Good, because you are using planemo test --galaxy_root ... you can preset the *.loc files as needed (because currently Planemo will not do this for you). See also Nicola's reply. Peter On Fri, Oct 7, 2016 at 5:49 PM, D K <danielfortin86@gmail.com> wrote:

Hi Peter,

This is the command I'm using to run planemo: . galaxy_test/.venv/bin/activate planemo test --test_data /home/galaxy-functional-testdata --galaxy_root galaxy-test/ --skip_venv test.xml

I'm getting no errors when using the planemo lint tool.

Thanks!

On Fri, Oct 7, 2016 at 2:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

Hi DK,

Looking at your XML that looks OK.

It might not be important, but how exactly are you running planemo test?

I'm asking because currently it will not create tool-data/twobit.loc for you from your sample file - although in that case I would have expected a different error message:

https://github.com/galaxyproject/planemo/issues/530 https://github.com/galaxyproject/planemo/issues/530

Is planemo lint happy with your tool?

Peter

On Thu, Oct 6, 2016 at 11:08 PM, D K <danielfortin86@gmail.com> 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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