Hi Nikos, In the very least, you’ll want to make sure that you have a bounding <actions></actions> tag set around your actions. It is probably also advisable to add a set of conditional/whens around the action, since you’re only setting the dbkey under certain circumstances. Thanks for using Galaxy, Dan On Oct 15, 2014, at 6:37 AM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of a parameter.
The parameter I want to use is genome.
<conditional name="bedgraph"> <param name="check" type="select" label="Produce BedGraph output" help="Can be displayed directly on UCSC browser. One file per normalisation method." > <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="bed_file" type="data" format="bed" label="Transcripts ins BED format" help="12 column BED file containing trancript definitions." /> <param name="genome" type="text" label="Genome Build" help="E.g. hg19" /> <param name="track_name" type="text" label="Track Name" size="20" value="Track Name" /> </when> <when value="no" /> </conditional>
and this is how I've set the output:
<data format="bedgraph" name="bedgraph_slograt" label="${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)" from_work_dir="output_dir/slograt.bedgraph"> <filter> bedgraph['check'] == 'yes' and slograt['check'] == 'yes' </filter> <action type="metadata" name="dbkey"> <option type="from_param" name="bedgraph.genome" param_attribute="value" /> </action> </data>
When I run the tool the dbkey isn't set to the output file. Does anyone know a workaround?
Bests, Nikos ___________________________________________________________ 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/
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