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Question: Test XML, how to select from table: <options from_data_table="blastdb">
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gravatar for danielfortin86
3.1 years ago by
danielfortin86 • 110
United States
danielfortin86 • 110 wrote:

When defining a test in the <tests> section of the xml, how does one refer to a specific value when the values are retrieved from a table such as blastdb.loc? 

e.g.

     <param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome">
      <options from_data_table="twobit_indexes" />
     </param>

...

<tests>

<test>

<param name="refGenomeSource_type" value="twoBitIndexElement/>

 

...

 
planemo test • 816 views
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modified 3.0 years ago • written 3.1 years ago by danielfortin86 • 110

Found these related comments....

https://github.com/peterjc/galaxy_blast/issues/52

https://github.com/peterjc/galaxy_blast/issues/53

ADD REPLY • link written 3.1 years ago by danielfortin86 • 110
1
gravatar for danielfortin86
3.0 years ago by
danielfortin86 • 110
United States
danielfortin86 • 110 wrote:

If any one is curious, I found an answer to this question in the Planemo documentation:

https://planemo.readthedocs.org/en/latest/writing_how_do_i.html

 

To create this kind of test, one simply needs to provide a tool_data_table_conf.xml.test beside your tool’s tool_data_table_conf.xml.sample file that specifies paths to test .loc files which in turn define paths to the test index data. Both the .loc files and the tool_data_table_conf.xml.test can use the value ${__HERE__} which will be replaced with the path to the directory the file lives in. This allows using relative-like paths in these files which is needed for portable tests.

An example commit demonstrating the application of this approach to a Picard tool can be found here.
ADD COMMENT • link written 3.0 years ago by danielfortin86 • 110
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