diff README @ 5:6e589f267c14

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+A collection of tools for converting genome annotation between GTF (Gene Transfer Format), 
+BED (Browser Extensible Data) and GFF (Generic Feature Format).
+
+INTRODUCTION
+
+Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs 
+they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested 
+with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the 
+instructions below to clone these tools into your galaxy instance.
+
+CONTENTS
+
+Tool configuration files in *.xml format. 
+
+    gtf_to_gff.xml
+    gff_to_gtf.xml
+    bed_to_gff.xml
+    gff_to_bed.xml
+    gbk_to_gff.xml
+    gff_fmap.xml
+
+Python based scripts. 
+
+    gtf_to_gff.py: convert data from GTF to valid GFF3.
+    gff_to_gtf.py: convert data from GFF3 to GTF.
+    bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3.
+    gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format.
+    gbk_to_gff.py: convert data from genbank format to GFF. 
+    gff_fmap.py: find the relation between different features described in a GFF file.  
+    GFFParser.py: Parse GFF/GTF files.  
+    helper.py: Utility functions.
+
+test-data: 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: 
+
+    exmaple: 
+    sh run_functional_tests.sh -id fml_gtf2gff
+
+REQUIREMENTS
+
+    python 
+
+COMMENTS/QUESTIONS 
+
+I can be reached at vipin [at] cbio.mskcc.org 
+
+LICENSE
+
+Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society
+              2013-2014 Memorial Sloan Kettering Cancer Center
+
+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.