Great, thanks!!!

From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Tuesday, October 18, 2011 10:24 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Trouble getting setting dbkey of output data

Hi Ilya,

The 'actions' tagset must be within the ''data' tagset, you have it outside. 
Try something like:

<data format="sam" name="output2" label="${tool.name} on ${on_string}:Output 
Sam File" >
      <actions>
       <action type="metadata" name="dbkey">
             <option type="from_data_table" name="RNASEQ_contams" column="1" 
offset="0">
                <filter type="param_value" column="0" value="#" 
compare="startswith" keep="False"/>
                <filter type="param_value" ref="input2" column="0"/>
             </option>
       </action>
      </actions>
</data>


Please let us know if we can provide additional assistance.

Thanks for using Galaxy,

Dan


On Oct 18, 2011, at 12:29 PM, Chorny, Ilya wrote:


Anybody, anybody?

Thanks,

Ilya


From: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu]<mailto:[mailto:galaxy-dev-boun...@lists.bx.psu.edu]>
 On Behalf Of Chorny, Ilya
Sent: Monday, October 17, 2011 9:31 AM
To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
Subject: [galaxy-dev] Trouble getting setting dbkey of output data

I am having trouble setting the dbkey of an output data set. The input and 
output, respectively, is shown below. I copied this from the bowtie_wrapper.xml 
 but the difference is that I do not have a condition on selecting the 
reference genome. My tool requires a .loc file. The tools completes correctly 
but the dbkey is not set. Any thoughts on what I may be doing wrong?

Thanks,

Ilya


<param name="input2" type="select" label="Select a reference genome">
       <options from_data_table="RNASEQ_contams">
          <filter type="sort_by" column="2" />
          <validator type="no_options" message="No indexes are available for 
the selected input dataset" />
       </options>
</param>

<data format="sam" name="output2" label="${tool.name} on ${on_string}:Output 
Sam File" />
      <actions>
       <action type="metadata" name="dbkey">
             <option type="from_data_table" name="RNASEQ_contams" column="1" 
offset="0">
                <filter type="param_value" column="0" value="#" 
compare="startswith" keep="False"/>
                <filter type="param_value" ref="input2" column="0"/>
             </option>
       </action>
      </actions>

Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>


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