I have created a set of apps for running a pipeline. The individual apps can be started from the command line and they have unified interface and parameters. For instance all of them have parameters:
--input # to tell that the input is a directory --workdir # working directory where the app must write all its output --conf # configuration file --cache # global sequence cache
Every app then creates $workdir, several directories in it and saves files there.
In the beginning, the first apps create configuration files, sequence cache, etc. These data need to be available to every downstream app, like a global state.
How can I implement this kind of behavior in Galaxy? How can I make all these data available to every app? How can I code this in custom tools' config XML? Or shall I first create apps and then it is possible to do this in Workflows?