Hi,


We have begun dabbling with a local instance of Galaxy (amazingly impressive !!).

I have 2 questions:

1.

I have written a tool to implement Lucy (http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1093).

I can figure out how to handle output when the command line has a -o option to explicitly state the output file name.
Or when the file output is always the same.

I am trying to make a tool where the java executable is launched and makes an output file. The output file is named
the same as the input file (input.txt) but has a new extension added to the end of it (.cal),

  i.e., inputfilename.txt.cal


I can't for the life of me figure out the XML syntax to read this file back into galaxy as an output.

Is the best strategy to write a wrapper in another language (perl, python, java), that will feed in $output,  then read in the ".cal" output and spew out a file
to satisfy $output for the XML ?



2.    For testing, what is the best way to do the testing?
I have written a few java based executable jars and the corresponding XML docs to go with them. I'd like to share with the world but I am not
sure the best way to go testing.




Thank you very much for your attention,
Rob Reid


Rob Reid, Ph.D. | Research Associate
UNC Charlotte | Dept. of Bioinformatics and Genomics
9201 University City Blvd. | Charlotte, NC 28223
Phone: 704-250-5766
rreid2@uncc.edu | http://www.uncc.edu
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