# HG changeset patch
# User iuc
# Date 1698063037 0
# Node ID e25d81465c23acf5161526874916b031ddd95874
# Parent 8e903cb3f91925708a15360d48b4e75f8ca19ce8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
diff -r 8e903cb3f919 -r e25d81465c23 macros.xml
--- a/macros.xml Thu Sep 22 20:30:20 2022 +0000
+++ b/macros.xml Mon Oct 23 12:10:37 2023 +0000
@@ -6,6 +6,7 @@
1.2.0
+ 0
21.05
diff -r 8e903cb3f919 -r e25d81465c23 ribowaltz.R
--- a/ribowaltz.R Thu Sep 22 20:30:20 2022 +0000
+++ b/ribowaltz.R Mon Oct 23 12:10:37 2023 +0000
@@ -21,6 +21,7 @@
"cds_coverage_info", "Z", 1, "character",
"psite_info_rdata", "O", 0, "character",
"refseq_sep", "s", 0, "character",
+ "indel_threshold", "t", 0, "integer",
"params_duplicate_filterting", "d", 0, "character",
"params_peridiocity_filterting", "l", 0, "character",
"params_custom_filterting", "c", 0, "character",
@@ -48,7 +49,7 @@
sep <- NULL
}
# convert alignments in BAM files into list of data tables
-reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep)
+reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep, indel_threshold = opt$indel_threshold)
library("jsonlite")
# remove duplicate reads
@@ -63,21 +64,21 @@
# selection of read lengths - periodicity filtering
if (!is.null(opt$params_peridiocity_filterting)) {
- json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
- reads_list <- length_filter(
- data = reads_list,
- length_filter_mode = "periodicity",
- periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
- )
+ json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
+ reads_list <- length_filter(
+ data = reads_list,
+ length_filter_mode = "periodicity",
+ periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
+ )
}
# selection of read lengths - length range filtering
if (!is.null(opt$params_custom_filterting)) {
- json_custom_filterting <- fromJSON(opt$params_custom_filterting)
- reads_list <- length_filter(
- data = reads_list,
- length_filter_mode = "custom",
- length_range = json_custom_filterting$length_range
- )
+ json_custom_filterting <- fromJSON(opt$params_custom_filterting)
+ reads_list <- length_filter(
+ data = reads_list,
+ length_filter_mode = "custom",
+ length_range = json_custom_filterting$length_range
+ )
}
# compute P-site offset
diff -r 8e903cb3f919 -r e25d81465c23 ribowaltz_plot.R
--- a/ribowaltz_plot.R Thu Sep 22 20:30:20 2022 +0000
+++ b/ribowaltz_plot.R Mon Oct 23 12:10:37 2023 +0000
@@ -118,7 +118,7 @@
print(metaprofile)
sample_list <- list()
for (sample_name in names(reads_psite_list)) {
- sample_list[[sample_name]] <- c(sample_name)
+ sample_list[[sample_name]] <- c(sample_name)
}
metaheatmap <- metaheatmap_psite(
reads_psite_list,
@@ -138,15 +138,15 @@
pdf("codon_usage.pdf", height = 6, width = 16)
json_codon_usage_psite <- fromJSON(opt$params_codon_usage_psite)
for (sample_name in names(reads_psite_list)) {
- cu_barplot <- codon_usage_psite(
- reads_psite_list,
- annotation_dt,
- sample = sample_name,
- fastapath = json_codon_usage_psite$fastapath,
- fasta_genome = FALSE,
- frequency_normalization = json_codon_usage_psite$frequency
- )
- print(cu_barplot[["plot"]])
+ cu_barplot <- codon_usage_psite(
+ reads_psite_list,
+ annotation_dt,
+ sample = sample_name,
+ fastapath = json_codon_usage_psite$fastapath,
+ fasta_genome = FALSE,
+ frequency_normalization = json_codon_usage_psite$frequency
+ )
+ print(cu_barplot[["plot"]])
}
dev.off()
}
diff -r 8e903cb3f919 -r e25d81465c23 ribowaltz_plot.xml
--- a/ribowaltz_plot.xml Thu Sep 22 20:30:20 2022 +0000
+++ b/ribowaltz_plot.xml Mon Oct 23 12:10:37 2023 +0000
@@ -1,11 +1,11 @@
-
+
visual inspection of ribosome profiling data
macros.xml
-
+