diff --git a/README.md b/README.md index 3b2af36..7b3599a 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,6 @@ r_code = retropath2( dmin=0, dmax=100, mwmax_source=1000, - mwmax_cof=1000, ) ``` diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py index e654881..dee1c52 100644 --- a/retropath2_wrapper/Args.py +++ b/retropath2_wrapper/Args.py @@ -101,7 +101,6 @@ def _add_arguments(parser): parser.add_argument('--dmin' , type=int, default=0) parser.add_argument('--dmax' , type=int, default=1000) parser.add_argument('--mwmax_source' , type=int, default=1000) - parser.add_argument('--mwmax_cof' , type=int, default=1000) parser.add_argument( '--timeout', type=int, diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py index 14e21bc..6e5ff21 100644 --- a/retropath2_wrapper/RetroPath2.py +++ b/retropath2_wrapper/RetroPath2.py @@ -130,7 +130,7 @@ def retropath2( max_steps: int = 3, topx: int = 100, dmin: int = 0, dmax: int = 100, - mwmax_source: int = 1000, mwmax_cof: int = 1000, + mwmax_source: int = 1000, timeout: int = DEFAULT_TIMEOUT, logger: Logger = getLogger(__name__) ) -> Tuple[str, Dict]: @@ -151,7 +151,6 @@ def retropath2( 'dmin' : dmin, 'dmax' : dmax, 'mwmax_source' : mwmax_source, - 'mwmax_cof' : mwmax_cof } logger.debug('rp2_params: ' + str(rp2_params)) @@ -623,7 +622,6 @@ def call_knime( + ' -workflow.variable=input.rulesfile,"' + files['rules'] + '",String' \ + ' -workflow.variable=input.topx,"' + str(params['topx']) + '",int' \ + ' -workflow.variable=input.mwmax-source,"' + str(params['mwmax_source']) + '",int' \ - + ' -workflow.variable=input.mwmax-cof,"' + str(params['mwmax_cof']) + '",int' \ + ' -workflow.variable=output.dir,"' + files['outdir'] + '",String' \ + ' -workflow.variable=output.solutionfile,"' + files['results'] + '",String' \ + ' -workflow.variable=output.sourceinsinkfile,"' + files['src-in-sk'] + '",String' diff --git a/retropath2_wrapper/__main__.py b/retropath2_wrapper/__main__.py index 6e6264a..238b539 100644 --- a/retropath2_wrapper/__main__.py +++ b/retropath2_wrapper/__main__.py @@ -105,7 +105,7 @@ def _cli(): sink_file=args.sink_file, source_file=args.source_file, rules_file=args.rules_file, outdir=args.outdir, kvars=kvars, - max_steps=args.max_steps, topx=args.topx, dmin=args.dmin, dmax=args.dmax, mwmax_source=args.mwmax_source, mwmax_cof=args.mwmax_cof, + max_steps=args.max_steps, topx=args.topx, dmin=args.dmin, dmax=args.dmax, mwmax_source=args.mwmax_source, rp2_version=args.rp2_version, timeout=args.timeout, logger=logger