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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="" class="moz-txt-link-rfc2396E" href="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&run=SRR445299&">"http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser&run=SRR445299&" 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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