Maybe I'm asking a beginner question, please bear with me.
I'm currently in charge of the integration of a tool into Galaxy (I am doing it for the first time, with modest programming skills). My tool (coded in C++) takes input files AND a configuration file (configfile.txt) as arguments. It generates 3 output files.
I'm having trouble deciding on a strategy to pass the arguments to my tool. to be exact, I am having trouble creating the configfile.txt needed from the parameters that the user enters, because, in my logic, that's what I should do since the execution of my tool requires this argument. Here's what I am thinking about :
1) In the Galaxy documentation I read about the <configfiles> tags (which I didn't fully understand, mainly because I can't really see how Cheetah works), is this what I need to describe the file?
2) I could write a shell script that catches the parameters entered in the form, creates the confgfile.txt, calls my program (with confgfile.txt as one of the arguments) and returns the output of my program.
How should I proceed ? is my logic correct ? (you never know)
Thank you !