Hello everyone,
I have a question about https://github.com/nturaga/bioc-galaxy-integration I am trying to convert a RScript into a Galaxy tool.
planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt --test_case Can only use the --test_case option if also specifying --example_command
planemo bioc_tool_init --rscript ./countsAroundTSS.R --example_command "Rscript countsAroundTSS.R--input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt” Error: no such option: --example_command
I am able to build a tool is I just run planemo bioc_tool_init --rscript ./countsAroundTSS.R --input ENCFF027UTM.bam --input mm10 --input 500 --input 500 --input transcripts_mm10_UCSC.sqlite --output ENCFF027UTM.txt
https://github.com/galaxyproject/planemo/issues/718
Thank you, Deepak