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>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to