On 02/06/2012 03:54 PM, Sarah Diehl wrote:
> I'm only guessing here, but maybe the issue is that the parameter names
> are all the same (namely "model"). Did you try with only unique names?
> Especially this one:
> <param name="models" type="select" label="model source"
> help="History or installed models?" value="local">
> should get it's own name.
Thank you, that was the first step to the solution. In fact I had used
different names before and failed, but what I left out was using
$ModelSource as a prefix to the actual variable name.
I had to rename the selection parameter "model" for local or history,
the two alternative parameters could stay with the same name ("model"),
since they are used mutually exclusive. Then, using $ModelSource.model
would give the correct result.
> On 02/06/2012 03:38 PM, Holger Klein wrote:
>> Dear all,
>> I'm working on a tool wrapper which for a sequence scoring tool.
>> It's supposed to score sequences either using a library installed to
>> galaxy (tool-data/models.loc) or datasets from the user history.
>> I tried to implement this behavior using the<conditional> /<when
>> value> mechanism, simplified code follows below.
>> Using locally installed models (from models.loc) fails with "NotFound:
>> cannot find 'models'", although in the details view of the failed tool
>> run "model database" points to the right file.
>> Using the model file from the history works.
>> Defining _only_ locally installed models from models.loc also works
>> (removing the<conditional> stuff and leaving only the part inside<when
>> value='local'> </when>).
>> The commandline might look a bit strange but is correct.
>> Can anybody spot what is going wrong here?
>> calcModels --scoreFasta -- --fa $fasta_in --bgFa $fasta_background
>> --models $models> $output_table
>> <param format="fasta" name="fasta_in" type="data" label="Input Fasta
>> File" />
>> <param format="fasta" name="fasta_background" type="data"
>> label="Background Fasta File" />
>> <conditional name="ModelSource">
>> <param name="models" type="select" label="model source"
>> help="History or installed models?" value="local">
>> <option value="local">Locally installed models</option>
>> <option value="history">Models from your history</option>
>> <when value="local">
>> <param name="models" type="select" label="model database">
>> <options from_file="models.loc">
>> <column name="name" index="1"/>
>> <column name="value" index="2"/>
>> <when value="history">
>> <param name="models" type="data" format="tabular" label="model
>> database" />
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
Tel: +49(6131) 39 21511
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