Off topic:cwl for a Phyloseq command

Question

[Shakuntala Baichoo]

Hi Michael! I have an R script that takes as input 3 files namely an OTU file, a map and a tree and generates a set of reports in the folder output and test.Rdata in current folder. At command line I call it as follows:

Rscript PhyloseqReport.R otus.tax.biom dog_stool_samples_metadata.tsv otus.tre output test.Rdata

I have started the following cwl script:

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
inputs:
otuFile:
  type: File
  inputBinding:
    position: 1
mapFile:
  type: File
  inputBinding:
    position: 2
tre:
  type: File
  inputBinding:
    position: 3

baseCommand: [ Rscript, PhyloSeqReport.R, "results.Rdata" ]

outputs:
  results:
    type: File
    outputBinding:
      glob: results.Rdata

How do I capture the fact that the set of reports generated should go in folder output?

Thank you.

Shakun