Yes!
Thank you very much Daniel.
On 15 October 2014 18:14, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Does removing the ‘param_attribute=“value"' attribute help?
>
>
> On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos <nikos.sid...@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 <d...@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.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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>>
>
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