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.sid...@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
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