Hi Fengyuan,
Try something like this:
<?xml version="1.0"?>
<tool name="Perform advanced genomic region search" id="intermine_export">
<description> with an InterMine instance</description>
<redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name}
INFO=${input1.info}</redirect_url_params>
<inputs>
<param format="bed" name="input1" type="data" label="Send this dataset to an
InterMine instance">
<validator type="unspecified_build" />
</param>
<conditional name="destination">
<param name="indexDestination" type="select" label="Select InterMine instance"
help="InterMine genomic region search service.">
<option value="flymine">FlyMine</option>
<option value="modmine">modMine</option>
<option value="metabolicmine">MetabolicMine</option>
</param>
<when value="flymine">
<param name="REDIRECT_URL" type="hidden"
value="http://www.flymine.org/query/genomicRegionSearch.do"; />
</when>
<when value="modmine">
<param name="REDIRECT_URL" type="hidden"
value="http://intermine.modencode.org/query/genomicRegionSearch.do"; />
</when>
<when value="metabolicmine">
<param name="REDIRECT_URL" type="hidden"
value="http://www.metabolicmine.org/beta/query/genomicRegionSearch.do"; />
</when>
</conditional>
<param name="DATA_URL" type="baseurl" value="/datasets" />
<param name="GALAXY_URL" type="baseurl"
value="/tool_runner?tool_id=intermine_import" />
<param name="REDIRECT_URL" type="hidden"
value="http://www.flymine.org/query/genomicRegionSearch.do"; />
</inputs>
<request_param_translation>
<request_param galaxy_name="REDIRECT_URL"
remote_name="destination|REDIRECT_URL"
missing="http://www.flymine.org/query/genomicRegionSearch.do"; />
</request_param_translation>
<outputs/>
<help>
some help text here...
</help>
</tool>
Where flymine is set as the default, but will be replaced based upon the user's
conditional selection. Please let us know if we can provide additional
assistance.
Thanks for using Galaxy,
Dan
On Sep 16, 2011, at 4:11 AM, Fengyuan Hu wrote:
> Hi,
>
> I don't mean to be pushy, but just in case my question is buried and
> forgotten to be viewed. Could someone have a look at this, please?
>
> Thanks
> Fengyuan
>
> On 12/09/11 10:20, Fengyuan Hu wrote:
>> Dear Galaxy developers,
>>
>> I'm trying to create a tool to export galaxy interval data to InterMine
>> instances.
>>
>> Firstly, based on the tool to send dataset to EpiGRAPH, I created one to
>> FlyMine, it's working on my local instance. Then I tried a bit complex one,
>> to integrate multiple mines in one tool, source xml as following:
>>
>> <?xml version="1.0"?>
>> <tool name="Perform advanced genomic region search" id="intermine_export">
>> <description> with an InterMine instance</description>
>> <redirect_url_params>GENOME=${input1.dbkey} NAME=${input1.name}
>> INFO=${input1.info}</redirect_url_params>
>> <inputs>
>> <param format="bed" name="input1" type="data" label="Send this dataset to an
>> InterMine instance">
>> <validator type="unspecified_build" />
>> </param>
>> <conditional name="destination">
>> <param name="indexDestination" type="select" label="Select InterMine
>> instance" help="InterMine genomic region search service.">
>> <option value="flymine">FlyMine</option>
>> <option value="modmine">modMine</option>
>> <option value="metabolicmine">MetabolicMine</option>
>> </param>
>> <when value="flymine">
>> <param name="REDIRECT_URL" type="hidden"
>> value="http://www.flymine.org/query/genomicRegionSearch.do"; />
>> </when>
>> <when value="modmine">
>> <param name="REDIRECT_URL" type="hidden"
>> value="http://intermine.modencode.org/query/genomicRegionSearch.do"; />
>> </when>
>> <when value="metabolicmine">
>> <param name="REDIRECT_URL" type="hidden"
>> value="http://www.metabolicmine.org/beta/query/genomicRegionSearch.do"; />
>> </when>
>> </conditional>
>> <param name="DATA_URL" type="baseurl" value="/datasets" />
>> <param name="GALAXY_URL" type="baseurl"
>> value="/tool_runner?tool_id=intermine_import" />
>> </inputs>
>> <outputs/>
>> <help>
>> some help text here...
>> </help>
>> </tool>
>>
>> I use <conditional> tag on intermine instances, it will be parsed to a
>> dropdown list in html page, every time I select a different mine, I'd like
>> the value of "REDIRECT_URL" param to change accordingly, but this is not
>> working. After testing and reading the doc a bit, I realised that
>> "REDIRECT_URL" will be renamed "destination | REDIRECT_URL" in the rendered
>> html, and the xml parser will only recognise the key word "REDIRECT_URL"
>> (reserved), is this the case?
>>
>> Can I still valid my logics in the xml?
>>
>> Thanks
>> Fengyuan
>>
>
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