def rename_command(self):
tmp = []
for _, this_template in self.template.items():
for parameter in util.alwayslist(this_template):
if isinstance(parameter.f, RenamedTemplateFile):
tmp.append(parameter.f.rename_command())
return ' && '.join(tmp)
def assign(self, snakemake_input):
for key, filenames in self._input_reader(snakemake_input):
if key not in self.rule_keys:
raise exception.RuleInputException(
'Unexpected input rule key: %s' % key)
this_template = util.alwayslist(self.template[key])
for filename, parameter in zip(filenames, this_template):
parameter.f.assign(filename)
def get_options(self):
options = []
for _, this_template in self.template.items():
for parameter in util.alwayslist(this_template):
if not parameter.used:
continue
fname, priority = parameter.f.infer_raw_name(
), parameter.priority
if parameter.option is not None:
option = ' '.join([parameter.option, fname])
options.append((option, priority))
else:
options.append((fname, priority))
return options
def _input_reader(self, snakemake_input):
for key, filenames in snakemake_input.items():
yield key, util.alwayslist(filenames)
def redirect_command(self):
for _, this_template in self.template.items():
for parameter in util.alwayslist(this_template):
if parameter.redirected:
return '> ' + parameter.f.infer_raw_name()
return ''