https://github.com/galaxyproject/galaxy
Tip revision: 9690680ec7256d979b8b11eb7d5f343a691c93f3 authored by mvdbeek on 15 March 2022, 19:46:24 UTC
Update version to 22.01.
Update version to 22.01.
Tip revision: 9690680
codingSnps_filter.py
#!/usr/bin/env python
# runs after the job (and after the default post-filter)
from galaxy.tools.parameters import DataToolParameter
def validate_input(trans, error_map, param_values, page_param_map):
dbkeys = set()
data_param_names = set()
data_params = 0
for name, param in page_param_map.items():
if isinstance(param, DataToolParameter):
# for each dataset parameter
if param_values.get(name, None) is not None:
dbkeys.add(param_values[name].dbkey)
data_params += 1
# check meta data
try:
param = param_values[name]
int(param.metadata.startCol)
int(param.metadata.endCol)
int(param.metadata.chromCol)
if param.metadata.strandCol is not None:
int(param.metadata.strandCol)
except Exception:
error_msg = ("The attributes of this dataset are not properly set. "
"Click the pencil icon in the history item to set the chrom, start, end and strand columns.")
error_map[name] = error_msg
data_param_names.add(name)
if len(dbkeys) > 1:
for name in data_param_names:
error_map[name] = "All datasets must belong to same genomic build, " \
"this dataset is linked to build '%s'" % param_values[name].dbkey
if data_params != len(data_param_names):
for name in data_param_names:
error_map[name] = "A dataset of the appropriate type is required"