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,

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