diff fml_gff_converter_programs/README @ 0:ed53dca1c6ff

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

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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
+
+galaxy: Contains tool configuration files in *.xml format. 
+
+    Tool configuration files. Please add right path to locate the scripts.
+
+    gtf_to_gff3.xml
+
+    gff3_to_gtf.xml
+
+    bed_to_gff3.xml
+
+    gff3_to_bed.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_gtf2gff3
+
+scripts: Python based and Perl based scripts. 
+
+    gtf_to_gff3_converter.py: This tool converts data from GTF format to valid GFF3 format.
+    
+    gff3_to_gtf_converter.pl: This tool converts data from GFF3 format to GTF format.
+
+    bed_to_gff3_converter.py: This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format.
+
+    gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.
+
+REQUIREMENTS
+
+    Python, Perl and if you are interested to use gff3_to_gtf_converter.pl please install Bio::Perl module.
+
+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.