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:


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?


--Mark Johnson
Staff Scientist

<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

   <!-- "action" is the thing the user interacts with -->
   <inputs action="" class="moz-txt-link-rfc2396E" href="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&amp;run=SRR445299&amp;">"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"/>

        <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" />

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

<help>Download SRA traces</help>

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