===========================
Galaxy wrapper for bamtobed
===========================

This wrapper is made by ALIS Marine and DINTILHAC Geoffrey, 2019.
Version 0.1.0.


Manual Installation
===================

To use bamtobed tool please follow these steps :

- Create a folder bamtobed in /galaxy/tools 

- Add the files "bamtobed.py" (Galaxy tool definition), "bamtobed.xml" (wrapper tool) and "readme.rst" in this folder

- In order to tell Galaxy this tool exists, a modification is needed, in the folder /galaxy/config : 
	* In the "tools_conf.xml" file, under the section "Convert Formats" (line :``<section id="convert" name="Convert Formats">``) add the line :
		<tool file="bamtobed_project/bamtobed.xml" />

	* Or if you rather add it in a new section, add (after all the sections) : 
		<section name="MyTools" id="mTools">
			<tool file="bamtobed_project/bamtobed.xml" />
		</section>


If you want to run the tests : 
    $ ./run_tests.sh -id bamtobed_project

This wrapper is available from the Galaxy Tool Shed at:
https://toolshed.g2.bx.psu.edu/view/geoffrey.dintilhac/bam_to_bed/68f7b5a4b1e2


What it does
============

This tool converts sequence alignments in BAM format into BED, BED12 or BEDPE format running the command "bamtobed" of bedtools (version 2.29.0).
The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.

For more informations about bamtobed command, please refer to this link : https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
For informations about BED and BEDPE format : https://bedtools.readthedocs.io/en/latest/content/general-usage.html

Warnings
========
- If you want a BEDPE output, your input has to be paired-end and sorted by read name.
- About score calculation : the option "another tag" is disallowed with BEDPE output.
- About the options -split and -cigar : 
	* -split is disallowed with edit-distance as a calculation for BED score. 
	* -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score.


MIT License
=============

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

NOTE: This is the licence for the Galaxy Wrapper only.
bedtools bamtobed is available and licenced separately.