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 <nsoranzo@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

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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