https://github.com/galaxyproject/galaxy
Tip revision: 18ef6a6ab0dcba1a1254a9d9f4273c346fdd1478 authored by Martin Cech on 24 May 2017, 14:47:27 UTC
Update version to 17.05
Update version to 17.05
Tip revision: 18ef6a6
codingSnps_filter.py
#!/usr/bin/env python
# runs after the job (and after the default post-filter)
from galaxy.tools.parameters import DataToolParameter
# Older py compatibility
try:
set()
except:
from sets import Set as set
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:
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"