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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 17:29:24 -0400
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 A set of tools for pre-processing genome annotation in Generic Feature Format (GFF)
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3 INTRODUCTION
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5 Here I am distributing a customized bio-python scripts to give details about the GFF file
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6 before you proceed with any analysis work. This programs allow you to get a better understanding
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7 about your GFF file and do necessary grooming procedure to make them valid for better use.
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8 Please follow the 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 gff_id_mapper.xml
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18 gff_available_limits.xml
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20 gff_loci_merge.xml
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23 t: Test data set. (move to your galaxy root folder/test-data/)
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25 You may need to move the test files into your test-data directory so galaxy can find them.
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26 If you want to run the functional tests eg as:
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28 sh run_functional_tests.sh -id fml_mergeloci
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30 scripts: Python based and Perl based scripts.
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32 gff_id_mapper.py : Provides feature to sub feature identifier mapping in a given GFF3 file ()
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34 gff_available_limits.py : This tool provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given GFF file.
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36 gff_loci_merge.py : This tool merge the feature annotation of same loci. MergeLoci will be able to merge several transcripts from single loci to a main feature instead of several features.
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38 REQUIREMENTS
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40 Python
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41
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42 COMMENTS/QUESTIONS
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43
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44 I can be reached at vipin.ts@tuebingen.mpg.de
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46 LICENSE
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47
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48 Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society
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49
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50 This program is free software; you can redistribute it and/or modify
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51 it under the terms of the GNU General Public License as published by
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52 the Free Software Foundation; either version 3 of the License, or
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53 (at your option) any later version.
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55 COURTESY
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56
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57 To the Galaxy Team.