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

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+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.