# HG changeset patch # User vipints # Date 1402444676 14400 # Node ID c6cf723c2ed449a5d32c5d543409f3c48ef3cdfb # Parent ed53dca1c6ff9f9f208f68e510f8f18378bee935 Uploaded version 2.0.0 of gfftools to integrate local Galaxy instances. diff -r ed53dca1c6ff -r c6cf723c2ed4 GFFtools-GX --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GFFtools-GX Tue Jun 10 19:57:56 2014 -0400 @@ -0,0 +1,906 @@ + + + + + + + + + + + + + vipints/GFFtools-GX ยท GitHub + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
+ + + + + + + +
+
+ + + + + +
+ Sign up + +
+ +
+ + +
+ +
+ + + +
+ + + +
+ + This repository + + + +
+ + + + + + + + +
+
+ +
+
+ + + +
+
+
+ +
+
+
+ + + + +

+ public + + /GFFtools-GX + + + + + +

+
+
+ +
+
+
+ + +
+
+ +
+ + + +
+
+ +
+ + + + +
+

HTTPS clone URL

+
+ + + + +
+
+ + + +
+

Subversion checkout URL

+
+ + + + +
+
+ + +

You can clone with + HTTPS + or Subversion. + + + + + +

+ + + + + + Download ZIP + +
+
+ +
+ + + + +
+
+

gfftools - Galaxy toolshed repository

+
+ + + +
+ +
+ +
+
+ + +
+
    +
  1. + + + Python + 100% + +
    2. +
+
+
+
+ +
+ +
+ + Python + +
+ + + +
+ + + + + + +
+ + + branch: + master + + + +
+ + +
GFFtools-GX /
+
+ + + + + + + +
+

+ text modified + +

+
+ + latest commit 86358adfbb + +
+ Vipin + + authored + +
+
+
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + test-data + + + functional test added with files + + + +
+ + + + GFFParser.py + + + added doc text to the functions + + + +
+ + + + README + + + text modified + + + +
+ + + + bed_to_gff.py + + + imporved the desc text in bed2gff + + + +
+ + + + bed_to_gff.xml + + + functional test done bed to gff conv + + + +
+ + + + gbk_to_gff.py + + + desc text added + + + +
+ + + + gbk_to_gff.xml + + + functional test added with files + + + +
+ + + + gff_to_bed.py + + + license information updated + + + +
+ + + + gff_to_bed.xml + + + functional test done + + + +
+ + + + gff_to_gtf.py + + + license information updated + + + +
+ + + + gff_to_gtf.xml + + + tool id changed + + + +
+ + + + gtf_to_gff.py + + + requirement field updated + + + +
+ + + + gtf_to_gff.xml + + + base template wrapper for gtf to gff program + + + +
+ + + + helper.py + + + doc text improved + + + +
+ + + + tool_conf.xml.sample + + + tool panel entries + + + +
+
+ + +
+ + + README + + + 
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
+
+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. 
+    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.
+
+
+ + +
+ +
+
+
+
+ + +
+ +
+
+ + + + + + + +
+
+ + +
+
+
+ +
+
+
+ + + + + + +
+
+ + + +
+ + + Something went wrong with that request. Please try again. +
+ + + + + + + + + +