From danielfortin86@gmail.com Thu Oct  6 18:08:57 2016
From: D K <danielfortin86@gmail.com>
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] planemo test with <options from_data_table>
Date: Thu, 06 Oct 2016 15:08:55 -0700
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 <CAHpuiyi4_je9AH0eZmwFGMnsRBUxRB-LJ-YYdbHdMghaua-+9w@mail.gmail.com>
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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=3D"refGenomeSource_type" type=3D"select" label=3D"Select a
> reference genome / transcriptome">
>       <options from_data_table=3D"type_indexes">
>       </options>
> </param>
> ...
>   <tests>
>       <test>
>         <param name=3D"refGenomeSource_type" value=3D"hsapiens"/>
>      </test>
>   </tests>
>
> From my "tool_data_table_conf.xml.sample" and
"tool_data_table_conf.xml.test" (mirrored)

> <table name=3D"type_indexes" comment_char=3D"#"
> allow_duplicate_entries=3D"False">
>         <columns>value, name, path</columns>
>         <file path=3D"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.GRC=
h38.cdna.all.fa


Any suggestions would be greatly appreciated!



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