# HG changeset patch
# User czouaoui
# Date 1526480590 14400
# Node ID 8a780635d8b4b78ecb92eda360ebfb0b060bff14
# Parent  a1f6c322aa2689d07bc22f87aac0aea91ab3397c
Deleted selected files

diff -r a1f6c322aa26 -r 8a780635d8b4 gc_cover_data/gc_cover_data.xml
--- a/gc_cover_data/gc_cover_data.xml	Wed May 16 10:12:05 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-<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="2.46.0">bioconductor-biostrings</requirement>
-		</requirements>
-    <command detect_errors="exit_code"><![CDATA[
-				Rscript $__tool_directory__/getGCCoverData.R $input1 $input2 "$input1.name"
-    ]]></command>
-    <inputs>
-        <param type="data" name="input1" format="fasta" label="DNA Sequence"/>
-				<param type="data" name="input2" format="txt" label="Coverage (Imagesmajik file)"/>
-    </inputs>
-    <outputs>
-        <data name= "output" format="rdata" label="${input1.name} - GCCover" from_work_dir="gcCover.RData"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input1" format="fasta" value="sequence.fasta"/>
-						<param name="input2" format="txt" value="covFile"/>
-            <output name="output" format="rdata" file="gcCover.RData"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        This tool is used to generate a R Data file from Fasta and Imagesmajik files. The data inside this file are used
-				to start the GC Cover Shiny application from Galaxy.
-    ]]></help>
-</tool>
diff -r a1f6c322aa26 -r 8a780635d8b4 gc_cover_data/getGCCoverData.R
--- a/gc_cover_data/getGCCoverData.R	Wed May 16 10:12:05 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-#!/usr/bin/env Rscript
-args = commandArgs(trailingOnly=TRUE)
-sessionInfo()
-library(Biostrings)
-sessionInfo()
-# test if there is at least one argument: if not, return an error
-if (length(args) != 3) {
-  stop("At least 3 arguments must be supplied (Fasta file, Coverage file, Fasta file name)", call.=FALSE)
-}
-
-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")