Hi Mark,

Try these changes:

<tool id="sra-trace-download" name="Download SRA data" tool_type="data_source">

and 

<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=sra-trace-download"/>

Although 'GALAXY_URL' should be generated automatically if it is not included explicitly for 'data_source' tool types.

Also, make sure that your application is including a "URL" parameter in the post back to Galaxy. Using GET requests should also work.


Please let us know if you encounter further difficulties.


Thanks for using Galaxy,

Dan


On Mar 22, 2012, at 10:53 AM, Mark Johnson wrote:

I'm working on an data source tool for NCBI's Sequence Read Archive (SRA). I'm currently targeting a small form in the existing SRA application, to allow downloading a part of a specific assembly. The form I'm talking about is labeled "Alignment" on this page:

http://www.ncbi.nlm.nih.gov/Traces/sra/?view=run_browser&run=SRR445299

The application is not yet Galaxy-aware (but it will be). I'm currently telling that form to POST to GALAXY_URL, which is defined in the tool file as /tool_runner/sra-trace-download
It will essentially do the same thing as the "File" button in that form, except (of course) download to Galaxy. (A related question: will Galaxy tool_runner accept GET requests, or must parameters be POSTed?)

The file I'm using appears below. Instead of a download, I simply get the Galaxy home page content (welcome.html) in the center iframe, and no download.

Is it clear from the XML what I'm missing?

Thanks

--Mark Johnson
Staff Scientist
NCBI


<tool id="sra-trace-download" name="Download SRA data" URL_method="post">
   <description>Download traces from NCBI SRA database</description>

   <!-- This is the program that processes the request. Currently just print the output filename -->
   <command interpreter="python">
print "Called tool, output=" % $output
   </command>

   <!-- "action" is the thing the user interacts with -->
   <inputs action="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&amp;run=SRR445299&amp;"  check_values="false" method="post">

    <param name="GALAXY_URL" type="baseurl" value="/tool_runner/sra-trace-download"/>
    <param name="sendToGalaxy" type="hidden" value="1"/>
   </inputs>

   <request_param_translation>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
        <request_param galaxy_name="URL" remote_name="URL" missing="" />
        <request_param galaxy_name="dbkey" remote_name="db" missing="sra" />
   </request_param_translation>

   <outputs>
     <data format="fasta" name="output"/>
   </outputs>

<help>Download SRA traces</help>
</tool>
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