Yup - thanks for the bug report. I have used your rna example to build
a minimal-ish example to fit into Galaxy's test tools framework here
https://github.com/galaxyproject/galaxy/pull/2795. I also tested in
16.01 and it worked - so this clearly broke in 16.04. I'll see if I
can track it down and we can move the discussion to the github PR.
Thanks a bunch for the detailed report Hans!

-John

On Tue, Aug 16, 2016 at 9:02 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> Hi Nicola and others on the list
>
> It looks like it has something to do with the 'conditional'
>
> I took the rnaStar xml file, and reduced it to the bare bones, just to
> reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It
> picks up the right dbkey.
>
> I made the xml file even simpler and removed the  'conditional' (see
> attachment: rg_rnaStar.simple_noCond  ). And now it no longer works (see
> attached screenshot)
>
> And just for completeness: There is nothing in the logs
>
>
> However, if I use the same two xml files on our current galaxy servers
> (running 15.10). It works in both cases. Each time, the right dbkey is
> picked up.
>
>
>  Hans-Rudolf
>
>
>
>
> On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote:
>>
>> Hi Nicola
>>
>> Many thanks for your comments/suggestions. I've just tested the rnaStar
>> wrapper, and it works as well.
>>
>> I will try to dig deeper
>>
>> Hans-Rudolf
>>
>>
>>
>>
>> On 08/16/2016 01:38 PM, Nicola Soranzo wrote:
>>>
>>> I've tested bowtie_wrapper on Galaxy release_16.04: <option
>>> type="from_data_table" name="bowtie_indexes" column="1" offset="0">
>>> works fine for me.
>>>
>>> Cheers,
>>> Nicola
>>>
>>> On 16/08/16 11:42, Nicola Soranzo wrote:
>>>>
>>>> Forget about my previous comment, I should have read your email
>>>> better, sorry!
>>>>
>>>> Your code similar to bowtie_wrapper is also used by
>>>>
>>>> https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml
>>>>
>>>> and I think it should work, not sure if it's a regression in Galaxy.
>>>>
>>>> Cheers,
>>>> Nicola
>>>>
>>>> On 16/08/16 11:29, Nicola Soranzo wrote:
>>>>>
>>>>> Hi Hans,
>>>>> see my comment below.
>>>>>
>>>>> On 16/08/16 09:51, Hans-Rudolf Hotz wrote:
>>>>>>
>>>>>> Dear All
>>>>>>
>>>>>>
>>>>>> I am trying to move our Galaxy installation to new hardware and at
>>>>>> the same time to a new version (the original is "15.10",minor
>>>>>> version "2" via mercurial; the new is "16.04" via github):
>>>>>>
>>>>>> So far, I am making good progress, but I am struggling with a tool
>>>>>> which was written by someone else who has left more than 2 years
>>>>>> ago. The problem is: it doesn't set the dbkey correctly.
>>>>>>
>>>>>> I get:
>>>>>> <Cheetah.Template.Template object at 0x7f1e40210f50>
>>>>>>
>>>>>>
>>>>>>
>>>>>> The tool xml is as follows:
>>>>>>
>>>>>> <inputs>
>>>>>>    <param name="sample_file" type="data"
>>>>>> format="qsamples,qsamplespaired" label="Sample File" help="set of
>>>>>> sequence files created by the 'select sequence files' tool">
>>>>>>    </param>
>>>>>>    <param name="index" type="select" label="Reference Genome"
>>>>>> help="all reads will be mapped to this reference">
>>>>>>       <options from_data_table="fmi__quasr_genomes"/>
>>>>>>    </param>
>>>>>>
>>>>>> ...
>>>>>> </inputs>
>>>>>> <outputs>
>>>>>>    <data name="output01" type="data" format="qproject"
>>>>>> label="qProject of ${sample_file.name}">
>>>>>>       <actions>
>>>>>>          <action type="metadata" name="dbkey">
>>>>>>             <option type="from_param" name="index"/>
>>>>>
>>>>>
>>>>> It seems you are missing a param_attribute="dbkey" here, it should be:
>>>>> <option type="from_param" name="index" param_attribute="dbkey"/>
>>>>>
>>>>> Cheers,
>>>>> Nicola
>>>>>
>>>>>> </action>
>>>>>>       </actions>
>>>>>>    </data>
>>>>>> </outputs>
>>>>>>
>>>>>>
>>>>>>
>>>>>> The user can select a genome (based on the Bioconductor BSgenome
>>>>>> packages) from the tab delimited fmi__quasr_genomes table, which
>>>>>> looks like:
>>>>>>
>>>>>> hg19BSg    hg19BSg    BSgenome Hsapiens (UCSC hg19)
>>>>>> BSgenome.Hsapiens.UCSC.hg19
>>>>>> hg18BSg    hg18BSg    BSgenome Hsapiens (UCSC hg18)
>>>>>> BSgenome.Hsapiens.UCSC.hg18
>>>>>> ce10BSg    ce10BSg    BSgenome Celegans (UCSC ce10)
>>>>>> BSgenome.Celegans.UCSC.ce10
>>>>>> ce6BSg    ce6BSg    BSgenome Celegans (UCSC ce6)
>>>>>> BSgenome.Celegans.UCSC.ce6
>>>>>> ...
>>>>>>
>>>>>>
>>>>>> The tool works:
>>>>>>  - it displays the available genomes (BSgenome Hsapiens (UCSC hg19),
>>>>>> hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc)
>>>>>>  - once the job is submitted, it uses the right Bioconductor package
>>>>>> (BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc)
>>>>>>
>>>>>> However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get:
>>>>>> <Cheetah.Template.Template object at 0x7f1e40210f50>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Has anything changed with the 'action' tag since release 15.10?
>>>>>> which makes this simple xml no longer working?
>>>>>>
>>>>>> I have to admit, it does look different than the example on the wiki
>>>>>>
>>>>>> (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set
>>>>>>
>>>>>> ). I tried the code from the wiki which is based on the
>>>>>> bowtie_wrapper
>>>>>>
>>>>>> (https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml)
>>>>>>
>>>>>> as well:
>>>>>>
>>>>>>
>>>>>>       <actions>
>>>>>>           <action type="metadata" name="dbkey">
>>>>>>           <option type="from_data_table" name="fmi__quasr_genomes"
>>>>>> column="1" offset="0">
>>>>>>              <filter type="param_value" column="0" value="#"
>>>>>> compare="startswith" keep="False"/>
>>>>>>              <filter type="param_value" ref="index" column="0"/>
>>>>>>           </option>
>>>>>>         </action>
>>>>>>       </actions>
>>>>>>
>>>>>>
>>>>>> but it results in the same kind of error:
>>>>>> <Cheetah.Template.Template object at 0x7ff82c0e43d0>
>>>>>>
>>>>>>
>>>>>> Thank you very much for any help/comments
>>>>>>
>>>>>> Regards, Hans-Rudolf
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> ___________________________________________________________
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>>>>
>>>>
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