From c1073fd36ae491bf32092e911792f38ddf03802e Mon Sep 17 00:00:00 2001
From: Ioannis Moustakas <i.moustakas@lumc.nl>
Date: Wed, 6 Jul 2016 17:18:45 +0200
Subject: [PATCH] Created a help page for BaseCounter. It is incomplete

---
 docs/tools/BaseCounter.md | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 docs/tools/BaseCounter.md

diff --git a/docs/tools/BaseCounter.md b/docs/tools/BaseCounter.md
new file mode 100644
index 000000000..7bceca336
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+++ b/docs/tools/BaseCounter.md
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+# BaseCounter 
+
+## Introduction
+This tool will generate Base count based on a bam file and a refflat file
+
+## Example
+Help menu
+~~~~
+Usage: BaseCounter [options]
+
+  -l <value> | --log_level <value>
+        Log level
+  -h | --help
+        Print usage
+  -v | --version
+        Print version
+  -r <file> | --refFlat <file>
+        refFlat file. Mandatory
+  -o <directory> | --outputDir <directory>
+        Output directory. Mandatory
+  -b <file> | --bam <file>
+        Bam file. Mandatory
+  -p <prefix> | --prefix 
+  
+ ~~~~
+ 
-- 
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