Mercurial > repos > galaxyp > cardinal_classification
changeset 9:24c000517173 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
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--- a/classification.xml Wed May 13 14:00:58 2020 -0400 +++ b/classification.xml Thu Sep 24 11:34:50 2020 +0000 @@ -1,11 +1,11 @@ -<tool id="cardinal_classification" name="MSI classification" version="@VERSION@.1"> +<tool id="cardinal_classification" name="MSI classification" version="@VERSION@.0"> <description>spatial classification of mass spectrometry imaging data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="2.3">r-gridextra</requirement> - <requirement type="package" version="3.2.1">r-ggplot2</requirement> + <requirement type="package" version="3.3.2">r-ggplot2</requirement> </expand> <command detect_errors="exit_code"> <![CDATA[ @@ -618,7 +618,23 @@ coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass") coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes) print(prediction_plot) + + + ## image with right and wrong classes: + comparison_df = cbind(prediction_df, y_vector) + comparison_df\$correct<- ifelse(comparison_df\$predicted_classes==comparison_df\$y_vector, T, F) + correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+ + geom_tile() + + coord_fixed()+ + ggtitle("Correctness of classification")+ + theme_bw()+ + theme(text=element_text(family="ArialMT", face="bold", size=15))+ + theme(legend.position="bottom",legend.direction="vertical")+ + guides(fill=guide_legend(ncol=2,byrow=TRUE)) + ## coord_labels = aggregate(cbind(x,y)~correct, data=comparison_df, mean, na.rm=TRUE, na.action="na.pass") + ##coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes) + print(correctness_plot) ## optional output as .RData #if $output_rdata: @@ -690,6 +706,25 @@ coord_labels = aggregate(cbind(x,y)~predicted_classes, data=prediction_df, mean, na.rm=TRUE, na.action="na.pass") coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes) print(prediction_plot) + + ## image with right and wrong classes: + + comparison_df = cbind(prediction_df, new_y_vector) + comparison_df\$correct<- as.factor(ifelse(comparison_df\$predicted_classes==comparison_df\$new_y_vector, T, F)) + + correctness_plot = ggplot(comparison_df, aes(x=x, y=y, fill=correct))+ + geom_tile()+ + scale_fill_manual(values = c("TRUE" = "orange","FALSE" = "darkblue"))+ + coord_fixed()+ + ggtitle("Correctness of classification")+ + theme_bw()+ + theme(text=element_text(family="ArialMT", face="bold", size=15))+ + theme(legend.position="bottom",legend.direction="vertical")+ + guides(fill=guide_legend(ncol=2,byrow=TRUE)) + ## coord_labels = aggregate(cbind(x,y)~correct, data=comparison_df, mean, na.rm=TRUE, na.action="na.pass") + ##coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$predicted_classes) + print(correctness_plot) + ## Summary table prediction summary_table = summary(prediction)\$accuracy[[names(prediction@resultData)]]
--- a/macros.xml Wed May 13 14:00:58 2020 -0400 +++ b/macros.xml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/112_auto_combined.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/112_auto_combined.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/112_auto_combined.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/112_auto_combined.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/123_combined.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/123_combined.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/123_combined.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/123_combined.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/123_combined_auto.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/123_combined_auto.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/123_combined_auto.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/123_combined_auto.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/12_combined.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/12_combined.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/12_combined.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/12_combined.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/2123_auto_combined.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/2123_auto_combined.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/2123_auto_combined.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/2123_auto_combined.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out3.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out3.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out3.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out3.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out4.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out4.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out4.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out4.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out5.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out5.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out5.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out5.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out6.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out6.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out6.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out6.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out7.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out7.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out7.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out7.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/out8.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out8.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/out8.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/out8.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/picked.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/picked.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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>
--- a/test-data/picked.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/picked.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -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
--- a/test-data/preprocessing_results4.imzml Wed May 13 14:00:58 2020 -0400 +++ b/test-data/preprocessing_results4.imzml Thu Sep 24 11:34:50 2020 +0000 @@ -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="c6122884-ceb5-46b6-9160-5d28e8862946" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9a685278-3bf0-48b5-b7c7-73a7a92625b2" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="036c4b8bf3f2f5a42a223ffd0b895f08b0a65f36" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - 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--- a/test-data/preprocessing_results4.imzml.txt Wed May 13 14:00:58 2020 -0400 +++ b/test-data/preprocessing_results4.imzml.txt Thu Sep 24 11:34:50 2020 +0000 @@ -1,4 +1,4 @@ imzML file: total 84 --rw-r--r-- 1 meli meli 63256 Mai 10 17:40 ibd --rw-r--r-- 1 meli meli 18199 Mai 10 17:40 imzml +-rw-rw-r-- 1 meli meli 62696 Sep 20 11:48 ibd +-rw-rw-r-- 1 meli meli 18199 Sep 20 11:48 imzml