I create an upload file button using upload.xml in one of my xml scripts. <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator)."> </param> But when I add it to a work flow and try to have it set the parameters at runtime, the set at runtime options fails. Any ideas why? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
Excerpts from Chorny, Ilya's message of 2011-10-19 23:41:28 +0000:
I create an upload file button using upload.xml in one of my xml scripts. ... But when I add it to a work flow and try to have it set the parameters at runtime, the set at runtime options fails. Any ideas why?
There is currently no support for upload tool parameters in workflows. What behavior are you looking for in this case? The upload tool is very special, and the parameters are quite interdependent. Are you trying to create a new dataset from the uploaded file or something else? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
I want to upload an experiment specific file from the workflow and bypass loading it into the history. -----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: Wednesday, October 19, 2011 4:50 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File Button Excerpts from Chorny, Ilya's message of 2011-10-19 23:41:28 +0000:
I create an upload file button using upload.xml in one of my xml scripts. ... But when I add it to a work flow and try to have it set the parameters at runtime, the set at runtime options fails. Any ideas why?
There is currently no support for upload tool parameters in workflows. What behavior are you looking for in this case? The upload tool is very special, and the parameters are quite interdependent. Are you trying to create a new dataset from the uploaded file or something else? -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
Excerpts from Chorny, Ilya's message of 2011-10-20 00:08:11 +0000:
I want to upload an experiment specific file from the workflow and bypass loading it into the history.
Galaxy doesn't really support this mode of operation. Data upload and tool/workflow execution are separated so that all data used by tools is captured within immutable datasets to ensure reproducibility. You could implement this, but unless you still create a dataset for the uploaded file, I think it would break other things (like re-running tools). -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
Yeah, I see. So in either case the file would have to be uploaded to history so it would not make sense to keep uploading the same file multiple times. Thanks, Ilya -----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: Wednesday, October 19, 2011 5:18 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File Button Excerpts from Chorny, Ilya's message of 2011-10-20 00:08:11 +0000:
I want to upload an experiment specific file from the workflow and bypass loading it into the history.
Galaxy doesn't really support this mode of operation. Data upload and tool/workflow execution are separated so that all data used by tools is captured within immutable datasets to ensure reproducibility. You could implement this, but unless you still create a dataset for the uploaded file, I think it would break other things (like re-running tools). -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
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James Taylor