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="${__HERE__}/test-data/twobit.loc" />
</table>
</tables>
tmp/tool-data/twobit.loc
hsapiens
/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
tmp/tool-data/twobit.loc
#
tmp/test-data/twobit.loc
hsapiens
/nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Rather than placing these twobit.loc files etc... under tmp with
test.xml I've also tried putting these files under
galaxy-test/tool-data, test-data, etc... and that didn't help either.
I'm not understanding what I'm doing wrong here. Any additional
suggestions would be appreciated.
Thanks!
On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <[email protected]
<mailto:[email protected]>> wrote:
Hi D K,
for a good example of how to test parameters from data tables,
please see:
https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers
<https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers>
Your tool_data_table_conf.xml.test should be different from your
.sample and contain:
<file path="${__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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