# HG changeset patch
# User artbio
# Date 1708418056 0
# Node ID 0adb846ca0567bb776490a7670414b5b53b4ff70
# Parent  bea8435e1e793679daa23d8b223e3ff4c46739b7
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage commit 668f7e9be66ae301f840b395d72ddcc311da7aa2

diff -r bea8435e1e79 -r 0adb846ca056 multicov.py
--- a/multicov.py	Thu Jun 03 23:59:31 2021 +0000
+++ b/multicov.py	Tue Feb 20 08:34:16 2024 +0000
@@ -53,6 +53,7 @@
         line_counter += 1
         suffix = '\t'.join(crossline)
         print('%s\t%s' % (prefix, suffix))
+    F.close()
 
 
 if __name__ == "__main__":
diff -r bea8435e1e79 -r 0adb846ca056 probecoverage.r
--- a/probecoverage.r	Thu Jun 03 23:59:31 2021 +0000
+++ b/probecoverage.r	Tue Feb 20 08:34:16 2024 +0000
@@ -1,9 +1,11 @@
 ## Setup R error handling to go to stderr
-options(show.error.messages = F,
-            error = function() {
-                cat(geterrmessage(), file = stderr()); q("no", 1, F)
-            }
-       )
+options(
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
+)
 warnings()
 library(optparse)
 library(ggplot2)
@@ -17,44 +19,44 @@
     make_option("--sample", type = "character", help = "a space separated of sample labels"),
     make_option("--method", type = "character", help = "bedtools or pysam"),
     make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot")
-    )
- 
+)
+
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
 args <- parse_args(parser)
 samples <- substr(args$sample, 2, nchar(args$sample) - 2)
 samples <- strsplit(samples, ", ")
- 
+
 # data frames implementation
 
-table <- read.delim(args$input, header = F)
+table <- read.delim(args$input, header = FALSE)
 headers <- c("chromosome", "start", "end", "id")
 for (i in seq(1, length(table) - 4)) {
     headers <- c(headers, samples[[1]][i])
-colnames(table) <- headers
+    colnames(table) <- headers
 }
 
 ## function
 if (args$method == "bedtools") {
     cumul <- function(x, y) sum(table[, y] / (table$end - table$start) > x) / length(table$chromosome)
-    } else {
+} else {
     cumul <- function(x, y) sum(table[, y] > x) / length(table$chromosome)
-    }
+}
 scale_fun <- function(x) sprintf("%.3f", x)
 
 ## end of function
 ## let's do a dataframe before plotting
 if (args$method == "bedtools") {
     maxdepth <- trunc(max(table[, 5:length(table)] / (table$end - table$start))) + 20
-    } else {
+} else {
     maxdepth <- trunc(max(table[, 5:length(table)])) + 20
-    }
+}
 
 graphpoints <- data.frame(1:maxdepth)
 i <- 5
 for (colonne in colnames(table)[5:length(colnames(table))]) {
-    graphpoints <- cbind(graphpoints,  mapply(cumul, 1:maxdepth, rep(i, maxdepth)))
+    graphpoints <- cbind(graphpoints, mapply(cumul, 1:maxdepth, rep(i, maxdepth)))
     i <- i + 1
-    }
+}
 colnames(graphpoints) <- c("Depth", colnames(table)[5:length(table)])
 maxfrac <- max(graphpoints[, 2:length(graphpoints)])
 
@@ -64,11 +66,13 @@
 
 pdf(file = args$output)
 ggplot(data = graphpoints, aes(x = Depth, y = sample_value, colour = Samples)) +
-      geom_line(size = 1) +
-      scale_x_continuous(trans = "log2", breaks = 2 ^ (seq(0, log(maxdepth, 2)))) +
-      scale_y_continuous(breaks = seq(0, maxfrac, by = maxfrac / 10), labels = scale_fun) +
-      labs(x = args$xlab, y = args$ylab, title = args$title) +
-      theme(legend.position = "top", legend.title = element_blank(),
-            legend.text = element_text(colour = "blue", size = 7))
+    geom_line(size = 1) +
+    scale_x_continuous(trans = "log2", breaks = 2^(seq(0, log(maxdepth, 2)))) +
+    scale_y_continuous(breaks = seq(0, maxfrac, by = maxfrac / 10), labels = scale_fun) +
+    labs(x = args$xlab, y = args$ylab, title = args$title) +
+    theme(
+        legend.position = "top", legend.title = element_blank(),
+        legend.text = element_text(colour = "blue", size = 7)
+    )
 
 devname <- dev.off()
diff -r bea8435e1e79 -r 0adb846ca056 probecoverage.xml
--- a/probecoverage.xml	Thu Jun 03 23:59:31 2021 +0000
+++ b/probecoverage.xml	Tue Feb 20 08:34:16 2024 +0000
@@ -1,19 +1,25 @@
-<tool id="probecoverage" name="Probe Coverage" version="0.7.0">
+<tool id="probecoverage" name="Probe Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
   <description></description>
-  <requirements>
-        <requirement type="package" version="1.10=h9402c20_2">samtools</requirement>
-        <requirement type="package" version="2.29.2=hc088bd4_0">bedtools</requirement>
-        <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
-        <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.17.3=py37h95a1406_0">numpy</requirement>
-        <requirement type="package" version="0.16.0.1">pysam</requirement>
-  </requirements>
+    <macros>
+        <token name="@TOOL_VERSION@">0.22.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
+    </macros>
+   <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pysam</requirement>
+        <requirement type="package" version="2.31.1">bedtools</requirement>
+        <requirement type="package" version="1.7.4">r-optparse</requirement>
+        <requirement type="package" version="3.4.4">r-ggplot2</requirement>
+        <requirement type="package" version="1.4.4">r-reshape2</requirement>
+        <requirement type="package" version="1.26.4">numpy</requirement>
+    </requirements>
   <stdio>
       <exit_code range="1:" level="fatal" description="Tool exception" />
   </stdio>
   <command detect_errors="exit_code"><![CDATA[
-      #for $file in $inputs
-          samtools index '$file' &&
+      #for $i, $file in enumerate($inputs):
+          ln -f -s '$file' ${i}.bam &&
+          ln -f -s '$file.metadata.bam_index' ${i}.bam.bai &&
       #end for
       #if $method == 'pysam':
           python $__tool_directory__/multicov.py
@@ -21,8 +27,8 @@
           bedtools multicov
       #end if
           -bams
-              #for $file in $inputs
-                  '$file'
+              #for $i, $file in enumerate($inputs):
+                  '${i}.bam'
               #end for
           -bed '$bed' > $coverage_dataframe &&
       Rscript '$__tool_directory__'/probecoverage.r
diff -r bea8435e1e79 -r 0adb846ca056 test-data/graph.pdf
Binary file test-data/graph.pdf has changed
diff -r bea8435e1e79 -r 0adb846ca056 test-data/graph_pysam.pdf
Binary file test-data/graph_pysam.pdf has changed