Hi, Nicholas, You'll almost certainly want to write a wrapper to create the plink command line and run it - a wrapper script can construct a correct plink command line and then do all sorts of post-plink transformation on the outputs as needed - which in my experience it usually is. Most of the rgenetics tools do just that so looking at the source under tools/rgenetics may provide some prototypes you can change to suit your needs - eg rgQC.py and rgQC.xml Plink spews out all sorts of stuff so you may want to explore the Html datatype - see http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003311.html for a brief explanation. On Wed, Nov 9, 2011 at 1:31 AM, Nicholas Robinson <nicholas.robinson@nofima.no> wrote:

Hi Galaxy users,

I am trying to write a simple tool that sends commands to shell to run Plink (and other analysis packages set up on our Galaxy server). I am new to this, but have managed to write some tools before that work in a similar fashion, at least when you can specify what input and output files will be produced. For plink there are a large number of options and different outputs possible. I have seen the discussion on the user group about how to handle multiple output files (eg. http://lists.bx.psu.edu/pipermail/galaxy-user/2009-September/000743.html). Normally to run plink you specify a single file name (eg. --out $output1) and the program can produce two, to a few, output files (eg depending on the analysis it might produce a $output1.log file and a $output1.cmh file if I do a certain test, otherwise it might produce the log file and two other files). If I add:

--out $output1 $output1.id $__new_file_path__

to the command line to try to capture all the output, as suggested for when the interpreter is python, then when I run the tool in galaxy it says:

ERROR: Problem parsing the command line arguments.

ie. plink makes a fuss about the addition to the command line (I suspect). Have any of you figured out a way to handle varying numbers of multiple output files under these circumstances? Please give me a simple reponse if you can, I am a new user.

Cheers,

Nick ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;