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author geoffrey.dintilhac
date Sat, 11 Jan 2020 12:23:57 -0500
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1
2 ===========================
3 Galaxy wrapper for bamtobed
4 ===========================
5
6 This wrapper is made by ALIS Marine and DINTILHAC Geoffrey, 2019.
7 Version 0.1.0.
8
9
10 Manual Installation
11 ===================
12
13 To use bamtobed tool please follow these steps :
14
15 - Create a folder bamtobed in /galaxy/tools
16
17 - Add the files "bamtobed.py" (Galaxy tool definition), "bamtobed.xml" (wrapper tool) and "readme.rst" in this folder
18
19 - In order to tell Galaxy this tool exists, a modification is needed, in the folder /galaxy/config :
20 * In the "tools_conf.xml" file, under the section "Convert Formats" (line :``<section id="convert" name="Convert Formats">``) add the line :
21 <tool file="bamtobed_project/bamtobed.xml" />
22
23 * Or if you rather add it in a new section, add (after all the sections) :
24 <section name="MyTools" id="mTools">
25 <tool file="bamtobed_project/bamtobed.xml" />
26 </section>
27
28
29 If you want to run the tests :
30 $ ./run_tests.sh -id bamtobed_project
31
32 This wrapper is available from the Galaxy Tool Shed at:
33 https://toolshed.g2.bx.psu.edu/view/geoffrey.dintilhac/bam_to_bed/68f7b5a4b1e2
34
35
36 What it does
37 ============
38
39 This tool converts sequence alignments in BAM format into BED, BED12 or BEDPE format running the command "bamtobed" of bedtools (version 2.29.0).
40 The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
41
42 For more informations about bamtobed command, please refer to this link : https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
43 For informations about BED and BEDPE format : https://bedtools.readthedocs.io/en/latest/content/general-usage.html
44
45 Warnings
46 ========
47 - If you want a BEDPE output, your input has to be paired-end and sorted by read name.
48 - About score calculation : the option "another tag" is disallowed with BEDPE output.
49 - About the options -split and -cigar :
50 * -split is disallowed with edit-distance as a calculation for BED score.
51 * -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score.
52
53
54 MIT License
55 =============
56
57 Permission is hereby granted, free of charge, to any person obtaining
58 a copy of this software and associated documentation files (the
59 "Software"), to deal in the Software without restriction, including
60 without limitation the rights to use, copy, modify, merge, publish,
61 distribute, sublicense, and/or sell copies of the Software, and to
62 permit persons to whom the Software is furnished to do so, subject to
63 the following conditions:
64
65 The above copyright notice and this permission notice shall be
66 included in all copies or substantial portions of the Software.
67
68 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
69 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
70 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
71 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
72 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
73 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
74 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
75 SOFTWARE
76
77 NOTE: This is the licence for the Galaxy Wrapper only.
78 bedtools bamtobed is available and licenced separately.
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