https://github.com/galaxyproject/galaxy
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Tip revision: 868acc362f6ce8a8b3559fcb88ebb4c060321905 authored by Martin Cech on 21 January 2016, 17:24:27 UTC
Merge pull request #1555 from natefoo/release_15.10
Tip revision: 868acc3
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.iteritems():
        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"
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