Hi John, 
 thanks for the response. So based on your updated documentation I’ve modified 
my script to take the identifiers as a second argument and with a bit of 
juggling I now have the command line:

        query_textgrids.py --textgrid "${",".join(map(str, $textgrid))}" 
--identifier "${",".join(map(str, [t.element_identifier for t in $textgrid]))}" 
--tier $tier --regex '$regex' --output_path $output

Note the juggling needed with list comprehension to get the list of identifiers 
from the textgrid argument.  This works ok and I can now get a result from my 
tool that includes the identifier:

start   end     duration        label   identifier
0.59    0.83    0.24    6:      1_1308_1_2_092-ch6-speaker16.TextGrid
1.56    1.77    0.21    I@      1_1308_1_2_094-ch6-speaker16.TextGrid
1.64    1.87    0.23    3:      1_1308_1_2_173-ch6-speaker16.TextGrid

in fact I’ll probably take the .TextGrid off the identifier so that it just 
names the recording I’m working with.  

What I’d like to do now is to write another tool that takes this as input along 
with another dataset collection who’s elements also have similar (or the same) 
identifiers but a different type (they will be acoustic features derived from 
an audio file.  I think I can see how to do this, the input to this tool will 
be similar to query_textgrids above and I’ll work through the identifiers and 
the table together.  

I saw your note on the issue re. galaxy.json and took a look in the sources for 
it, so this is a secret way of communicating dataset metadata back to the 
system? Sounds like it might be useful.  I may be able to get someone to work 
on this so if you have time to elaborate your ideas then please go ahead.

It seems that if I was to write my python script in the .xml file (as cheetah) 
I’d get access to a bunch of things that are opaque to a separate script. Would 
it be a useful goal to have a richer galaxy-tool interface that could make all 
information available to the tool wrapper visible to my Python script? One way 
to do that would just be to bundle everything up in JSON and send it to the 

Again, thanks for the help.


Department of Computing, Macquarie University

> On 27 Jul 2016, at 12:29 AM, John Chilton <jmchil...@gmail.com> wrote:
> Thanks for the questions - I have tried to revise the planemo docs to
> be more explicit about what collection identifiers are and where they
> come from 
> (https://github.com/galaxyproject/planemo/commit/a811e652f23d31682f862f858dc792c1ef5a99ce).
> http://planemo.readthedocs.io/en/latest/writing_advanced.html#collections
> I think this might be a case where I'm too close the problem - I
> implemented collections, the tooling around them, and planemo docs so
> there is probably a lot that I just assume is implicit when it is
> completely non-obvious.
> The collection identifier in your case is going to be something like:
> 1_1308_1_2_092-ch6-speaker16. The designation in the previous step -
> the outputing a collection with discovered datasets - if it is
> producing a collection should actually be called "identifier". The
> terms "desigination" and "identifier" are inter-changable from a
> Galaxy perspective - but I prefer using the term "identifier" for
> collections and the older "desigination" when discovered un-collected
> individual datasets.
> There was a little warning explaining the odd whitespace replacement
> stuff that got shifted around at some point in the planemo docs - I
> think I have corrected that now. The explanation for fixing up the
> identifier was this:
> "Here we are rewriting the element identifiers to assure everything is
> safe to put on the command-line. In the future, collections will not
> be able to contain keys that are potentially harmful and this won't be
> necessary."
> So yes this is the name you are after.
> As for the quesstion, "Is a manifest-based approach a silly idea?" -
> not at all, not in the least. I'd prefer to have both options
> available - this current option is nice because it doesn't require a
> "wrapper" script - you can build command lines and such from the
> cheetah template - but definitely people already working with and
> thinking about collections from inside some sort of script should have
> the option to consume and produce manifests of files.
> I've created an issue for this idea here -
> https://github.com/galaxyproject/galaxy/issues/2658. I'm not sure if
> I'll have time to get to it anytime soon - but if you or someone else
> is eager to tackle the problem I could scope out an implementation
> plan for this.
> Thanks for the e-mail and I hope this helps,
> -John
> On Tue, Jul 26, 2016 at 1:59 AM, Steve Cassidy <steve.cass...@mq.edu.au> 
> wrote:
>> Hi all,
>>   I’m staring at the discussion of handling dataset collections:
>> http://planemo.readthedocs.io/en/latest/_writing_collections.html
>> but failing to see the solution to my problem.
>> I have a tool that creates a dataset collection, a group of files with names
>> like 1_1308_1_2_092-ch6-speaker16.TextGrid where the 1_1308_1_2_092 part is
>> a unique identifier that I’d like to keep track of.  I’ve used a
>> discover_datasets tag in the tool xml file to match my output filenames and
>> extract the designation (1_1308_1_2_092-ch6-speaker16.TextGrid) and the ext
>> (TextGrid).
>> I have another tool that runs a query over these files and generates a
>> single tabular result that will ideally include the identifier in some form.
>> Here’s the command section for that tool:
>>        query_textgrids.py --textgrid "${",".join(map(str, $textgrid))}"
>> --tier $tier --regex '$regex' --output_path $output
>> where ‘$textgrid’ is one of my input parameters that has multiple=“true” set
>> so that it can be a dataset collection.  That works ok but the input I get
>> are the filenames (dataset_1.dat, etc.) not the name of the datasets.
>> The page above mentions something called the ‘element_identifier’ and gives
>> this funky example:
>> merge_rows --name "${re.sub('[^\w\-_]', '_', $input.element_identifier)}"
>> --file "$input" --to $output;
>> I can’t see what this element_identifier thing is - the suggestion is that
>> it might be the dataset name, but I’m not sure.  Also I don’t understand why
>> the command above is doing replacement of whitespace with underscores.
>> If this is the name I’m after, it would seem that I’d need to pass these
>> names along with the textgrid files and then pair them up inside my script -
>> is that what I need to do?
>> All of this cries out to me for a more explicit representation of a dataset
>> collection that my tool can create and consume rather than this hacky
>> treatment of filenames.   If I could generate a manifest file of some kind
>> describing my dataset collection then none of this parsing of filenames
>> would be needed.  I could also consume the manifest file as well and it
>> could be used for collection level metadata.  Is this a silly idea?
>> Anyway, any help with my immediate problem would be appreciated.
>> Thanks,
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
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