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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 16:41:06 -0400
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4c459744cab1 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 A collection of tools for converting genome annotation between GTF (Gene Transfer Format), BED (Browser Extensible Data) and GFF (Generic Feature Format)
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3 INTRODUCTION
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5 Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs
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6 they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested
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7 with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the
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8 instructions below to clone these tools into your galaxy instance.
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10 CONTENTS
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12 galaxy: Contains tool configuration files in *.xml format.
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14 Tool configuration files. Please add right path to locate the scripts.
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16 gtf_to_gff3.xml
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18 gff3_to_gtf.xml
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20 bed_to_gff3.xml
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22 gff3_to_bed.xml
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24 t: Test data set. (move to your galaxy root folder/test-data/)
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26 You may need to move the test files into your test-data directory so galaxy can find them.
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27 If you want to run the functional tests eg as:
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29 sh run_functional_tests.sh -id fml_gtf2gff3
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31 scripts: Python based and Perl based scripts.
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33 gtf_to_gff3_converter.py: This tool converts data from GTF format to valid GFF3 format.
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35 gff3_to_gtf_converter.pl: This tool converts data from GFF3 format to GTF format.
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37 bed_to_gff3_converter.py: This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format.
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39 gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.
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41 REQUIREMENTS
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43 Python, Perl and if you are interested to use gff3_to_gtf_converter.pl please install Bio::Perl module.
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44
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45 COMMENTS/QUESTIONS
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47 I can be reached at vipin.ts@tuebingen.mpg.de
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49 LICENSE
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50
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51 Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society
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52
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53 This program is free software; you can redistribute it and/or modify
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54 it under the terms of the GNU General Public License as published by
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55 the Free Software Foundation; either version 3 of the License, or
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56 (at your option) any later version.
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58 COURTESY
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60 To the Galaxy Team.