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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