# HG changeset patch
# User iuc
# Date 1747314151 0
# Node ID 653803fab9212a88c9b1f6c9d406e5c9a1e54681
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 57b86418a4f032a5664b8dc1c9585a11be629158
diff -r 000000000000 -r 653803fab921 ggplot2_boxplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ggplot2_boxplot.xml Thu May 15 13:02:31 2025 +0000
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+
+ Boxplot visualization tool using ggplot2
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+ macros.xml
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+ r-tidyr
+ r-arrow
+ r-rlang
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+ > $script
+ #end if
+ ]]>
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+ export_R_script
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\ No newline at end of file
diff -r 000000000000 -r 653803fab921 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 15 13:02:31 2025 +0000
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+ r-ggplot2
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+ ggplot2
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+ 3.5.1
+ 1
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+ @book{wickham2009ggplot2,
+ author = {Hadley Wickham},
+ title = {ggplot2: Elegant Graphics for Data Analysis},
+ publisher = {Springer-Verlag New York},
+ year = {2009},
+ isbn = {978-0-387-98140-6},
+ url = {https://ggplot2.tidyverse.org/},
+ }
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+ out['additional_output_format'] != "none"
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diff -r 000000000000 -r 653803fab921 test-data/barplot_test_data.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barplot_test_data.txt Thu May 15 13:02:31 2025 +0000
@@ -0,0 +1,10 @@
+Condition Replicate Value ID
+ctrl 1 12 1
+ctrl 2 4 2
+ctrl 3 10 3
+trtA 1 50 4
+trtA 2 52 5
+trtA 3 49 6
+trtB 1 15 7
+trtB 2 10 8
+trtB 3 9 9
\ No newline at end of file
diff -r 000000000000 -r 653803fab921 test-data/boxplot_test_data.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/boxplot_test_data.txt Thu May 15 13:02:31 2025 +0000
@@ -0,0 +1,15 @@
+RowID File_1 File_2 File_3 File_4 File_5 File_6 File_7 File_8 File_9
+12 95.97218086 42.13959786 6.11506479 30.15646347 94.23814082 57.36969732 60.86347654 19.91409937 68.71355704
+14 59.66064371 64.93522126 32.32890474 40.14978233 2.891311477 32.96107785 66.75097997 0.920440008 24.22636581
+5 38.66154396 36.42452677 84.36958354 10.69964404 39.46448065 77.47277323 32.52771639 97.57285906 93.70459001
+36 32.97909046 43.52631758 59.83839323 69.87436805 98.12738555 4.751636512 47.47689026 41.3876903 67.78716531
+89 83.25413765 7.549367861 20.50592254 0.349459671 73.89946997 31.40388713 4.366449277 38.84340215 95.44116332
+965 71.74909204 40.82129731 21.73719426 32.67826786 93.7897543 92.54811762 57.16246361 98.97950241 38.61134734
+11 40.10030753 0.619259961 89.65946872 82.98278412 5.022064589 35.6513286 91.42743566 1.293400215 95.96990548
+2 82.35962922 25.48196256 47.51041934 71.45794006 90.23170047 34.52642435 88.0453423 63.2896977 28.82679247
+456 69.23813955 53.77332434 84.61367461 51.17705197 69.40525804 79.68268428 4.526957668 46.81700494 80.93458495
+68 88.78897848 85.84282896 51.53708603 71.26727107 94.03802875 77.02830433 50.12587615 30.93374275 15.06805862
+90 15.55940741 75.14719125 78.0377742 51.71345723 59.47299196 79.63191036 86.12417779 66.88062611 11.96856299
+23 51.55755631 26.99985192 85.64996749 74.54372275 97.09925394 47.50634659 43.94265016 60.73243208 89.94399967
+44 38.5549221 96.81614325 99.76966908 75.41077107 75.34246484 83.57435092 73.67006881 81.33326567 37.3100164
+567 72.74969753 17.0015972 64.01806032 37.71428705 41.30061893 84.5375675 44.21028268 9.076252458 50.67516692
diff -r 000000000000 -r 653803fab921 test-data/boxplot_test_expDesign.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/boxplot_test_expDesign.txt Thu May 15 13:02:31 2025 +0000
@@ -0,0 +1,10 @@
+SampleID Condition Replicate Batch
+File_1 control 1 1
+File_2 control 2 1
+File_3 control 3 1
+File_4 treatment_A 1 1
+File_5 treatment_A 2 1
+File_6 treatment_A 3 2
+File_7 treatment_B 1 2
+File_8 treatment_B 2 2
+File_9 treatment_B 3 2
diff -r 000000000000 -r 653803fab921 test-data/ggplot_heatmap_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_histogram_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_line_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_pca_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_point_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_point_result2.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_point_result3.pdf
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diff -r 000000000000 -r 653803fab921 test-data/ggplot_violin_result1.pdf
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diff -r 000000000000 -r 653803fab921 test-data/mtcars.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mtcars.txt Thu May 15 13:02:31 2025 +0000
@@ -0,0 +1,33 @@
+brand mpg cyl disp hp drat wt qsec vs am gear carb
+Mazda RX4 21 6 160 110 3.9 2.62 16.46 0 1 4 4
+Mazda RX4 Wag 21 6 160 110 3.9 2.875 17.02 0 1 4 4
+Datsun 710 22.8 4 108 93 3.85 2.32 18.61 1 1 4 1
+Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
+Hornet Sportabout 18.7 8 360 175 3.15 3.44 17.02 0 0 3 2
+Valiant 18.1 6 225 105 2.76 3.46 20.22 1 0 3 1
+Duster 360 14.3 8 360 245 3.21 3.57 15.84 0 0 3 4
+Merc 240D 24.4 4 146.7 62 3.69 3.19 20 1 0 4 2
+Merc 230 22.8 4 140.8 95 3.92 3.15 22.9 1 0 4 2
+Merc 280 19.2 6 167.6 123 3.92 3.44 18.3 1 0 4 4
+Merc 280C 17.8 6 167.6 123 3.92 3.44 18.9 1 0 4 4
+Merc 450SE 16.4 8 275.8 180 3.07 4.07 17.4 0 0 3 3
+Merc 450SL 17.3 8 275.8 180 3.07 3.73 17.6 0 0 3 3
+Merc 450SLC 15.2 8 275.8 180 3.07 3.78 18 0 0 3 3
+Cadillac Fleetwood 10.4 8 472 205 2.93 5.25 17.98 0 0 3 4
+Lincoln Continental 10.4 8 460 215 3 5.424 17.82 0 0 3 4
+Chrysler Imperial 14.7 8 440 230 3.23 5.345 17.42 0 0 3 4
+Fiat 128 32.4 4 78.7 66 4.08 2.2 19.47 1 1 4 1
+Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
+Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.9 1 1 4 1
+Toyota Corona 21.5 4 120.1 97 3.7 2.465 20.01 1 0 3 1
+Dodge Challenger 15.5 8 318 150 2.76 3.52 16.87 0 0 3 2
+AMC Javelin 15.2 8 304 150 3.15 3.435 17.3 0 0 3 2
+Camaro Z28 13.3 8 350 245 3.73 3.84 15.41 0 0 3 4
+Pontiac Firebird 19.2 8 400 175 3.08 3.845 17.05 0 0 3 2
+Fiat X1-9 27.3 4 79 66 4.08 1.935 18.9 1 1 4 1
+Porsche 914-2 26 4 120.3 91 4.43 2.14 16.7 0 1 5 2
+Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2
+Ford Pantera L 15.8 8 351 264 4.22 3.17 14.5 0 1 5 4
+Ferrari Dino 19.7 6 145 175 3.62 2.77 15.5 0 1 5 6
+Maserati Bora 15 8 301 335 3.54 3.57 14.6 0 1 5 8
+Volvo 142E 21.4 4 121 109 4.11 2.78 18.6 1 1 4 2
diff -r 000000000000 -r 653803fab921 utils.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/utils.r Thu May 15 13:02:31 2025 +0000
@@ -0,0 +1,13 @@
+# Function for the data input
+load_data <- function(file_name, file_extension) {
+ if (file_extension == "csv") {
+ data_input <- read.csv(file_name, check.names = "false")
+ } else if (file_extension %in% c("tsv", "txt", "tabular")) {
+ data_input <- read.delim(file_name, sep = "\t", check.names = "false")
+ } else if (file_extension == "parquet") {
+ data_input <- arrow::read_parquet(file_name)
+ } else {
+ stop("Unsupported file format.")
+ }
+ return(data_input)
+}