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