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2013/11: VelvetG error on CloudMan Instance: cannot find 'cov_cutoff'

Topic

VelvetG error on CloudMan instance: cannot find 'cov_cutoff'

Date
2013/11/13
Who

Dave Clements

Resolution
Fixed XML wrapper

VelvetG started at 15:50 And got an error:

 NotFound: cannot find 'cov_cutoff' while searching for 'expected.cov_cutoff'

Problem was In velvetg.xml. Here's the fixed version

           #if $coverage.cutoff == "auto":
               -cov_cutoff auto
           #elif $coverage.cutoff == "value":
               -cov_cutoff $coverage.cov_cutoff
           #end if
           #if $expected.coverage == "auto":
               -exp_cov auto
           #elif $expected.coverage == "value":
               -exp_cov $expected.exp_cov
           #end if                                                      

Fix was based on this from later in the file:

   1     <conditional name="coverage">
   2       <param name="cutoff" type="select" label="Coverage cutoff" help="">
   3         <option value="none">None</option>
   4         <option value="auto">Automatically Determined</option>
   5         <option value="value">Specify Cutoff Value</option>
   6       </param>
   7       <when value="none"/>
   8       <when value="auto"/>
   9       <when value="value">
  10         <param name="cov_cutoff" value = "10.0" label="Remove nodes with coverage below" type="float" />
  11       </when>
  12     </conditional>
  13 
  14     <conditional name="expected">
  15       <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
  16         <option value="none">None</option>
  17         <option value="auto">Automatically Determined</option>
  18         <option value="value">Specify Expected Value</option>
  19       </param>
  20       <when value="none"/>
  21       <when value="auto"/>
  22       <when value="value">
  23         <param name="exp_cov" value = "10.0" label="Remove nodes with coverage below" type="float" />
  24       </when>
  25     </conditional>

Restarted Galaxy

Restarted velvetg at 18:08

All was happy.

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