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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