# HG changeset patch
# User iuc
# Date 1686254273 0
# Node ID d6b5fc94062ca5488cd08c26bb4cce078b8affc2
# Parent d3e447dd52c8310283f3cb947e129fb65e40889b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 10e44e324ee754d81a1b9d990ee0932b37e7a9bc
diff -r d3e447dd52c8 -r d6b5fc94062c macros.xml
--- a/macros.xml Wed Jun 07 11:47:30 2023 +0000
+++ b/macros.xml Thu Jun 08 19:57:53 2023 +0000
@@ -8,7 +8,7 @@
0.30.1
- 1
+ 2
20.01
diff -r d3e447dd52c8 -r d6b5fc94062c sleuth.R
--- a/sleuth.R Wed Jun 07 11:47:30 2023 +0000
+++ b/sleuth.R Thu Jun 08 19:57:53 2023 +0000
@@ -51,15 +51,11 @@
read.table(file = args$metadata_file,
header = TRUE,
sep = "\t")
- paths <- c()
- for (x in s2c$data_filename) {
- paths <- c(paths, paste("./kallisto_outputs/", x, sep = ""))
+
+ s2c$path <- file.path("./kallisto_outputs/", paste(s2c$path, ".h5", sep = ""))
+ for (f in args$factorLevel_counts) {
+ file.rename(f, paste(f, ".h5", sep = ""))
}
- for (f in paths) {
- file.rename(f, gsub(".fastq.*", "", f))
- file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
- }
- s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")
so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
so <- sleuth_fit(so)
diff -r d3e447dd52c8 -r d6b5fc94062c sleuth.xml
--- a/sleuth.xml Wed Jun 07 11:47:30 2023 +0000
+++ b/sleuth.xml Thu Jun 08 19:57:53 2023 +0000
@@ -67,7 +67,7 @@
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@@ -82,7 +82,7 @@
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/design.tab
--- a/test-data/design.tab Wed Jun 07 11:47:30 2023 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-sample condition data_filename
-CAM_01 CAM kallisto_output_01.h5
-CAM_02 CAM kallisto_output_02.h5
-reC3_01 reC3 kallisto_output_03.h5
-reC3_02 reC3 kallisto_output_04.h5
diff -r d3e447dd52c8 -r d6b5fc94062c test-data/design_three_factors.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/design_three_factors.tab Thu Jun 08 19:57:53 2023 +0000
@@ -0,0 +1,5 @@
+sample condition path colour
+CAM_01 CAM kallisto_output_01.h5 blue
+CAM_02 CAM kallisto_output_02.h5 green
+reC3_01 reC3 kallisto_output_03.h5 yellow
+reC3_02 reC3 kallisto_output_04.h5 blue
diff -r d3e447dd52c8 -r d6b5fc94062c test-data/design_two_factors.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/design_two_factors.tab Thu Jun 08 19:57:53 2023 +0000
@@ -0,0 +1,5 @@
+sample condition path
+CAM_01 CAM kallisto_output_01.h5
+CAM_02 CAM kallisto_output_02.h5
+reC3_01 reC3 kallisto_output_03.h5
+reC3_02 reC3 kallisto_output_04.h5
diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test01_density.pdf
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test01_pca.pdf
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test02_density.pdf
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test02_pca.pdf
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test03_density.pdf
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diff -r d3e447dd52c8 -r d6b5fc94062c test-data/test03_pca.pdf
Binary file test-data/test03_pca.pdf has changed