,8 +9,8 @@\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:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{D767424F-5E74-45AB-AF1B-0D25244B435B}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="445E32981D0B3D08ED2BA74E11500A3A08CDB9B7" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="f367e393-ca54-4bcc-bc17-10f87a3e41d0" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b9439af71c5fb6703e3fe571d12a1f9b6f90d82c" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\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\t<cvParam cvRef="MS" accession="MS:1000095" name="linear" 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="32-bit float" />\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" 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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results3.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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| @@ -1,4 +1,4 @@ imzML file: -total 36 --rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml +total 24 +-rw-r--r-- 1 meli meli 136 Mär 24 11:10 ibd +-rw-r--r-- 1 meli meli 18088 Mär 24 11:10 imzml |
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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results4.imzml Wed Mar 25 05:31:15 2020 -0400 |
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| b'@@ -9,8 +9,8 @@\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="{FE932E04-42E4-4D89-B721-2A6CE83250B6}" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="36C7C916C176DD85CBBF4B7FA969C92B9403768D" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="db79298c-8368-42d7-84fc-18cad6ef1924" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="18bae3cc87b4c9aab2577cffe2fbc7425a93270b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -22,19 +22,18 @@\n \t\t</referenceableParamGroup>\n \t\t<referenceableParamGroup id="scan1">\n \t\t\t<cvParam cvRef="MS" 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| diff -r 4a05e47cd0ea -r 25b83cbd596a test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Fri Dec 13 13:51:29 2019 -0500 +++ b/test-data/preprocessing_results4.imzml.txt Wed Mar 25 05:31:15 2020 -0400 |
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