Thanks Nicola,

That fixed it when all of the files are in the tmp/ directory

Is this file/directory structure required when doing this?

When I try putting the relevant entries in
"galaxy-test/tool_data_table_conf.xml.test" and
 "galaxy-test/tool_data_table_conf.xml.sample" and the "twobit.loc" in
"galaxy-test/test-data" and "galaxy-test/tool-data" then I get the same
error again. I'd like to be able to put the files here instead of in their
own directory structure.

Thanks!

On Fri, Oct 7, 2016 at 10:04 AM, D K <danielforti...@gmail.com> 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="${__HERE__}/test-data/twobit.loc" />
>>     </table>
>> </tables>
>
>
> tmp/tool-data/twobit.loc
>
>> hsapiens       /nfs/seqdata/reference_genome/
>> MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> tmp/tool-data/twobit.loc
>
>> #
>
>
> tmp/test-data/twobit.loc
>
>> hsapiens       /nfs/seqdata/reference_genome/
>> MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>
>
> Rather than placing these twobit.loc files etc... under tmp with test.xml
> I've also tried putting these files under galaxy-test/tool-data, test-data,
> etc... and that didn't help either.
>
> I'm not understanding what I'm doing wrong here. Any additional
> suggestions would be appreciated.
>
> Thanks!
>
> On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsora...@tiscali.it>
> wrote:
>
>> Hi D K,
>> for a good example of how to test parameters from data tables, please
>> see: https://github.com/galaxyproject/tools-devteam/tree/master/
>> tools/bowtie_wrappers
>>
>> Your tool_data_table_conf.xml.test should be different from your .sample
>> and contain:
>>
>> <file path="${__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/refer
>>> ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
>>
>>
>> Any suggestions would be greatly appreciated!
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to