Re: [galaxy-dev] Multiple fastq files per forward/reverse mates (tophat and related tools)

2011-07-15 Thread Jeremy Goecks
Gus, Good to hear about your progress. Please send me a patch of your changes and I'll take a look. You can create a patch using Mercurial from the command line as follows. % hg diff tophat.patch Thanks, J. On Jul 13, 2011, at 7:37 PM, W. Augustine Dunn III wrote: First off thank you

Re: [galaxy-dev] Multiple fastq files per forward/reverse mates (tophat and related tools)

2011-07-13 Thread W. Augustine Dunn III
First off thank you heartily for pointing me in the right direction here. It SEEMS like i have managed to accomplish this. Meaning: i finally got the run to get past the parsing of the config file and now have a process running on the cpu and the server log shows a command line string that

Re: [galaxy-dev] Multiple fastq files per forward/reverse mates (tophat and related tools)

2011-07-11 Thread Sarah Diehl
Hi Gus, for parameters of the type select you can enable the option to select multiple options. However, this isn't really suitable for files, I think. I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make

Re: [galaxy-dev] Multiple fastq files per forward/reverse mates (tophat and related tools)

2011-07-11 Thread Jeremy Goecks
I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files. Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag. Gus, if you end