Mercurial > repos > xuebing > sharplabtool
view tools/samtools/sam_merge_code.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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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.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"