dynamic column names and R ExpressionSet files
Hi All, I'm trying to dynamically load labels from a BioConductor ExpressionSet file (binary .RData) into a select item type. This works just fine, but with a few caveats. Example (for reference, this is from a modification of https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.x...): <code file="CL_code.py"/> ... <page> <param name="eset" type="data" label="Expression set" format="rdata" force_select="True" help="An R data file containing an ExpressionSet"/> </page> <page> <param name="label" type="select" dynamic_options="get_label(eset,False,'class')" force_select="True" label="Variable to test" size="20" help="Name of the variable subject to testing" /> ... I would like to remove the deprecated page tags here (also then the tool can be added to a workflow). However if I do that and then select an ExpressionSet file, the select list does not update. It only works when loading the page for the first time, or when I use the page tags. For text files the solution would be easy; just use type="data_column" and data_ref="yourinputfileparamname" and it auto-updates the select field (though not with the actual column names but that is another issue). With a binary file this is not possible, therefore the dynamic_options feature is needed to do this. Does anyone know of a way to get this to work without using the page tags? Kind regards, Bas Horsman Dept. Bioinformatics Erasmus MC
Options and filters should work for what you need: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Coption.... http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.... Best, J. On Nov 22, 2012, at 4:49 AM, S. Horsman wrote:
Hi All,
I'm trying to dynamically load labels from a BioConductor ExpressionSet file (binary .RData) into a select item type. This works just fine, but with a few caveats.
Example (for reference, this is from a modification of https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.x...):
<code file="CL_code.py"/> ... <page> <param name="eset" type="data" label="Expression set" format="rdata" force_select="True" help="An R data file containing an ExpressionSet"/> </page> <page> <param name="label" type="select" dynamic_options="get_label(eset,False,'class')" force_select="True" label="Variable to test" size="20" help="Name of the variable subject to testing" /> ...
I would like to remove the deprecated page tags here (also then the tool can be added to a workflow). However if I do that and then select an ExpressionSet file, the select list does not update. It only works when loading the page for the first time, or when I use the page tags. For text files the solution would be easy; just use type="data_column" and data_ref="yourinputfileparamname" and it auto-updates the select field (though not with the actual column names but that is another issue). With a binary file this is not possible, therefore the dynamic_options feature is needed to do this.
Does anyone know of a way to get this to work without using the page tags?
Kind regards,
Bas Horsman Dept. Bioinformatics Erasmus MC
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But how does that let me read from a binary file? Bas From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: 22 November 2012 15:59 To: S. Horsman Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] dynamic column names and R ExpressionSet files Options and filters should work for what you need: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Coption.... http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.... Best, J. On Nov 22, 2012, at 4:49 AM, S. Horsman wrote: Hi All, I'm trying to dynamically load labels from a BioConductor ExpressionSet file (binary .RData) into a select item type. This works just fine, but with a few caveats. Example (for reference, this is from a modification of https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.x...): <code file="CL_code.py"/> ... <page> <param name="eset" type="data" label="Expression set" format="rdata" force_select="True" help="An R data file containing an ExpressionSet"/> </page> <page> <param name="label" type="select" dynamic_options="get_label(eset,False,'class')" force_select="True" label="Variable to test" size="20" help="Name of the variable subject to testing" /> ... I would like to remove the deprecated page tags here (also then the tool can be added to a workflow). However if I do that and then select an ExpressionSet file, the select list does not update. It only works when loading the page for the first time, or when I use the page tags. For text files the solution would be easy; just use type="data_column" and data_ref="yourinputfileparamname" and it auto-updates the select field (though not with the actual column names but that is another issue). With a binary file this is not possible, therefore the dynamic_options feature is needed to do this. Does anyone know of a way to get this to work without using the page tags? Kind regards, Bas Horsman Dept. Bioinformatics Erasmus MC ___________________________________________________________ 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/
Apologies, I didn't see that the file was binary. You're right - my suggestion will only help if your file is tabular. One simple option is to provide an RData to tabular converter for now. Currently, I think your approach is the best way given the binary dataset. In the future, it'd be nice if dynamic options allowed a function to be used for retrieving options from a dataset. Best, J. On Nov 28, 2012, at 9:39 AM, S. Horsman wrote:
But how does that let me read from a binary file?
Bas
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: 22 November 2012 15:59 To: S. Horsman Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] dynamic column names and R ExpressionSet files
Options and filters should work for what you need:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Coption.... http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter....
Best, J.
On Nov 22, 2012, at 4:49 AM, S. Horsman wrote:
Hi All,
I'm trying to dynamically load labels from a BioConductor ExpressionSet file (binary .RData) into a select item type. This works just fine, but with a few caveats.
Example (for reference, this is from a modification of https://trac.nbic.nl/galaxytools/browser/trunk/tools/proteomics/NPC/AMC/DE.x...):
<code file="CL_code.py"/> ... <page> <param name="eset" type="data" label="Expression set" format="rdata" force_select="True" help="An R data file containing an ExpressionSet"/> </page> <page> <param name="label" type="select" dynamic_options="get_label(eset,False,'class')" force_select="True" label="Variable to test" size="20" help="Name of the variable subject to testing" /> ...
I would like to remove the deprecated page tags here (also then the tool can be added to a workflow). However if I do that and then select an ExpressionSet file, the select list does not update. It only works when loading the page for the first time, or when I use the page tags. For text files the solution would be easy; just use type="data_column" and data_ref="yourinputfileparamname" and it auto-updates the select field (though not with the actual column names but that is another issue). With a binary file this is not possible, therefore the dynamic_options feature is needed to do this.
Does anyone know of a way to get this to work without using the page tags?
Kind regards,
Bas Horsman Dept. Bioinformatics Erasmus MC
___________________________________________________________ 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:
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