| Previous changeset 8:525f201b86c1 (2020-05-13) Next changeset 10:c3eb5cd37ebe (2020-09-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" |
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modified:
combine.xml macros.xml 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_combined.ibd test-data/123_combined.imzml test-data/123_combined.imzml.txt 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_combined.ibd test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/12_combined_QC.pdf test-data/2123_auto_combined.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/centroids_proc.pdf test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf test-data/kmeans_analyze.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/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/pca_imzml.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked_QC.pdf test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a combine.xml --- a/combine.xml Wed May 13 14:08:25 2020 -0400 +++ b/combine.xml Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.1"> +<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.0"> <description> combine several mass spectrometry imaging datasets into one </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.2.1">r-ggplot2</requirement> + <requirement type="package" version="3.3.2">r-ggplot2</requirement> <requirement type="package" version="0.12">r-maldiquantforeign</requirement> <requirement type="package" version="1.19.3">r-maldiquant</requirement> </expand> @@ -110,17 +110,15 @@ msidata_$i\$column4 = NULL msidata_$i\$column5 = NULL msidata_$i\$combined_sample = NULL + msidata_$i <- as(msidata_$i, "MSImagingExperiment") #end if - ## coercion into MSImageSet - msidata_$i = as(msidata_$i, "MSImageSet") - ## remove duplicated coordinates, otherwise combine will fail print(paste0(sum(duplicated(coord(msidata_$i))), " duplicated coordinates were removed from input file")) msidata_${i} <- msidata_${i}[,!duplicated(coord(msidata_${i}))] ## same name for MSI data files necessary to combine data into one single coordinate system - sampleNames(msidata_$i) = "msidata" + run(msidata_$i) = "msidata" ############ 3) Read and process annotation tabular files ###################### @@ -252,7 +250,7 @@ ## combine only valid datasets valid_data = list(#echo ','.join($msidata)#)[valid_dataset] - msidata = do.call(combine, valid_data) + msidata = do.call(cbind, valid_data) print("Valid datasets in order of input bottom to top:") print(valid_dataset) writeImzML(msidata, "out") @@ -280,13 +278,13 @@ datasetlist = list() count = 1 for (usable_dataset in list(#echo ','.join($msidata)#)){ - pixelsofinterest = pixels(usable_dataset)[names(pixels(usable_dataset)) %in% rownames(coordinates_combined)] + + pixelsofinterest = paste(coord(usable_dataset)\$x, coord(usable_dataset)\$y, sep="_") %in% paste(coordinates_combined\$x, coordinates_combined\$y, sep="_") filtered_dataset = usable_dataset[,pixelsofinterest] if (ncol(filtered_dataset) > 0 ){ datasetlist[[count]] = filtered_dataset} count = count +1} - - msidata = do.call(combine, datasetlist) + msidata = do.call(cbind, datasetlist) writeImzML(msidata, "out") #else @@ -362,7 +360,7 @@ <inputs> <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" label="MSI data" - help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> + help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal 'MSImageSet' or 'MSImagingExperiment' saved as RData (regular upload)"/> <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> <conditional name="processed_cond"> <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a macros.xml --- a/macros.xml Wed May 13 14:08:25 2020 -0400 +++ b/macros.xml Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,10 +1,10 @@ <macros> - <token name="@VERSION@">2.4.0</token> + <token name="@VERSION@">2.6.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <requirement type="package" version="3.6.1">r-base</requirement> + <!--requirement type="package" version="3.6.1">r-base</requirement--> <yield/> </requirements> </xml> @@ -175,7 +175,7 @@ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - - Cardinal "MSImageSet" data saved as .RData + - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData ]]></token> <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - Optional tabular file with m/z values: @@ -243,7 +243,7 @@ </param> <when value="no_processed"/> <when value="processed"> - <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/> <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> <option value="mz" >mz</option> <option value="ppm" selected="True" >ppm</option> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/112_auto_combined.ibd |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/112_auto_combined.imzml --- a/test-data/112_auto_combined.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/112_auto_combined.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="de720b1f-c3fa-4596-b054-284efaff29fc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="040b9782d76e25ebe9a6b7c27fdda7e27e711674" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="23f1e1c8-aaa5-4d04-ab81-da14f7d24507" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b2e009b6e72791420e704b751b4fc1a0f36bf420" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/112_auto_combined.imzml.txt --- a/test-data/112_auto_combined.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/112_auto_combined.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 556 --rw-r--r-- 1 meli meli 537552 Apr 21 12:46 ibd --rw-r--r-- 1 meli meli 27497 Apr 21 12:46 imzml +-rw-rw-r-- 1 meli meli 537552 Aug 30 13:50 ibd +-rw-rw-r-- 1 meli meli 27497 Aug 30 13:50 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/123_combined.imzml --- a/test-data/123_combined.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/123_combined.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="c9f19079-a92c-4995-b4ee-48d2766994a8" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="889b1020d3d844330f13a360be4b2bd0b65d11a1" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="383dcc6e-fa4e-4ffe-8523-9cd0c3bd2571" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2cd98028c7ab9bd53b698168b508a0ac74f256c9" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/123_combined.imzml.txt --- a/test-data/123_combined.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/123_combined.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 452 --rw-r--r-- 1 meli meli 436764 Apr 21 12:41 ibd --rw-r--r-- 1 meli meli 22855 Apr 21 12:41 imzml +-rw-rw-r-- 1 meli meli 436764 Aug 30 13:46 ibd +-rw-rw-r-- 1 meli meli 22855 Aug 30 13:46 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/123_combined_auto.imzml --- a/test-data/123_combined_auto.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/123_combined_auto.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="386d1a7c-e065-4bf1-96a6-019586133b29" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bdafd878211e7d0c8fd0ef11bd534cbacfe7d40" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ae23e625-6ac2-4a33-be4a-b73af67bc0dd" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1b81e4b14567ea9da1177c0490f636d0823b2aac" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/123_combined_auto.imzml.txt --- a/test-data/123_combined_auto.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/123_combined_auto.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 452 --rw-r--r-- 1 meli meli 436764 Apr 21 12:43 ibd --rw-r--r-- 1 meli meli 22860 Apr 21 12:43 imzml +-rw-rw-r-- 1 meli meli 436764 Aug 30 13:48 ibd +-rw-rw-r-- 1 meli meli 22860 Aug 30 13:48 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/12_combined.imzml --- a/test-data/12_combined.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/12_combined.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="57f26041-833d-4843-ba25-0037f2c35f51" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c271b37214900da9960cd3bcb748cc5bc377cfec" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="85ec7820-8e87-4fb2-b74a-5b9cd8cf24d6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d8a4e14091441873e8969f3b6b249f55b4d95146" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/12_combined.imzml.txt --- a/test-data/12_combined.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/12_combined.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 352 --rw-r--r-- 1 meli meli 335976 Apr 21 12:45 ibd --rw-r--r-- 1 meli meli 18225 Apr 21 12:45 imzml +-rw-rw-r-- 1 meli meli 335976 Aug 30 13:49 ibd +-rw-rw-r-- 1 meli meli 18225 Aug 30 13:49 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/2123_auto_combined.imzml --- a/test-data/2123_auto_combined.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/2123_auto_combined.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="1c0a127a-8417-47ef-a049-553b9d56de81" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5113bf7d09e0b1a584238aa6c5242f50eeef839b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d5abe155-9afd-4249-aaf3-8fc631c1fd10" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="3c93096f299dc50ca088d712feca19f8bf2d5152" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/2123_auto_combined.imzml.txt --- a/test-data/2123_auto_combined.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/2123_auto_combined.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 656 --rw-r--r-- 1 meli meli 638340 Apr 21 12:46 ibd --rw-r--r-- 1 meli meli 32132 Apr 21 12:46 imzml +-rw-rw-r-- 1 meli meli 638340 Aug 30 13:50 ibd +-rw-rw-r-- 1 meli meli 32132 Aug 30 13:50 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out3.imzml --- a/test-data/out3.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out3.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6cc990a-d910-4c17-aedd-ceb204b4d105" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out3.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd --rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml +-rw-rw-r-- 1 meli meli 9616 Aug 23 17:39 ibd +-rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out4.ibd |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out4.imzml --- a/test-data/out4.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out4.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="b0dec95e-b66f-4c3f-86df-166d942f42c3" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out4.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 44 --rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd --rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml +-rw-rw-r-- 1 meli meli 28792 Aug 23 17:39 ibd +-rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out5.ibd |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out5.imzml --- a/test-data/out5.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out5.imzml Thu Sep 24 11:38:29 2020 +0000 |
| 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="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="30751422-deca-429e-9f8e-24639c108d6d" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out5.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 20 --rw-r--r-- 1 meli meli 380 Mär 24 19:24 ibd --rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml +-rw-rw-r-- 1 meli meli 380 Aug 23 17:40 ibd +-rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out6.imzml --- a/test-data/out6.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out6.imzml Thu Sep 24 11:38:29 2020 +0000 |
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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="8b625a26-987e-4e32-b7d4-729efe840814" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="254b991f-92f5-46d5-8069-6f9ecd53b05a" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out6.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 164 --rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd --rw-r--r-- 1 meli meli 18221 Mär 24 19:25 imzml +-rw-rw-r-- 1 meli meli 146896 Aug 23 17:41 ibd +-rw-rw-r-- 1 meli meli 18221 Aug 23 17:41 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out7.ibd |
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| Binary file test-data/out7.ibd has changed |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out7.imzml --- a/test-data/out7.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out7.imzml Thu Sep 24 11:38:29 2020 +0000 |
| 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="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="227ecc2e-a494-4018-afc5-45eaa790e812" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="e22162d1dd762607ca6d31c0b8892e0ae5a3a772" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out7.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 116 --rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd --rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml +-rw-rw-r-- 1 meli meli 95976 Aug 23 17:41 ibd +-rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out8.imzml --- a/test-data/out8.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out8.imzml Thu Sep 24 11:38:29 2020 +0000 |
| 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="ace74b18-25e2-4722-89f4-6eedc2b62ed8" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="91ed729b-0b8d-49f6-b832-e4d3834fe733" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="efd09bddeebeb334efe9dffad3a4f3bed35442d1" /> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/out8.imzml.txt --- a/test-data/out8.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/out8.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +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 +-rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd +-rw-rw-r-- 1 meli meli 12402 Aug 23 17:42 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/pca_imzml.pdf |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/picked.ibd |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/picked.imzml --- a/test-data/picked.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/picked.imzml Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -8,8 +8,8 @@ <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cb7c9edc-eee3-4159-a8a1-efdf5fc56a13}"/> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="f3e61f4699108e65bb678cfbbd6208be562f11c9"/> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{19bd2a62-4cc1-4316-b173-25f1de3871f6}"/> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ca84032e28aa3c04e4f41b74b85ccd1bd6e44107"/> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/> <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/> </fileContent> |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/picked.imzml.txt --- a/test-data/picked.imzml.txt Wed May 13 14:08:25 2020 -0400 +++ b/test-data/picked.imzml.txt Thu Sep 24 11:38:29 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 192 --rw-r--r-- 1 meli meli 157984 Apr 21 12:42 ibd --rw-r--r-- 1 meli meli 35012 Apr 21 12:42 imzml +-rw-rw-r-- 1 meli meli 157984 Aug 30 13:47 ibd +-rw-rw-r-- 1 meli meli 35012 Aug 30 13:47 imzml |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/picked_QC.pdf |
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| diff -r 525f201b86c1 -r 7e18fcb92a6a test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Wed May 13 14:08:25 2020 -0400 +++ b/test-data/preprocessing_results4.imzml Thu Sep 24 11:38:29 2020 +0000 |
| 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:1000128" name="profile spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6122884-ceb5-46b6-9160-5d28e8862946" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9a685278-3bf0-48b5-b7c7-73a7a92625b2" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="036c4b8bf3f2f5a42a223ffd0b895f08b0a65f36" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -42,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" 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