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1 # before running the qc, need to rename various output files
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2 # <data format="html" name="html_file" />
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3 # <data format="txt" name="log_file" parent="html_file" />
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4 # <data format="tabular" name="marker_file" parent="html_file" />
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5 # <data format="tabular" name="subject_file" parent="html_file" />
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6
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7 from galaxy import datatypes,model
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8 import sys,string
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9
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10 def get_columns( input ):
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11 columns = []
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12 elems = []
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13 if input and input.metadata.columns:
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14 ncols = input.metadata.columns
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15 colnames = ['Col%d' % x for x in range(1,ncols+1)]
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16 for i, line in enumerate( file ( input.file_name ) ):
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17 valid = True
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18 if line and not line.startswith( '#' ):
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19 line = line.rstrip('\r\n')
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20 elems = line.split( '\t' )
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21
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22 """
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23 Since this tool requires users to select only those columns
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24 that contain numerical values, we'll restrict the column select
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25 list appropriately.
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26 """
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27 if len(elems) > 0:
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28 for col in range(len(elems)): # zero offset
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29 if i == 0: # header row
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30 colnames[col] = elems[col]
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31 else:
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32 val = elems[col]
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33 try:
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34 val = float(val)
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35 valid = True
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36 except:
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37 valid = False
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38 if valid:
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39 option = colnames[col]
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40 columns.append((option,str(col),False))
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41 if len(columns) > 0:
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42 """
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43 We have our select list built, so we can break out of the outer most for loop
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44 """
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45 break
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46 if i == 30:
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47 break # Hopefully we never get here...
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48 else:
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49 columns = [('?','?',False),]
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50 return columns
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