root/galaxy-central/tools/evolution/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"