Mercurial > repos > vipints > fml_mergeloci
diff fml_gff_groomer/README @ 0:79726c328621 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | vipints |
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date | Tue, 07 Jun 2011 17:29:24 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_groomer/README Tue Jun 07 17:29:24 2011 -0400 @@ -0,0 +1,57 @@ +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 vipin.ts@tuebingen.mpg.de + +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.