Dear Galaxy team,

I just realized that the “merge” tool in the ‘Operate on Genomic intervals” section has been modified (for both the test and the main sites). When I used it before, it gave me only three columns as output (start, end and chromosome) regardless of the number of columns present in the original file. That was actually very handy for me, because it meant that after merging output files from different programs individually, I could join those into one without problem because the columns ended up being the same in all files. Now the tool conserves the column number by adding dot columns to reproduce the original number of columns. I wonder if there is the possibility to leave this as an option, so that the user can choose among conserving number of columns or getting a simplified version with only three output columns like before. I know I can simply cut the columns I want out to another file, but it is an additional step, and when processing a lot of files, if the connection is slow or the server is busy it takes ages :(

Otherwise I would be very happy if someone can tell me how to use galaxy directly from the command line… That would make my life so much easier :)

Thank you,

Iris