Re: [galaxy-dev] The need for wrappers

2011-10-13 Thread Edward Kirton
wrappers are also used when a tool produces several files in an output folder (i.e. executable takes outdir parameter, not explicitly named outfile paths) and you would like to move these to the desired paths under files/ (i.e. a composite datatype is not desired) and/or cleanup unnecessary files.

Re: [galaxy-dev] The need for wrappers

2011-09-20 Thread Peter Cock
Hi Timothy, On Tuesday, September 20, 2011, Timothy Wu 2hug...@gmail.com wrote: Hi, Looking under the tools directory I realized that some tools comes with *_wrapper.py. I wonder under what circumstances is this needed? Mostly messing about with stderr (there is a long standing bug open

[galaxy-dev] The need for wrappers

2011-09-19 Thread Timothy Wu
Hi, Looking under the tools directory I realized that some tools comes with *_wrapper.py. I wonder under what circumstances is this needed? I'm trying to do a quickie for RepeatMasker. It looks to me like the tool does not allow one to specify the name of the output files. It also appears to me