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

Did you try what Dan suggested ? Which issues did you find by doing so ? PD: Someone should put the "repy to:" munging in this mailing list so that it keeps the responses in the list automatically, there's a mailman setting for this (reply_goes_to_list): http://www.gnu.org/s/mailman/mailman-admin/node11.html Ignore the "considered harmful" nonsense, in my experience it does help a lot in mailing lists such as this. 16 sep 2011 kl. 10:11 skrev Fengyuan Hu:

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

___________________________________________________________ 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/