# HG changeset patch # User galaxyp # Date 1585138021 14400 # Node ID 8da3511c9467e9d02647da335d0fd1db5f89016b # Parent 90d2e00e1304d4218c81e83fd4f0c5650e56bd69 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c" diff -r 90d2e00e1304 -r 8da3511c9467 macros.xml --- a/macros.xml Fri Dec 13 13:56:29 2019 -0500 +++ b/macros.xml Wed Mar 25 08:07:01 2020 -0400 @@ -1,316 +1,322 @@ - - 1.12.1 - - - - bioconductor-cardinal - r-base - - - - - - /dev/null | grep -v -i "WARNING: ") - ]]> - - - - - - - - - - - - 0, for if conditions - npeaks= sum(spectra(msidata)>0, na.rm=TRUE) - ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata))) - ## Number of duplicated coordinates - dupl_coord = sum(duplicated(coord(msidata))) - - properties = c("Number of m/z features", - "Range of m/z values", - "Number of pixels", - "Range of x coordinates", - "Range of y coordinates", - "Range of intensities", - "Number of NA intensities", - "Number of Inf intensities", - "Number of duplicated coordinates") - - values = c(paste0(maxfeatures), - paste0(minmz, " - ", maxmz), - paste0(pixelcount), - paste0(minimumx, " - ", maximumx), - paste0(minimumy, " - ", maximumy), - paste0(minint, " - ", maxint), - paste0(NAcount), - paste0(infcount), - paste0(dupl_coord)) - - property_df = data.frame(properties, values) - ]]> - - `_ - ]]> - `_ - - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - - Cardinal "MSImageSet" data saved as .RData - ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1093/bioinformatics/btv146 - - - - - - - - - - - - - - - - + + 1.12.1 + + + + bioconductor-cardinal + r-base + + + + + + /dev/null | grep -v -i "WARNING: ") + ]]> + + + + + + + + + + + + 0, for if conditions + npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + ## Number of NA in spectra matrix + NAcount = sum(is.na(spectra(msidata))) + ## Number of NA in spectra matrix + infcount = sum(is.infinite(spectra(msidata))) + ## Number of duplicated coordinates + dupl_coord = sum(duplicated(coord(msidata))) + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates", + "Range of intensities", + "Number of NA intensities", + "Number of Inf intensities", + "Number of duplicated coordinates") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy), + paste0(minint, " - ", maxint), + paste0(NAcount), + paste0(infcount), + paste0(dupl_coord)) + + property_df = data.frame(properties, values) + ]]> + + `_ + ]]> + `_ + - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) + - Cardinal "MSImageSet" data saved as .RData + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btv146 + + + + + + + + + + + + + + + + + + + + + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/Analyze75.hdr diff -r 90d2e00e1304 -r 8da3511c9467 test-data/Analyze75.img diff -r 90d2e00e1304 -r 8da3511c9467 test-data/Analyze75.t2m diff -r 90d2e00e1304 -r 8da3511c9467 test-data/Example_Continuous.ibd diff -r 90d2e00e1304 -r 8da3511c9467 test-data/Example_Continuous.imzML diff -r 90d2e00e1304 -r 8da3511c9467 test-data/analyze75_filtered2.pdf Binary file test-data/analyze75_filtered2.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/imzml_filtered3.pdf Binary file test-data/imzml_filtered3.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/imzml_filtered4.pdf Binary file test-data/imzml_filtered4.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/imzml_filtered5.pdf Binary file test-data/imzml_filtered5.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/imzml_filtered8.pdf Binary file test-data/imzml_filtered8.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out3.ibd Binary file test-data/out3.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out3.imzml --- a/test-data/out3.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out3.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out3.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out4.ibd Binary file test-data/out4.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out4.imzml --- a/test-data/out4.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out4.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out5.ibd Binary file test-data/out5.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out5.imzml --- a/test-data/out5.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out5.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out5.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out6.ibd Binary file test-data/out6.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out6.imzml --- a/test-data/out6.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out6.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + @@ -235,6 +252,8 @@ + + @@ -262,6 +281,8 @@ + + @@ -289,6 +310,8 @@ + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out6.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out7.ibd Binary file test-data/out7.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out7.imzml --- a/test-data/out7.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out7.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,6 +78,8 @@ + + @@ -100,6 +107,8 @@ + + @@ -127,6 +136,8 @@ + + @@ -154,6 +165,8 @@ + + @@ -181,6 +194,8 @@ + + @@ -208,6 +223,8 @@ + + @@ -235,6 +252,8 @@ + + @@ -262,6 +281,8 @@ + + @@ -289,6 +310,8 @@ + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/out7.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out8.ibd Binary file test-data/out8.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out8.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -0,0 +1,224 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/out8.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results1.ibd Binary file test-data/preprocessing_results1.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results1.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,21 +78,23 @@ + + - - + + - - - + + + @@ -100,21 +107,23 @@ + + - - + + - - - + + + @@ -127,21 +136,23 @@ + + - - + + - - - + + + @@ -154,21 +165,23 @@ + + - - + + - - - + + + @@ -181,21 +194,23 @@ + + - - + + - - - + + + @@ -208,21 +223,23 @@ + + - - + + - - - + + + @@ -235,21 +252,23 @@ + + - - + + - - - + + + @@ -262,21 +281,23 @@ + + - - + + - - - + + + @@ -289,21 +310,23 @@ + + - - + + - - - + + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results1.pdf Binary file test-data/preprocessing_results1.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results2.ibd Binary file test-data/preprocessing_results2.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results2.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,18 +42,24 @@ - + - + + + + + - + + + @@ -73,21 +78,23 @@ + + - - + + - - - + + + @@ -100,21 +107,23 @@ + + - - + + - - - + + + @@ -127,21 +136,23 @@ + + - - + + - - - + + + @@ -154,21 +165,23 @@ + + - - + + - - - + + + @@ -181,21 +194,23 @@ + + - - + + - - - + + + @@ -208,21 +223,23 @@ + + - - + + - - - + + + @@ -235,21 +252,23 @@ + + - - + + - - - + + + @@ -262,21 +281,23 @@ + + - - + + - - - + + + @@ -289,21 +310,23 @@ + + - - + + - - - + + + @@ -316,21 +339,23 @@ + + - - + + - - - + + + @@ -343,21 +368,23 @@ + + - - + + - - - + + + @@ -370,21 +397,23 @@ + + - - + + - - - + + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results2.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results2.pdf Binary file test-data/preprocessing_results2.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results3.ibd Binary file test-data/preprocessing_results3.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results3.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,21 +78,23 @@ + + - - + + - - - + + + @@ -100,21 +107,23 @@ + + - - + + - - - + + + @@ -127,21 +136,23 @@ + + - - + + - - - + + + @@ -154,21 +165,23 @@ + + - - + + - - - + + + @@ -181,21 +194,23 @@ + + - - + + - - - + + + @@ -208,21 +223,23 @@ + + - - + + - - - + + + @@ -235,21 +252,23 @@ + + - - + + - - - + + + @@ -262,21 +281,23 @@ + + - - + + - - - + + + @@ -289,21 +310,23 @@ + + - - + + - - - + + + diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results3.imzml.txt Wed Mar 25 08:07:01 2020 -0400 @@ -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 diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results3.pdf Binary file test-data/preprocessing_results3.pdf has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results4.ibd Binary file test-data/preprocessing_results4.ibd has changed diff -r 90d2e00e1304 -r 8da3511c9467 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Fri Dec 13 13:56:29 2019 -0500 +++ b/test-data/preprocessing_results4.imzml Wed Mar 25 08:07:01 2020 -0400 @@ -9,8 +9,8 @@ - - + + @@ -22,19 +22,18 @@ - - + - + @@ -43,7 +42,7 @@ - + @@ -51,10 +50,16 @@ + + + + - + + + @@ -73,21 +78,23 @@ + + - - + + - - - + + + @@ -100,21 +107,23 @@ + + - - + + - - - + + + @@ -127,21 +136,23 @@ + + - - + + - - - + + + @@ -154,21 +165,23 @@ + + - - + + - - - + + + @@ -181,21 +194,23 @@ + + - - + + - - - + + + @@ -208,21 +223,23 @@ + + - - + + - - - + + + @@ -235,21 +252,23 @@ + + - - - - - @@ -262,21 +281,23 @@ + + @@ -289,21 +310,23 @@