Hi D K,
I think that the problem may be that the table name is different in your test.xml , tool_data_table_conf.xml.sample and tool_data_table_conf.xml.test files (type_indexes, twobit_indexes and twobit respectively), should always be twobit.

Cheers,
Nicola

On 07/10/16 18:04, D K wrote:
Hi Nicola,

Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error.
I've changed my file structure to look like this:

tmp/test.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>


tmp/tool_data_table_conf.xml.sample:

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


tmp/tool_data_table_conf.xml.test:

    <tables>
        <!-- Locations of indexes in the 2bit format -->
        <table name="twobit" comment_char="#"
    allow_duplicate_entries="False">
            <columns>value, path</columns>
            <file path="${__HERE__}/test-data/twobit.loc" />
        </table>
    </tables>


tmp/tool-data/twobit.loc

    hsapiens
    
/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


tmp/tool-data/twobit.loc

    #


tmp/test-data/twobit.loc

    hsapiens
    
/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa


Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either.

I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated.

Thanks!

On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsora...@tiscali.it <mailto:nsora...@tiscali.it>> wrote:

    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
    
<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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