Thank you dan, it works!
On 16/09/11 14:42, Daniel Blankenberg wrote:
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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