def run_checkM_lineage_wf(self, ctx, params):
"""
:param params: instance of type "CheckMLineageWfParams" (input_ref -
reference to the input Assembly or BinnedContigs data (could be
expanded to include Genome objects as well)) -> structure:
parameter "input_ref" of String, parameter "workspace_name" of
String, parameter "save_output_dir" of type "boolean" (A boolean -
0 for false, 1 for true. @range (0, 1)), parameter
"save_plots_dir" of type "boolean" (A boolean - 0 for false, 1 for
true. @range (0, 1))
:returns: instance of type "CheckMLineageWfResult" -> structure:
parameter "report_name" of String, parameter "report_ref" of String
"""
# ctx is the context object
# return variables are: result
#BEGIN run_checkM_lineage_wf
print('--->\nRunning kb_Msuite.run_checkM_lineage_wf\nparams:')
print(json.dumps(params, indent=1))
cmu = CheckMUtil(self.config)
result = cmu.run_checkM_lineage_wf(params)
#END run_checkM_lineage_wf
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError('Method run_checkM_lineage_wf return value ' +
'result is not type dict as required.')
# return the results
return [result]
def run_checkM_lineage_wf_withFilter(self, ctx, params):
"""
:param params: instance of type "CheckMLineageWf_withFilter_Params"
(input_ref - reference to the input BinnedContigs data) ->
structure: parameter "input_ref" of String, parameter
"workspace_name" of String, parameter "reduced_tree" of type
"boolean" (A boolean - 0 for false, 1 for true. @range (0, 1)),
parameter "save_output_dir" of type "boolean" (A boolean - 0 for
false, 1 for true. @range (0, 1)), parameter "save_plots_dir" of
type "boolean" (A boolean - 0 for false, 1 for true. @range (0,
1)), parameter "completeness_perc" of Double, parameter
"contamination_perc" of Double, parameter
"output_filtered_binnedcontigs_obj_name" of String, parameter
"threads" of Long
:returns: instance of type "CheckMLineageWf_withFilter_Result" ->
structure: parameter "report_name" of String, parameter
"report_ref" of String, parameter "binned_contig_obj_ref" of type
"obj_ref" ("WS_ID/OBJ_ID/VER")
"""
# ctx is the context object
# return variables are: result
#BEGIN run_checkM_lineage_wf_withFilter
print(
'--->\nRunning kb_Msuite.run_checkM_lineage_wf_withFilter\nparams:'
)
print(json.dumps(params, indent=1))
cmu = CheckMUtil(self.config, ctx)
result = cmu.run_checkM_lineage_wf(params)
#END run_checkM_lineage_wf_withFilter
# At some point might do deeper type checking...
if not isinstance(result, dict):
raise ValueError(
'Method run_checkM_lineage_wf_withFilter return value ' +
'result is not type dict as required.')
# return the results
return [result]