On Wed, Jul 10, 2013 at 8:03 PM, Björn Grüning <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > Hi VJ, > > you only can have one <command> tag in a tool, afaik. You can try to > write it with cheetah and concatenate several shell commands with && or > you can extend your python script to call your java tool at first step. > > Cheers, > Bjoern >
Also this part will break - Galaxy is telling you the filename, if you add .txt to it then it no longer points to a file on disk: >> input_file = sys.argv[1] >> ... >> txt_in = input_file + '.txt' Likewise Galaxy has told you which output filename to use, if you add .pdf to it Galaxy won't find it: >> output_file = sys.argv[2] >> .. >> pdf_out = output_file + '.pdf' The tool should just use the filenames Galaxy tells it (and they will end in .dat regardless of the datatype). Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
