Great, thanks!!!

From: Daniel Blankenberg [mailto:dan@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Monday, October 17, 2011 9:31 AM
To: 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: ichorny@illumina.com

Website: www.illumina.com

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