Setting the output label based on input parameters?
Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik.
Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: <outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs> Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
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Hi Kanwei, I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I couldn't get it to work. Also, in the example below the "%" should really be "#" right? Anything anyone can think of that I might be doing wrong? - Nik. On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li <kanwei@gmail.com> wrote:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
___________________________________________________________ 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:
you can use label="${input.name}" Shaun Quoting Nikhil Joshi <najoshi@ucdavis.edu> on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the output name BEFORE execution... although that doesn't make sense. In any case, I couldn't get it to work. Also, in the example below the "%" should really be "#" right? Anything anyone can think of that I might be doing wrong?
- Nik.
On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li <kanwei@gmail.com> wrote:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
I meant to say label="${input}" or label="${input.value}. If it's a select field then you can change the option values to the text you want to add to your output label. Shaun Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work. - Nik. On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk>wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the text you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section: <param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/> and in the output section: <data format="fasta" name="output_fasta" label="$filter_reads"/> This seems wrong to do, but it does work. If anyone has a better method, please let me know! - Nik. On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk>wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the text you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
- Nik.
______________________________**_____________________________ 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:
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell. This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output: <data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/> There's even a built in ${on_string} if you just want the file name plus some history ids? On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the text you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want the output label to be different if the user sets a particular parameter to be true.
Hi Ross, Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way. - Nik. On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.lazarus@gmail.com> wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within
parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any
way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the
text
you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi all,
Is there a way to set the label of the output based on the input parameters? Perhaps by using the <action> tag? Basically, I want
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote: the the
output label to be different if the user sets a particular parameter to be true.
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values. One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :) On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.lazarus@gmail.com> wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the text you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
<outputs> %if param == True: <data format="txt" name="blah" label="Label1" /> %else <data format="txt" name="blah" label="Label2" /> %endif </outputs>
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
> Hi all, > > Is there a way to set the label of the output based on the input > parameters? Perhaps by using the <action> tag? Basically, I want > the > output label to be different if the user sets a particular parameter > to > be > true. >
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes. In brief, here's what I did: The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method. I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables. In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action... The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually. So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger" A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab". Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace. The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers). I welcome any feedback and am more than happy to share the code back to the galaxy community. Dave On 8/29/11 6:20 PM, "Ross" <ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.lazarus@gmail.com> wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote:
I meant to say label="${input}" or label="${input.value}.
If it's a select field then you can change the option values to the text you want to add to your output label.
Shaun
Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 -0400:
> Hi Nikhil, > > The tool templates are Cheetah templates, so you can do things like: > > <outputs> > %if param == True: > <data format="txt" name="blah" label="Label1" /> > %else > <data format="txt" name="blah" label="Label2" /> > %endif > </outputs> > > Thanks, > > K > > On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> > wrote: > >> Hi all, >> >> Is there a way to set the label of the output based on the input >> parameters? Perhaps by using the <action> tag? Basically, I want >> the >> output label to be different if the user sets a particular parameter >> to >> be >> true. >>
FWIW: This sounds like a useful idea to me. My users are struggling with output names currently being generated by complex workflows where many tools do something like label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that might be ok for a single step but after traveling through a few of those, the base name (which we routinely use for metadata needed at some final amalgamation step, such as experimental condition) is hard to find in all the cruft. On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton <Dave.Walton@jax.org> wrote:
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes.
In brief, here's what I did:
The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method.
I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables.
In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action...
The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually.
So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger
Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger"
A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace.
The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
I welcome any feedback and am more than happy to share the code back to the galaxy community.
Dave
On 8/29/11 6:20 PM, "Ross" <ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.lazarus@gmail.com> wrote:
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote: > > I meant to say label="${input}" or label="${input.value}. >
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It's actually a boolean checkbox..... so I basically want the label to change based upon whether or not the checkbox is checked. Is there any way to do that? Again, I've tried using the Cheetah syntax to do the #if #end inside the <output> tags.... but that didn't work.
- Nik.
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> wrote: > > I meant to say label="${input}" or label="${input.value}. > > If it's a select field then you can change the option values to the > text > you want to add to your output label. > > Shaun > > > > > > Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 > -0400: > >> Hi Nikhil, >> >> The tool templates are Cheetah templates, so you can do things like: >> >> <outputs> >> %if param == True: >> <data format="txt" name="blah" label="Label1" /> >> %else >> <data format="txt" name="blah" label="Label2" /> >> %endif >> </outputs> >> >> Thanks, >> >> K >> >> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> >> wrote: >> >>> Hi all, >>> >>> Is there a way to set the label of the output based on the input >>> parameters? Perhaps by using the <action> tag? Basically, I want >>> the >>> output label to be different if the user sets a particular parameter >>> to >>> be >>> true.
This is a big part of the reason we did this. I will push it out for the galaxy team to look at. If for some reason the don't approve it I can share our change directly with you. Dave On Sep 1, 2011, at 6:39 PM, "Ross" <ross.lazarus@gmail.com> wrote:
FWIW: This sounds like a useful idea to me.
My users are struggling with output names currently being generated by complex workflows where many tools do something like label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that might be ok for a single step but after traveling through a few of those, the base name (which we routinely use for metadata needed at some final amalgamation step, such as experimental condition) is hard to find in all the cruft.
On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton <Dave.Walton@jax.org> wrote:
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes.
In brief, here's what I did:
The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method.
I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables.
In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action...
The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually.
So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger
Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger"
A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace.
The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
I welcome any feedback and am more than happy to share the code back to the galaxy community.
Dave
On 8/29/11 6:20 PM, "Ross" <ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross <ross.lazarus@gmail.com> wrote:
> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> > wrote: >> >> I meant to say label="${input}" or label="${input.value}. >>
Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
It looks like the Cheetah syntax only is parsed within the <command> tags.... so I figured out a way to do it... but it seems hackish. I basically changed the string values of truevalue and falsevalue within the parameter to be an English sentence that would become the label for the output. I.e., in the input section:
<param name="filter_reads" type="boolean" truevalue="Filtered Reads Fasta" falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
and in the output section:
<data format="fasta" name="output_fasta" label="$filter_reads"/>
This seems wrong to do, but it does work. If anyone has a better method, please let me know!
- Nik.
On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote: > > It's actually a boolean checkbox..... so I basically want the label to > change based upon whether or not the checkbox is checked. Is there any > way > to do that? Again, I've tried using the Cheetah syntax to do the #if > #end > inside the <output> tags.... but that didn't work. > > - Nik. > > On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB <swebb1@staffmail.ed.ac.uk> > wrote: >> >> I meant to say label="${input}" or label="${input.value}. >> >> If it's a select field then you can change the option values to the >> text >> you want to add to your output label. >> >> Shaun >> >> >> >> >> >> Quoting Kanwei Li <kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 >> -0400: >> >>> Hi Nikhil, >>> >>> The tool templates are Cheetah templates, so you can do things like: >>> >>> <outputs> >>> %if param == True: >>> <data format="txt" name="blah" label="Label1" /> >>> %else >>> <data format="txt" name="blah" label="Label2" /> >>> %endif >>> </outputs> >>> >>> Thanks, >>> >>> K >>> >>> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi <najoshi@ucdavis.edu> >>> wrote: >>> >>>> Hi all, >>>> >>>> Is there a way to set the label of the output based on the input >>>> parameters? Perhaps by using the <action> tag? Basically, I want >>>> the >>>> output label to be different if the user sets a particular parameter >>>> to >>>> be >>>> true.
While ${on_string} works well for items in the history, I found that for a dataset in a data table, for example in the 'all_fasta' table, the content of ${on_string} is the null string. Is that expected? Is there a better to get the name or some sort of identifier of the dataset? Thank you, Florent On 02/09/11 08:52, Dave Walton wrote:
This is a big part of the reason we did this.
I will push it out for the galaxy team to look at. If for some reason the don't approve it I can share our change directly with you.
Dave
On Sep 1, 2011, at 6:39 PM, "Ross"<ross.lazarus@gmail.com> wrote:
FWIW: This sounds like a useful idea to me.
My users are struggling with output names currently being generated by complex workflows where many tools do something like label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that might be ok for a single step but after traveling through a few of those, the base name (which we routinely use for metadata needed at some final amalgamation step, such as experimental condition) is hard to find in all the cruft.
On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton<Dave.Walton@jax.org> wrote:
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes.
In brief, here's what I did:
The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method.
I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables.
In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action...
The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually.
So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger
Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger"
A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace.
The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
I welcome any feedback and am more than happy to share the code back to the galaxy community.
Dave
On 8/29/11 6:20 PM, "Ross"<ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi<najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross<ross.lazarus@gmail.com> wrote:
>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB<swebb1@staffmail.ed.ac.uk> >> wrote: >>> I meant to say label="${input}" or label="${input.value}. >>> Nikhil, did you try as Shaun and others have suggested? Any available string parameter can be used in a label as far as I can tell.
This is a common idiom - ask for a string ('title') to describe the job/output for posterity, then in an output:
<data format="foo" name="output1" metadata_source="input1" label="${title}.myext"/>
There's even a built in ${on_string} if you just want the file name plus some history ids?
On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi<najoshi@ucdavis.edu> wrote: > It looks like the Cheetah syntax only is parsed within the<command> > tags.... so I figured out a way to do it... but it seems hackish. I > basically changed the string values of truevalue and falsevalue within > the > parameter to be an English sentence that would become the label for the > output. I.e., in the input section: > > <param name="filter_reads" type="boolean" truevalue="Filtered Reads > Fasta" > falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/> > > and in the output section: > > <data format="fasta" name="output_fasta" label="$filter_reads"/> > > This seems wrong to do, but it does work. If anyone has a better > method, > please let me know! > > - Nik. > > On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi<najoshi@ucdavis.edu> > wrote: >> It's actually a boolean checkbox..... so I basically want the label to >> change based upon whether or not the checkbox is checked. Is there any >> way >> to do that? Again, I've tried using the Cheetah syntax to do the #if >> #end >> inside the<output> tags.... but that didn't work. >> >> - Nik. >> >> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB<swebb1@staffmail.ed.ac.uk> >> wrote: >>> I meant to say label="${input}" or label="${input.value}. >>> >>> If it's a select field then you can change the option values to the >>> text >>> you want to add to your output label. >>> >>> Shaun >>> >>> >>> >>> >>> >>> Quoting Kanwei Li<kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 >>> -0400: >>> >>>> Hi Nikhil, >>>> >>>> The tool templates are Cheetah templates, so you can do things like: >>>> >>>> <outputs> >>>> %if param == True: >>>> <data format="txt" name="blah" label="Label1" /> >>>> %else >>>> <data format="txt" name="blah" label="Label2" /> >>>> %endif >>>> </outputs> >>>> >>>> Thanks, >>>> >>>> K >>>> >>>> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi<najoshi@ucdavis.edu> >>>> wrote: >>>> >>>>> Hi all, >>>>> >>>>> Is there a way to set the label of the output based on the input >>>>> parameters? Perhaps by using the<action> tag? Basically, I want >>>>> the >>>>> output label to be different if the user sets a particular parameter >>>>> to >>>>> be >>>>> true.
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:
on_string seems to be defined for datatool parameters only. There's a common idiom for looking up fields from the relevant .loc files for things like all_fasta - it's not pretty but it does work - eg from the bowtie wrapper: --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" As you can see, it will pass the last column from the relevant row of the loc file pointed at by the tool_data_table.xml entry for bowtie_indexes_color To get a name instead of a path, you could replace the column selector with (eg) 2 if that's the column you want from the .loc file? It's complex but do-able - I hope this helps... On Fri, Sep 16, 2011 at 1:19 PM, Florent Angly <florent.angly@gmail.com> wrote:
While ${on_string} works well for items in the history, I found that for a dataset in a data table, for example in the 'all_fasta' table, the content of ${on_string} is the null string. Is that expected? Is there a better to get the name or some sort of identifier of the dataset? Thank you, Florent
On 02/09/11 08:52, Dave Walton wrote:
This is a big part of the reason we did this.
I will push it out for the galaxy team to look at. If for some reason the don't approve it I can share our change directly with you.
Dave
On Sep 1, 2011, at 6:39 PM, "Ross"<ross.lazarus@gmail.com> wrote:
FWIW: This sounds like a useful idea to me.
My users are struggling with output names currently being generated by complex workflows where many tools do something like label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that might be ok for a single step but after traveling through a few of those, the base name (which we routinely use for metadata needed at some final amalgamation step, such as experimental condition) is hard to find in all the cruft.
On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton<Dave.Walton@jax.org> wrote:
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes.
In brief, here's what I did:
The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method.
I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables.
In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action...
The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually.
So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger
Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger"
A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace.
The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
I welcome any feedback and am more than happy to share the code back to the galaxy community.
Dave
On 8/29/11 6:20 PM, "Ross"<ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi<najoshi@ucdavis.edu> wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes based on whether or not you've checked a checkbox (or a way to change the label of the output based on whether or not the checkbox was checked). So my idea below did work, but it seems like a hack. Which is why I was wondering if there was a better way.
- Nik.
On Mon, Aug 29, 2011 at 2:55 AM, Ross<ross.lazarus@gmail.com> wrote: >>> >>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN >>> WEBB<swebb1@staffmail.ed.ac.uk> >>> wrote: >>>> >>>> I meant to say label="${input}" or label="${input.value}. >>>> > Nikhil, did you try as Shaun and others have suggested? Any available > string parameter can be used in a label as far as I can tell. > > This is a common idiom - ask for a string ('title') to describe the > job/output for posterity, then in an output: > > <data format="foo" name="output1" metadata_source="input1" > label="${title}.myext"/> > > There's even a built in ${on_string} if you just want the file name > plus some history ids? > > > On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi<najoshi@ucdavis.edu> > wrote: >> >> It looks like the Cheetah syntax only is parsed within the<command> >> tags.... so I figured out a way to do it... but it seems hackish. I >> basically changed the string values of truevalue and falsevalue >> within >> the >> parameter to be an English sentence that would become the label for >> the >> output. I.e., in the input section: >> >> <param name="filter_reads" type="boolean" truevalue="Filtered Reads >> Fasta" >> falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/> >> >> and in the output section: >> >> <data format="fasta" name="output_fasta" label="$filter_reads"/> >> >> This seems wrong to do, but it does work. If anyone has a better >> method, >> please let me know! >> >> - Nik. >> >> On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi<najoshi@ucdavis.edu> >> wrote: >>> >>> It's actually a boolean checkbox..... so I basically want the label >>> to >>> change based upon whether or not the checkbox is checked. Is there >>> any >>> way >>> to do that? Again, I've tried using the Cheetah syntax to do the >>> #if >>> #end >>> inside the<output> tags.... but that didn't work. >>> >>> - Nik. >>> >>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN >>> WEBB<swebb1@staffmail.ed.ac.uk> >>> wrote: >>>> >>>> I meant to say label="${input}" or label="${input.value}. >>>> >>>> If it's a select field then you can change the option values to >>>> the >>>> text >>>> you want to add to your output label. >>>> >>>> Shaun >>>> >>>> >>>> >>>> >>>> >>>> Quoting Kanwei Li<kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 >>>> -0400: >>>> >>>>> Hi Nikhil, >>>>> >>>>> The tool templates are Cheetah templates, so you can do things >>>>> like: >>>>> >>>>> <outputs> >>>>> %if param == True: >>>>> <data format="txt" name="blah" label="Label1" /> >>>>> %else >>>>> <data format="txt" name="blah" label="Label2" /> >>>>> %endif >>>>> </outputs> >>>>> >>>>> Thanks, >>>>> >>>>> K >>>>> >>>>> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil >>>>> Joshi<najoshi@ucdavis.edu> >>>>> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> Is there a way to set the label of the output based on the input >>>>>> parameters? Perhaps by using the<action> tag? Basically, I >>>>>> want >>>>>> the >>>>>> output label to be different if the user sets a particular >>>>>> parameter >>>>>> to >>>>>> be >>>>>> true.
___________________________________________________________ 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:
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi Florent, A quick follow up. This has become easier somewhat recently. If you are using datatables, you can define additional fields and access them using e.g. $parameter_name.fields.datatable_key. This is often used for passing the path to tools, when it differers from the name, value used on the tool forms, but could also be used to pull out descriptions, etc. The bfast tool (tools/sr_mapping/bfast_wrapper.xml) is one tool that accesses a defined path attribute: --ref="${ refGenomeSource.indices.fields.path }" Thanks for using Galaxy, Dan On Sep 16, 2011, at 12:07 AM, Ross wrote:
on_string seems to be defined for datatool parameters only.
There's a common idiom for looking up fields from the relevant .loc files for things like all_fasta - it's not pretty but it does work - eg from the bowtie wrapper:
--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }"
As you can see, it will pass the last column from the relevant row of the loc file pointed at by the tool_data_table.xml entry for bowtie_indexes_color To get a name instead of a path, you could replace the column selector with (eg) 2 if that's the column you want from the .loc file?
It's complex but do-able - I hope this helps...
On Fri, Sep 16, 2011 at 1:19 PM, Florent Angly <florent.angly@gmail.com> wrote:
While ${on_string} works well for items in the history, I found that for a dataset in a data table, for example in the 'all_fasta' table, the content of ${on_string} is the null string. Is that expected? Is there a better to get the name or some sort of identifier of the dataset? Thank you, Florent
On 02/09/11 08:52, Dave Walton wrote:
This is a big part of the reason we did this.
I will push it out for the galaxy team to look at. If for some reason the don't approve it I can share our change directly with you.
Dave
On Sep 1, 2011, at 6:39 PM, "Ross"<ross.lazarus@gmail.com> wrote:
FWIW: This sounds like a useful idea to me.
My users are struggling with output names currently being generated by complex workflows where many tools do something like label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that might be ok for a single step but after traveling through a few of those, the base name (which we routinely use for metadata needed at some final amalgamation step, such as experimental condition) is hard to find in all the cruft.
On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton<Dave.Walton@jax.org> wrote:
This is similar to something we've done for workflows in our instance of Galaxy. Dannon actually suggested I push a copy of my changes out so he can review them and potentially add them to galaxy central. I've been delinquent in doing this push. It's not exactly what you are talking about but similar (IMHO)... If folks are interested in this functionality I'll get off my butt and make the time to share the changes.
In brief, here's what I did:
The change is totally isolated to lib/galaxy/jobs/actions/post.py in the RenameDatasetAction.execute method.
I have introduced syntax similar to the ${variable} syntax that is used for creating workflow variables.
In my case the syntax is as follows: #{inputs_file_variable | option 1 | option n} where: input_file_variable = is the name of a module input variable | = the delimiter for added options. Optional if no options. options = basename, upper, lower basename = keep all of the file name except the extension (everything before the final ".") upper = force the file name to upper case lower = force the file name to lower case suggested additions: "replace" option so you can replace a portion of the name, support multiple #{name} in one rename action...
The choice of the character "#" instead of "$" was relatively arbitrary... It was that or "!" actually.
So an example might be: I have a workflow with an Input Dataset and a FASTQ Groomer. In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the "New output name:" field I might type: #{input_file | basename | upper}.fastqsanger
Assume the original input file name to the Input Dataset was s_1_1_PWDxNOD.txt The variable in the FastQ Groomer module for that file is "input_file". When I run the workflow, the resulting output file from the groomer would be "S_1_1_PWDXNOD.fastqsanger"
A much simpler example might just be "#{input_file}.fastqsanger". This is perfectly legal syntax, but the downside is if you have a lengthy workflow and you are continually appending new extentions, you could end up with something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
Like the first of the two suggested additions I mention above, I could see you deciding to add more possible operations in addition to basename, upper, lower and replace.
The concept of the markup I used for adding the operations was taken from "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
I welcome any feedback and am more than happy to share the code back to the galaxy community.
Dave
On 8/29/11 6:20 PM, "Ross"<ross.lazarus@gmail.com> wrote:
Most times I need a user supplied label substring. I'm not sure how else to conditionally set a string to a predetermined value other than with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now deprecated) post job exec hook to change the output dataset name based on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi<najoshi@ucdavis.edu> wrote: > > Hi Ross, > > Yes, I did try that... but what I want is string parameter that > changes > based on whether or not you've checked a checkbox (or a way to change > the > label of the output based on whether or not the checkbox was checked). > So > my idea below did work, but it seems like a hack. Which is why I was > wondering if there was a better way. > > - Nik. > > On Mon, Aug 29, 2011 at 2:55 AM, Ross<ross.lazarus@gmail.com> wrote: >>>> >>>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN >>>> WEBB<swebb1@staffmail.ed.ac.uk> >>>> wrote: >>>>> >>>>> I meant to say label="${input}" or label="${input.value}. >>>>> >> Nikhil, did you try as Shaun and others have suggested? Any available >> string parameter can be used in a label as far as I can tell. >> >> This is a common idiom - ask for a string ('title') to describe the >> job/output for posterity, then in an output: >> >> <data format="foo" name="output1" metadata_source="input1" >> label="${title}.myext"/> >> >> There's even a built in ${on_string} if you just want the file name >> plus some history ids? >> >> >> On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi<najoshi@ucdavis.edu> >> wrote: >>> >>> It looks like the Cheetah syntax only is parsed within the<command> >>> tags.... so I figured out a way to do it... but it seems hackish. I >>> basically changed the string values of truevalue and falsevalue >>> within >>> the >>> parameter to be an English sentence that would become the label for >>> the >>> output. I.e., in the input section: >>> >>> <param name="filter_reads" type="boolean" truevalue="Filtered Reads >>> Fasta" >>> falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/> >>> >>> and in the output section: >>> >>> <data format="fasta" name="output_fasta" label="$filter_reads"/> >>> >>> This seems wrong to do, but it does work. If anyone has a better >>> method, >>> please let me know! >>> >>> - Nik. >>> >>> On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi<najoshi@ucdavis.edu> >>> wrote: >>>> >>>> It's actually a boolean checkbox..... so I basically want the label >>>> to >>>> change based upon whether or not the checkbox is checked. Is there >>>> any >>>> way >>>> to do that? Again, I've tried using the Cheetah syntax to do the >>>> #if >>>> #end >>>> inside the<output> tags.... but that didn't work. >>>> >>>> - Nik. >>>> >>>> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN >>>> WEBB<swebb1@staffmail.ed.ac.uk> >>>> wrote: >>>>> >>>>> I meant to say label="${input}" or label="${input.value}. >>>>> >>>>> If it's a select field then you can change the option values to >>>>> the >>>>> text >>>>> you want to add to your output label. >>>>> >>>>> Shaun >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> Quoting Kanwei Li<kanwei@gmail.com> on Wed, 24 Aug 2011 20:34:57 >>>>> -0400: >>>>> >>>>>> Hi Nikhil, >>>>>> >>>>>> The tool templates are Cheetah templates, so you can do things >>>>>> like: >>>>>> >>>>>> <outputs> >>>>>> %if param == True: >>>>>> <data format="txt" name="blah" label="Label1" /> >>>>>> %else >>>>>> <data format="txt" name="blah" label="Label2" /> >>>>>> %endif >>>>>> </outputs> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> K >>>>>> >>>>>> On Wed, Aug 24, 2011 at 8:24 PM, Nikhil >>>>>> Joshi<najoshi@ucdavis.edu> >>>>>> wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> Is there a way to set the label of the output based on the input >>>>>>> parameters? Perhaps by using the<action> tag? Basically, I >>>>>>> want >>>>>>> the >>>>>>> output label to be different if the user sets a particular >>>>>>> parameter >>>>>>> to >>>>>>> be >>>>>>> true.
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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participants (7)
-
Daniel Blankenberg -
Dave Walton -
Florent Angly -
Kanwei Li -
Nikhil Joshi -
Ross -
SHAUN WEBB