Hello:

I would like to convert .gff3 file to 12-column .bed file, as in this link under "BED Format" (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

I have thus far used Galaxy from Penn State, but it outputs a 6-column .bed file.

Any advice is greatly appreciated!

Thank you
The UCSC Genome Browser [hosts conversion utilities][1] that you can run from your command line to accomplish the gff3 to BED12 conversion. Note utilities are OS specific and need to be given permission to execute with "chmod +x utilityName". 

Here's an example of how I did a conversion using the following steps:

 - wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.basic.annotation.gff3.gz
 - gunzip gencode.v31.basic.annotation.gff3.gz 
 - ./gff3ToGenePred
   gencode.v31.basic.annotation.gff3 gencode.v31.basic.genePred
 - ./genePredToBed gencode.v31.basic.genePred gencode.v31.basic.bed 

Disclaimer that I work for the UCSC Genome Browser. :)

  [1]: http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads