+
+ + GFFtools-GXA collection of tools for converting genome annotation between GTF, BED, GenBank and GFF.
+ ++
+ + INTRODUCTIONSeveral genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. These programs can be easily integrated into your galaxy instance.
+ ++
+ + CONTENTSIncluded utilities are:
+ +BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
+GBK-to-GFF: convert data from genbank format to GFF
+GFF-to-BED: convert data from GFF to 12 column BED format
+GFF-to-GTF: convert data from GFF to GTF
+GTF-to-GFF: convert data from GTF to valid GFF
+
+
+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
+
+
++
+ + REQUIREMENTSpython2.6 or 2.7 and biopython
+
+Galaxy should be able to automatically install biopython via Galaxy toolshed.
+
+
++
+ + COMMENTS/QUESTIONSI can be reached at vipin [at] cbio.mskcc.org
+ ++
+ + LICENSECopyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society
+ + 2013-2015, Memorial Sloan Kettering Cancer Center
+ Vipin T Sreedharan <vipin@cbio.mskcc.org>
+
+
+All rights reserved.
+ +Licensed under the BSD 2-Clause License: http://opensource.org/licenses/BSD-2-Clause
+ +Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
++
+ + COURTESYTo the Galaxy Team.
+