https://github.com/galaxyproject/galaxy
Tip revision: 9cb113bcb5aed7da86348edb8ba2c35c2a104fe4 authored by Nate Coraor on 02 June 2014, 20:27:48 UTC
Update stable branch from next-stable for release.
Update stable branch from next-stable for release.
Tip revision: 9cb113b
codingSnps_filter.py
#!/usr/bin/env python
# runs after the job (and after the default post-filter)
import os
from galaxy import eggs
from galaxy import jobs
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.iteritems():
if isinstance( param, DataToolParameter ):
# for each dataset parameter
if param_values.get(name, None) != None:
dbkeys.add( param_values[name].dbkey )
data_params += 1
# check meta data
try:
param = param_values[name]
startCol = int( param.metadata.startCol )
endCol = int( param.metadata.endCol )
chromCol = int( param.metadata.chromCol )
if param.metadata.strandCol is not None:
strandCol = int ( param.metadata.strandCol )
else:
strandCol = 0
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"