# HG changeset patch
# User czouaoui
# Date 1526541057 14400
# Node ID ec0d59a927e2a302bf04f7c25efdf05af7f8ce7a
# Parent  55f4ada53e504e80cde995624dd46485551d37dd
Uploaded

diff -r 55f4ada53e50 -r ec0d59a927e2 gc_cover_data/gc_cover_data.xml
--- a/gc_cover_data/gc_cover_data.xml	Thu May 17 03:02:16 2018 -0400
+++ b/gc_cover_data/gc_cover_data.xml	Thu May 17 03:10:57 2018 -0400
@@ -1,7 +1,5 @@
 <tool id="gc_cover_data" name="Generating R Data to run GC Cover Shiny app inside Galaxy" version="0.1.0">
 		<requirements>
-			<requirement type="package" version="2.12.0">bioconductor-iranges</requirement>
-			<requirement type="package" version="2.46.0">bioconductor-biostrings</requirement>
 			<requirement type="package" version="3.4_5">r-seqinr</requirement>
 		</requirements>
     <command detect_errors="exit_code"><![CDATA[
diff -r 55f4ada53e50 -r ec0d59a927e2 gc_cover_data/getGCCoverData.R
--- a/gc_cover_data/getGCCoverData.R	Thu May 17 03:02:16 2018 -0400
+++ b/gc_cover_data/getGCCoverData.R	Thu May 17 03:10:57 2018 -0400
@@ -1,7 +1,6 @@
 #!/usr/bin/env Rscript
 args = commandArgs(trailingOnly=TRUE)
 library(seqinr)
-library(Biostrings)
 
 # test if there is at least one argument: if not, return an error
 if (length(args) != 3) {
@@ -9,8 +8,7 @@
 }
 
 seqString <- read.fasta(args[1], seqonly=TRUE)
-sequence <- DNAString(seqString[[1]])
 covData <- scan(args[2], integer(), sep =",", skip = 1)
 seqName <- strsplit(args[3], '[.].*')
 
-save(sequence, covData, seqName, file="gcCover.RData")
+save(seqString, covData, seqName, file="gcCover.RData")