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.
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