# HG changeset patch
# User Joachim Jacob <joachim.jacob@gmail.com>
# Date 1363768507 -3600
# Node ID 3d690162d6297dedcda88a72f0fa9cbe4376268f
# Parent  9537dd9dd18b240c262952ff36f2003842e6157a
Added more details for the required dependencies.

diff -r 9537dd9dd18b -r 3d690162d629 README
--- a/README	Tue Feb 12 04:50:47 2013 -0500
+++ b/README	Wed Mar 20 09:35:07 2013 +0100
@@ -1,4 +1,4 @@
-qualimap - 1.0.0
+qualimap - 1.0.1
 =====================================================================
 <joachim.jacob@vib.be>
 
@@ -15,16 +15,19 @@
 -----------------------------
 Install this tool in your Galaxy via the Toolshed
 
-   ) Third party code installation
-	Required: qualimap JAR archives.  
+   ) Required dependencies:
+	- Qualimap available in the PATH
+	- Perl 
+	- Perl core module File::Temp and File::Basename
+	- Perl module Log::Log4perl	
 
    ) Integration into Galaxy
 	Please use the toolshed
 
 DETAILS AND ISSUES
 ------------------
-   ) Only bamqc provided in this first version
-   ) bamqc: allow passing number of threads, and take into account number of 'chunks'
-   ) bamqc: 
+   ) Qualimap suite provide various quality control tools to apply 
+     after mapping. Only bamqc is provided in this first version
+   ) bamqc reports various statistics of an alignment.
 
 =====================================================================
diff -r 9537dd9dd18b -r 3d690162d629 bamqc.xml
--- a/bamqc.xml	Tue Feb 12 04:50:47 2013 -0500
+++ b/bamqc.xml	Wed Mar 20 09:35:07 2013 +0100
@@ -1,5 +1,5 @@
 
-<tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="0.0.1">
+<tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="1.0.1">
     <!-- Additional info: wrapper compatible with versions ..... -->
     <description>
 		to asses mapping quality metrics.
diff -r 9537dd9dd18b -r 3d690162d629 bamqc_wrapper.pl
--- a/bamqc_wrapper.pl	Tue Feb 12 04:50:47 2013 -0500
+++ b/bamqc_wrapper.pl	Wed Mar 20 09:35:07 2013 +0100
@@ -65,19 +65,6 @@
 mkdir "$tempdir", 077 unless -d "$tempdir";
 INFO "\nTemporary directory:\n$tempdir";
 
-
-# ---------------------- Output files ---------------------------------#
-########################################################################
-# Two possible scenarios
-# - output is written to the file at the output location in config file
-# - output is moved to the output file location
-
-# open (SAMOUTPUT, ">$para{'output_sam'}") 
-# 	or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die );
-# print SAMOUTPUT "Here comes sam\n";
-# close (SAMOUTPUT);	
-
-
 # -------------------- Assembling command  ----------------------------#
 ########################################################################
 my $outdir="bamqc_output";