Hello, I had an issue with the "merge tool some time ago and I sent a message to this board on the 20th of November last year. I got a reply linking me to the explanation of the new operations, which I found awesome! Especially for the Cluster tool :) I did reply to that message, but it seems like it did not come through. In that mail I wrote the following: --- If the Merge tool should output only three columns then there might be something wrong with it because it actually replaces all the columns that are not start, end and chromosome with dots instead of eliminating them, resulting in files with different numbers of columns. On the other hand, the concatenate tool does combine datasets that have the same columns in different orders. But if there are additional columns beside of start, end and chromosome (like the dot columns in the results from the merge tool), then it gives me an error: An error occurred running this job: Traceback (most recent call last): File "./tools/new_operations/gops_concat.py", line 69, in ? main() File "./tools/new_operations/gops_concat.py", line 62, in main for line in concat([g1, g2], sameformat=sameformat): File "build/bdist.linux Here I can’t see the whole error message, so I don’t know if this is useful. --- The "merge" tool actually continues adding those funny dots for the additional columns, which I then need to eliminated to continue performing operations on the file. Therefore I would ask you please to have a look at it and maybe give the user the choice as to how many columns are needed in the output (i.e. 1-conserve number of columns or 2-reduce to three columns). Thanks again, Iris ====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048 ----- Original Message ----- From: "Anton Nekrutenko" <anton@bx.psu.edu> To: "Iris Vargas Jentzsch" <imj15@student.canterbury.ac.nz> Cc: <galaxy-dev@bx.psu.edu> Sent: Wednesday, November 22, 2006 3:01 AM Subject: Re: [galaxy-user] modified "merge" tool Iris: The merge tool still gives you three columns as before. The concatenate tool now fills absent fields with dots. Here is a detailed description of new operations: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/GopsDesc You can use new operation from command line. For this you will need to download Galaxy and look at how commands are formed within tool configuration files. Let us know if you need any help with that. anton Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu On Nov 19, 2006, at 8:46 PM, Iris Vargas Jentzsch wrote:

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

====================================== Iris M. Vargas Jentzsch School of Biological Sciences University of Canterbury Private Bag 4800 Christchurch - New Zealand phone: +64 (0) 3 364 2987 ext 7048 _______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user