# HG changeset patch
# User artbio
# Date 1506291012 14400
# Node ID daec4df60281cc6e08b28fd554ef390fb8ca9dba
# Parent  4f744d3aaf0b2c9dee5a77905414176f589bd2ae
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 2b4a222804a40730abdaec6fb6aefc2295e89e11

diff -r 4f744d3aaf0b -r daec4df60281 probecoverage.r
--- a/probecoverage.r	Sun Sep 24 14:47:11 2017 -0400
+++ b/probecoverage.r	Sun Sep 24 18:10:12 2017 -0400
@@ -40,7 +40,12 @@
 
 ## end of function
 ## let's do a dataframe before plotting
-maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
+if (args$method == 'bedtools') {
+    maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20
+    } 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))]) {
diff -r 4f744d3aaf0b -r daec4df60281 probecoverage.xml
--- a/probecoverage.xml	Sun Sep 24 14:47:11 2017 -0400
+++ b/probecoverage.xml	Sun Sep 24 18:10:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="probecoverage" name="Probe Coverage" version="0.4.0">
+<tool id="probecoverage" name="Probe Coverage" version="0.4.1">
   <description></description>
   <requirements>
         <requirement type="package" version="1.4.1">samtools</requirement>
diff -r 4f744d3aaf0b -r daec4df60281 test-data/graph_pysam.pdf
Binary file test-data/graph_pysam.pdf has changed