# HG changeset patch # User galaxyp # Date 1600947584 0 # Node ID e92efed8320847ddf4a325d795067070e0ae9958 # Parent a8157342d9a3362929683c952cebaeaf6ecd5f99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" diff -r a8157342d9a3 -r e92efed83208 filtering.xml --- a/filtering.xml Wed May 13 14:11:34 2020 -0400 +++ b/filtering.xml Thu Sep 24 11:39:44 2020 +0000 @@ -5,7 +5,7 @@ r-gridextra - r-ggplot2 + r-ggplot2 @@ -365,7 +365,7 @@ theme(plot.title = element_text(hjust = 0.5))+ theme(legend.position="bottom",legend.direction="vertical")+ guides(fill=guide_legend(ncol=5,byrow=TRUE)) - print(pixel_image) + print(pixel_image + scale_fill_manual(values=c("#00BFC4", "#F8766D"))) ### visual mz feature control @@ -384,7 +384,8 @@ theme(legend.position="bottom",legend.direction="vertical")+ labs(title="Overview of filtered m/z", x="m/z", y = "count") + guides(fill=guide_legend(ncol=5,byrow=TRUE)) - print(histogram_mz) + print(histogram_mz + scale_fill_manual(values=c("#00BFC4", "#F8766D"))) + dev.off() @@ -525,7 +526,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 macros.xml --- a/macros.xml Wed May 13 14:11:34 2020 -0400 +++ b/macros.xml Thu Sep 24 11:39:44 2020 +0000 @@ -1,10 +1,10 @@ - 2.4.0 + 2.6.0 bioconductor-cardinal - r-base + @@ -175,7 +175,7 @@ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format `_ - 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 ]]> - + diff -r a8157342d9a3 -r e92efed83208 test-data/112_auto_combined.ibd Binary file test-data/112_auto_combined.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/112_auto_combined.imzml --- a/test-data/112_auto_combined.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/112_auto_combined.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/112_auto_combined.imzml.txt --- a/test-data/112_auto_combined.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/112_auto_combined.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/112_auto_combined_QC.pdf Binary file test-data/112_auto_combined_QC.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined.ibd Binary file test-data/123_combined.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined.imzml --- a/test-data/123_combined.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/123_combined.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined.imzml.txt --- a/test-data/123_combined.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/123_combined.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined_QC.pdf Binary file test-data/123_combined_QC.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined_auto.ibd Binary file test-data/123_combined_auto.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined_auto.imzml --- a/test-data/123_combined_auto.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/123_combined_auto.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined_auto.imzml.txt --- a/test-data/123_combined_auto.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/123_combined_auto.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/123_combined_auto.pdf Binary file test-data/123_combined_auto.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/12_combined.ibd Binary file test-data/12_combined.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/12_combined.imzml --- a/test-data/12_combined.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/12_combined.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/12_combined.imzml.txt --- a/test-data/12_combined.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/12_combined.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/12_combined_QC.pdf Binary file test-data/12_combined_QC.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/2123_auto_combined.ibd Binary file test-data/2123_auto_combined.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/2123_auto_combined.imzml --- a/test-data/2123_auto_combined.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/2123_auto_combined.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/2123_auto_combined.imzml.txt --- a/test-data/2123_auto_combined.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/2123_auto_combined.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/2123_auto_combined_QC.pdf Binary file test-data/2123_auto_combined_QC.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Heatmaps_LM8_file16.pdf Binary file test-data/Heatmaps_LM8_file16.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Heatmaps_analyze75.pdf Binary file test-data/Heatmaps_analyze75.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Heatmaps_imzml.pdf Binary file test-data/Heatmaps_imzml.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Heatmaps_processed.pdf Binary file test-data/Heatmaps_processed.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Heatmaps_rdata.pdf Binary file test-data/Heatmaps_rdata.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_analyze75.pdf Binary file test-data/Plot_analyze75.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_analyze75_allpixels.pdf Binary file test-data/Plot_analyze75_allpixels.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_imzml.pdf Binary file test-data/Plot_imzml.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_picked.pdf Binary file test-data/Plot_picked.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_processed.pdf Binary file test-data/Plot_processed.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/Plot_rdata.pdf Binary file test-data/Plot_rdata.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/QC_analyze75.pdf Binary file test-data/QC_analyze75.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/QC_empty_spectra.pdf Binary file test-data/QC_empty_spectra.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/QC_imzml.pdf Binary file test-data/QC_imzml.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/QC_rdata.pdf Binary file test-data/QC_rdata.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/analyze75_filtered2.pdf Binary file test-data/analyze75_filtered2.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/centroids_proc.pdf Binary file test-data/centroids_proc.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/centroids_rdata.pdf Binary file test-data/centroids_rdata.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/cluster_skm.RData Binary file test-data/cluster_skm.RData has changed diff -r a8157342d9a3 -r e92efed83208 test-data/imzml_filtered3.pdf Binary file test-data/imzml_filtered3.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/imzml_filtered4.pdf Binary file test-data/imzml_filtered4.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/imzml_filtered5.pdf Binary file test-data/imzml_filtered5.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/imzml_filtered8.pdf Binary file test-data/imzml_filtered8.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/kmeans_analyze.pdf Binary file test-data/kmeans_analyze.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out3.ibd Binary file test-data/out3.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out3.imzml --- a/test-data/out3.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out3.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out3.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/out4.ibd Binary file test-data/out4.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out4.imzml --- a/test-data/out4.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out4.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out4.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/out5.ibd Binary file test-data/out5.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out5.imzml --- a/test-data/out5.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out5.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out5.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/out6.ibd Binary file test-data/out6.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out6.imzml --- a/test-data/out6.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out6.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out6.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/out7.ibd Binary file test-data/out7.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out7.imzml --- a/test-data/out7.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out7.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out7.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/out8.ibd Binary file test-data/out8.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/out8.imzml --- a/test-data/out8.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out8.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + diff -r a8157342d9a3 -r e92efed83208 test-data/out8.imzml.txt --- a/test-data/out8.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/out8.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/pca_imzml.pdf Binary file test-data/pca_imzml.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/picked.ibd Binary file test-data/picked.ibd has changed diff -r a8157342d9a3 -r e92efed83208 test-data/picked.imzml --- a/test-data/picked.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/picked.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -8,8 +8,8 @@ - - + + diff -r a8157342d9a3 -r e92efed83208 test-data/picked.imzml.txt --- a/test-data/picked.imzml.txt Wed May 13 14:11:34 2020 -0400 +++ b/test-data/picked.imzml.txt Thu Sep 24 11:39:44 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 diff -r a8157342d9a3 -r e92efed83208 test-data/picked_QC.pdf Binary file test-data/picked_QC.pdf has changed diff -r a8157342d9a3 -r e92efed83208 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Wed May 13 14:11:34 2020 -0400 +++ b/test-data/preprocessing_results4.imzml Thu Sep 24 11:39:44 2020 +0000 @@ -9,8 +9,8 @@ - - + + @@ -42,7 +42,7 @@ - + @@ -86,15 +86,15 @@ - - + + - - - + + + @@ -115,15 +115,15 @@ - - + + - - - + + + @@ -144,15 +144,15 @@ - - + + - - - + + + @@ -173,15 +173,15 @@ - - + + - - - + + + @@ -202,15 +202,15 @@ - 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