The remaining part of the GUI template are output options. The order can then later, in the execution network, be retrieved.įor a better visual appearance, elements are arranged in a 3x3 grid. We thus need an ordered group (ordered=true). Trimmomatic is a special case, because the order of the parameters can alter the result.

Unfortunately netcat behaves differently on virtually every operating system, we must call netcat differently on Mac OS and Ubuntu, to ensure that the connection is closed upon sending the EOF. The user's IP address is given as fourth parameter to the install module, the corresponding port as the fifth parameter. This is done via a TCP connection (because std-out and std-err are already used by the install module). Now we need to transfer the template to bioGUI. Example: Trimmomatic Dependency/Install Partįor the install module, we start with the shebang which gives the module its name:ĪPPBINARYESC= ' $ ' fi Note that this action button has the program attribute set! Sometimes not all are documented or some are used so seldom, that it is not worth to include them as visual checkboxes.Ī simple input element can serve as container for user-defined command line arguments. Report alignments tailored specifically for Cufflinks Report alignments tailored for transcript assemblers including StringTie Guarantees output to be in order of input Search at most x distinct, primary alignments for each readĭo not attempt to align unpaired reads to the forward reference strandĭo not attempt to align unpaired reads to the reverse reference strandĭisable mixed alignments (if no conc/disc)ĭo not look for discordant alignments if no concordant are available Reads are files with one input sequence per line

Trimmomatic crop example