I am new to Galaxy and I am trying to learn how to use the Galaxy API with the BioBlend package.
When describing the Galaxy API, Galaxy mentions that it is useful to use the API and tools such a BioBlend in the following cases:
Running a workflow against multiple datasets (which can be done with the web interface, but is tedious)
When the analysis involves complex control, such as looping and branching
I was therefore hoping that I would be able to programmatically create workflows with BioBlend, not only invoke them. however, the documentation for BioBlend doesn’t seem to indicate that I can make workflows. Am I correct in thinking that I cannot create workflows? Is this something that Parsec might be able to do?
An example of I was hoping to do. I want to automate RNAseq differential expression starting from a single matrix produced with featureCounts. I have 3 groups I need to compare (so 3 inputs for edgeR). However, in the Galaxy GUI, I have been unable to seperate my matrix count into 3 noodles going into edgeR. In other words, if I want edgeR to have 3 input groups, I need to create 3 separate matrix counts. See image below. I was hoping to be able to programmatically create a workflow with BioBlend that would help me around this problem.
Any help would be deeply appreciated.