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.commailto:ichorny@illumina.com Website: www.illumina.comhttp://www.illumina.com