changeset 7:3bddd7ab96e3 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1010eff91c8ce7415d50adaf2f83ecc278295df8"

--- a/barplot.r	Mon Oct 07 08:40:41 2019 -0400
+++ b/barplot.r	Sun Oct 24 23:52:11 2021 +0000
@@ -3,10 +3,13 @@
   q("no")
 }
 
-
 # load packages that are provided in the conda env
-options( show.error.messages=F,
-       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F,
+       error = function() {
+           cat(geterrmessage(), file = stderr())
+                           q("no", 1, F)
+       }
+)
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 warnings()
 library(optparse)
@@ -14,55 +17,50 @@
 library(ggrepel)
 library(RColorBrewer)
 
-
-#Arguments
-option_list = list(
+option_list <- list(
   make_option(
     c("-i", "--input"),
     default = NA,
-    type = 'character',
+    type = "character",
     help = "Input file that contains count data (no header)"
   ),
   make_option(
     c("-o", "--barplot"),
     default = NA,
-    type = 'character',
+    type = "character",
     help = "PDF output file"
   )
 )
 
-opt = parse_args(OptionParser(option_list = option_list),
+opt <- parse_args(OptionParser(option_list = option_list),
                  args = commandArgs(trailingOnly = TRUE))
 
-
-## 
-annotations = read.delim(opt$input, header=F)
-colnames(annotations) = c("sample", "class", "percent_of_reads", "total")
-annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2)
-# ggplot2 plotting
+annotations <- read.delim(opt$input, header = F)
+colnames(annotations) <- c("sample", "class", "percent_of_reads", "total")
+annotations$percent <- round(annotations$percent_of_reads / annotations$total * 100,
+                            digits = 2)
+## ggplot2 plotting
 
 # Define the number of colors you want
-Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231',
-                              '#911eb4', '#46f0f0', '#f032e6', '#bcf60c',
-                              '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000',
-                              '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080')
-nb.cols <- 19  # 10 with colorRampPalette
-# mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols)
-mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols]
-
-ggtitle('Class proportions') 
-ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) +
-       geom_bar(position="fill", stat="identity") + 
-       facet_wrap(~sample, ncol=3 ) +
-       geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
-       coord_polar(theta="y") +
+mycolors <- c("#e6194b", "#3cb44b", "#ffe119", "#4363d8", "#f58231",
+                              "#911eb4", "#46f0f0", "#f032e6", "#bcf60c",
+                              "#008080", "#e6beff", "#9a6324", "#fffac8", "#800000",
+                              "#aaffc3", "#808000", "#ffd8b1", "#000075", "#808080")
+ggtitle("Class proportions")
+ggplot(annotations, aes(x = total / 2, y = percent_of_reads, fill = class, width = total)) +
+       geom_bar(position = "fill", stat = "identity") +
+       facet_wrap(~sample, ncol = 3) +
+       geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5),
+                        size = 2, show.legend = F) +
+       coord_polar(theta = "y") +
        labs(x = "Class fractions (%)") +
        scale_fill_manual(values = mycolors) +
        theme(axis.text = element_blank(),
              axis.ticks = element_blank(),
              panel.grid  = element_blank(),
              axis.title.y = element_blank(),
-             legend.position="bottom") +
-       geom_text(aes(x = total/2, y= .5, label = paste(round(total/1000000, digits=3), "M"), vjust = 4, hjust=-1), size=2)
-ggsave(file=opt$barplot, device="pdf")
-
+             legend.position = "bottom") +
+       geom_text(aes(x = total / 2, y = .5, label = paste(round(total / 1000000, digits = 3),
+                     "M"),
+                 vjust = 4, hjust = -1), size = 2)
+ggsave(file = opt$barplot, device = "pdf")

--- a/sr_bowtie_dataset_annotation.xml	Mon Oct 07 08:40:41 2019 -0400
+++ b/sr_bowtie_dataset_annotation.xml	Sun Oct 24 23:52:11 2021 +0000
@@ -1,10 +1,10 @@
-<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.4.0">
+<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.5.0">
   <description>by iterative alignments with sRbowtie</description>
   <requirements>
-        <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="package" version="1.6.0">r-optparse</requirement>
-        <requirement type="package" version="3.1.0">r-ggplot2</requirement>
-        <requirement type="package" version="0.8.0">r-ggrepel</requirement>
+        <requirement type="package" version="1.3.1">bowtie</requirement>
+        <requirement type="package" version="1.7.1">r-optparse</requirement>
+        <requirement type="package" version="3.3.5">r-ggplot2</requirement>
+        <requirement type="package" version="0.9.1">r-ggrepel</requirement>
   </requirements>
   <command  detect_errors="exit_code"><![CDATA[
         #if $refGenomeSource1.genomeSource == "history":