I have to fill parameters manually into my workflow which are mostly file names and sample names. I have to select from about 7 files about 20 times and enter similar but slightly different sample names (e. g. wn0552.A7CE75785, wn0552.A7CE75785_tumor, wn0552.A7CE75785_normal) for another 20 times. As you may guess, it is time consuming, error prone and in general not exactly the kind of work i dreamed of.
But i suspect i can automate this process. If it were linux command line, all i need were echo, cat, ln etc., and some rarely used ascii symbols. However in galaxy i found only cat.
So essentially i want:
Tool that receives one file and sends it to the output intact so i could connect its output to all steps using some specific file and set its name only once. In linux it may be cat or cp, but i would prefer ln or even variable definition to save disk space and time.
Tool that receives some string and output it intact like echo.
Tool that receives two string and concatenates them like echo $a$b . So i could set my sample name to e. g. wn0552.A7CE75785, derive other important strings from it and use these strings in all my steps using “add connection to module”.
And also tool that gives the number of processors on current machine to set the number of threads in some tools.
Is this possible in galaxy? Or maybe there is an easier way to automate workflows? Or i have to write wrappers for all these tools myself?
Thanks in advance.