root/galaxy-central/tools/evolution/codingSnps_filter.py

リビジョン 2, 1.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

  • 属性 svn:executable の設定値 *
行番号 
1#!/usr/bin/env python
2
3# runs after the job (and after the default post-filter)
4import os
5from galaxy import eggs
6from galaxy import jobs
7from galaxy.tools.parameters import DataToolParameter
8# Older py compatibility
9try:
10    set()
11except:
12    from sets import Set as set
13
14def validate_input( trans, error_map, param_values, page_param_map ):
15    dbkeys = set()
16    data_param_names = set()
17    data_params = 0
18    for name, param in page_param_map.iteritems():
19        if isinstance( param, DataToolParameter ):
20            # for each dataset parameter
21            if param_values.get(name, None) != None:
22                dbkeys.add( param_values[name].dbkey )
23                data_params += 1
24                # check meta data
25                try:
26                    param = param_values[name]
27                    startCol = int( param.metadata.startCol )
28                    endCol = int( param.metadata.endCol )
29                    chromCol = int( param.metadata.chromCol )
30                    if param.metadata.strandCol is not None:
31                        strandCol = int ( param.metadata.strandCol )
32                    else:
33                        strandCol = 0
34                except:
35                    error_msg = "The attributes of this dataset are not properly set. " + \
36                    "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
37                    error_map[name] = error_msg
38            data_param_names.add( name )
39    if len( dbkeys ) > 1:
40        for name in data_param_names:
41            error_map[name] = "All datasets must belong to same genomic build, " \
42                "this dataset is linked to build '%s'" % param_values[name].dbkey
43    if data_params != len(data_param_names):
44        for name in data_param_names:
45            error_map[name] = "A dataset of the appropriate type is required"
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