Hi D K,
for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers

Your tool_data_table_conf.xml.test should be different from your .sample and contain:

<file path="${__HERE__}/test-data/twobit.loc" />

Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc

Cheers,
Nicola

On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,

I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type 
requires a value, but has no legal values defined.\n

From my script XML:

     <param name="refGenomeSource_type" type="select" label="Select a
    reference genome / transcriptome">
          <options from_data_table="type_indexes">
          </options>
    </param>
    ...
      <tests>
          <test>
            <param name="refGenomeSource_type" value="hsapiens"/>
         </test>
      </tests>

From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)

    <table name="type_indexes" comment_char="#"
    allow_duplicate_entries="False">
            <columns>value, name, path</columns>
            <file path="tool-data/twobit.loc" />
    </table>


and from twobit.loc (where the columns are tab separated):

    hsapiens        H. sapiens (hg38)
    
/remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Any suggestions would be greatly appreciated!



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