Re: [galaxy-dev] A tool with no inputs
One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). From: Duddy, John jdu...@illumina.com Doesn't this violate one of the basic tenets of Galaxy - reproducibility? Without the ability to provide full traceability to the inputs, one can make no guarantees about the outputs. I think that condition is being met - the resulting dataset depends on no inputs but the time of fetching, and so traceability is satisfied, just like many remote and updating data sources. In any event, our pragmatic need in this case is for such a tool without any need for reproducibility. Which leads me to note the strange behaviour seen when the only input is a hidden field. When the inputs are: inputs param name=input_seq_file type=data format=fasta label=Input sequences help=The sequences to have MLST profiles constructed for. / param name=offset type=hidden value=0 / /inputs this works as expected: a dataset selection dropdown and a hidden field (seen in the source). But if you delete the non-hidden parameter: inputs param name=offset type=hidden value=0 / /inputs Galaxy doesn't generate an error, reports loading the tool, and puts an entry in the tool panel. However the link for the tool in question is malformed, missing a tool identifier and when clicked only reloads the middle welcome panel. I haven't worked out where and why this is happening, but at the least it's an uninformative error. Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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/
[galaxy-dev] A tool with no inputs
One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). It is admittedly a fairly niche use-case and we could put in a dummy field and simply not use it, but that seems inelegant. Any suggestions? Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **___ 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/
Re: [galaxy-dev] A tool with no inputs
Doesn't this violate one of the basic tenets of Galaxy - reproducibility? Without the ability to provide full traceability to the inputs, one can make no guarantees about the outputs. John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.commailto:jdu...@illumina.com From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Paul-Michael Agapow Sent: Monday, May 16, 2011 7:45 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] A tool with no inputs One of my colleagues is having trouble developing a peculiar tool: it has no inputs. This makes sense in our local context - it fetches some constantly updating remote data for the current user - but implementing it has escaped our skill. Galaxy complains about a tool with no params (i.e. an empty inputs). It complains about a tool with no inputs tag. Hidden input fields don't seem to work (i.e. looks like I'm getting the cached value of the form). It is admittedly a fairly niche use-case and we could put in a dummy field and simply not use it, but that seems inelegant. Any suggestions? Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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/
