Hi!
I am trying to run skesa (a NGS assembler) in a Galaxy instance through API ([bioblend.galaxy.GalaxyInstance.ToolClient.run_tool()])(API documentation for interacting with Galaxy — BioBlend 1.5.0 documentation) in python code. I am using a paired fastq in one of my histories. My code looks like:
my_history = my_galaxy_instance.histories.get_histories()
tool_client = ToolClient(my_galaxy_instance)
tool_id = “toolshed.g2.bx.psu.edu/repos/cstrittmatter/skesa/skesa/0.24”
skesa_input = {
“fastq”: {
“id”: “56a201aaf82840b5”, #id of the paired fastq
“src”: “hdca”
}
}
result_skesa = tool_client.run_tool(my_history[0][“id”], tool_id, skesa_input)
I want to use all default settings for skesa. The command for skesa would be: “skesa -fastq forward_read_file,reverse_read_file”. The format of “skesa_input” seems incompatible with my Galaxy instance. What would be the correct format for “skesa_input”? Thank you.