--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Wed Apr 12 17:52:09 2017 -0400
@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 Rémi Marenco
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Apr 12 17:52:09 2017 -0400
@@ -0,0 +1,2 @@
+# bamToBigwig
+Galaxy wrapper for Bam to Bigwig conversion

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig.xml	Wed Apr 12 17:52:09 2017 -0400
@@ -0,0 +1,30 @@
+<tool id="bam_to_bigwig" name="Convert Bam to BigWig" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.0">ucsc_tools_340</requirement>
+        <requirement type="package" version="2.24">bedtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        faToTwoBit $input_reference_fasta two_bit.2bit;
+        twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes;
+        bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg;
+        bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
+    ]]></command>
+    <inputs>
+        <param format="bam" name="input_bam" type="data" label="Choose BAM file" />
+        <param format="fasta" name="input_reference_fasta"
+               type="data" label="Choose Reference Genome (Fasta)" />
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="output_bigwig" />
+    </outputs>
+    <help>
+        This tool converts a Bam file to a BigWig file.
+
+        It needs:
+            - A Bam file
+            - The reference genome as a Fasta file
+    </help>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Apr 12 17:52:09 2017 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ucsc_tools_340" version="1.0">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>                       
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>    
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+         </install>
+         <readme>The well known UCSC tools from Jim Kent.</readme>
+    </package>
+
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+</tool_dependency>