# HG changeset patch
# User geoffrey.dintilhac
# Date 1578763437 18000
# Node ID 59907c23e75e70a8fd7fdbf446a2d94ab3d1ae0c
# Parent  fef10ad6ee1569844313e51e1135f659ff0f4e45
Uploaded

diff -r fef10ad6ee15 -r 59907c23e75e readme.txt
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+
+===========================
+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.
+
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