annotate fml_gff_groomer/README @ 0:79726c328621 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

A set of tools for pre-processing genome annotation in Generic Feature Format (GFF)

INTRODUCTION

Here I am distributing a customized bio-python scripts to give details about the GFF file 
before you proceed with any analysis work. This programs allow you to get a better understanding 
about your GFF file and do necessary grooming procedure to make them valid for better use.
Please follow the instructions below to clone these tools into your galaxy instance.

CONTENTS

galaxy: Contains tool configuration files in *.xml format. 

    Tool configuration files. Please add right path to locate the scripts.

    gff_id_mapper.xml

    gff_available_limits.xml

    gff_loci_merge.xml


t: Test data set. (move to your galaxy root folder/test-data/)
    
    You may need to move the test files into your test-data directory so galaxy can find them. 
    If you want to run the functional tests eg as: 

    sh run_functional_tests.sh -id fml_mergeloci

scripts: Python based and Perl based scripts. 

    gff_id_mapper.py : Provides feature to sub feature identifier mapping in a given GFF3 file ()

    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.

    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.

REQUIREMENTS

    Python 

COMMENTS/QUESTIONS 

I can be reached at [e-mail]

LICENSE

Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

COURTESY

To the Galaxy Team.