this question was asked on https://www.biostars.org/p/158324/ initially, following a recommendation I put it here, too:
I would like to implement a command line shell or python wrapper for the CloudMap workflow (www: http://hobertlab.org/cloudmap/ galaxy implementation: https://usegalaxy.org/u/gm2123/p/cloudmap). Therefore I want to know which software tools are used and what are the minimum/basic arguments for this analysis. I know I can use the workflow tools from galaxyproject.org to investigate the code, but:
I would like to know if there exists a a web post which shows the summarized command line tool chain used for the CloudMap workflow.
I would appreciate if people could share links or even post an example!