Revision f722e122f723ec37b95aa669a1f60f53260e0f71 authored by Matthias Bernt on 08 June 2023, 13:54:28 UTC, committed by Matthias Bernt on 08 June 2023, 13:54:28 UTC
1 parent 1ee21e3
workflow_execute_parameters.py
#!/usr/bin/env python
"""
# ---------------------------------------------- #
# PARKLAB, Author: RPARK
# ---------------------------------------------- #
Execute workflows from the command line.
Example calls:
python workflow_execute.py <api_key> <galaxy_url>/api/workflows <workflow_id> 'hist_id=<history_id>' '38=hda=<file_id>' 'param=tool=name=value'
python workflow_execute_parameters.py <api_key> http://localhost:8080/api/workflows 1cd8e2f6b131e891 'Test API' '69=ld=a799d38679e985db' '70=ld=33b43b4e7093c91f' 'param=peakcalling_spp=aligner=bowtie' 'param=bowtie_wrapper=suppressHeader=True' 'param=peakcalling_spp=window_size=1000'
"""
import os
import sys
from common import submit
def main():
try:
print("workflow_execute:py:")
data = {}
data["workflow_id"] = sys.argv[3]
data["history"] = sys.argv[4]
data["ds_map"] = {}
# Trying to pass in parameter for my own dictionary
data["parameters"] = {}
# DBTODO If only one input is given, don't require a step
# mapping, just use it for everything?
for v in sys.argv[5:]:
print("Multiple arguments ")
print(v)
try:
step, src, ds_id = v.split("=")
data["ds_map"][step] = {"src": src, "id": ds_id}
except ValueError:
print("VALUE ERROR:")
wtype, wtool, wparam, wvalue = v.split("=")
try:
data["parameters"][wtool] = {"param": wparam, "value": wvalue}
except ValueError:
print("TOOL ID ERROR:")
except IndexError:
print("usage: %s key url workflow_id history step=src=dataset_id" % os.path.basename(sys.argv[0]))
sys.exit(1)
submit(sys.argv[1], sys.argv[2], data)
if __name__ == "__main__":
main()
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