Dear galaxy users,
My team is involved in the NGS field. We have our own local cluster and we are looking for a workflow management system. Currently we are trying to set up and test galaxy.
For our quality control analysis pipeline, R statistical software will be used. So we want to be able to call R scripts from galaxy.
I know that it is possible and the xy_plot.xml is a really good example (conditional & when, repeat tags). Also, in this example a <configfile> tag is used. Within this tag you put your R code. And moreover you can add lines beginning with only one '#' which will be interpreted with *cheetah template engine*. This is helpful to create dynamic content of your R code with respect to your submitted parameters. (an old screencast introduces this example)
My question is : is there a way to avoid the <configfile> section and to let all the R code be outside the tool's xml config file? If yes, how can we specify an output file in the xml conf that will catch, for instance, a write.table() call in the R script ?
Best regards,
Anthony