Re: [galaxy-dev] Set output dbkey from parameter value

15 Oct 2014

      Yes!

Thank you very much Daniel.

On 15 October 2014 18:14, Daniel Blankenberg <dan@bx.psu.edu> wrote:
...
Does removing the ‘param_attribute=“value"' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos <nikos.sidiro@gmail.com> wrote:
...
Hi Daniel,
Thanks for the response.
I've edited the output to:
<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>
           <actions>
               <conditional name="bedgraph.check">
                   <when value="yes">
                       <action type="metadata" name="dbkey">
                           <option type="from_param"
name="bedgraph.genome" param_attribute="value" />
                       </action>
                   </when>
               </conditional>
           </actions>
       </data>
Now I'm getting a tool execution error.
Error executing tool: 'unicode' object has no attribute 'value'
I've tried to change the param_attribute to "ext", "dbkey" (ones that
I know that exist) and got a similar error.
Bests,
Nikos
On 15 October 2014 16:58, Daniel Blankenberg <dan@bx.psu.edu> wrote:
...
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/