Get unsanitized access to tags in the tool xml

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#1

I’m currently using the following line to get tags of datasets to the underlying tool:

#set tags = ','.join(str(t.value) for t in $dataset.tags)

This however this does not return the original tags, they get truncated (losing # and the name:), converted to lowercase and special characters are removed. Is there a better way to get access to tags in the tool xml?

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#2

You need to get t.name and t.value. .name is the first part before the :

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#3

Thanks @mvdbeek, can the tool also get access to unsanitized or at least preserved casing of tag values? e.g. #hello:YoU vs #hello:you

#4

There’s no sanitization anywhere, but tags are linked via lowercase, so maybe you’d need to use
user_tname and user_value

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#5

Thanks @mvdbeek that works, although not that easy(or I might also just be doing something wrong) and I guess the cheetah templating is then still sanitizing characters like $ ?
Anyway the following snippet works for me to get both the named:tags and simpletags:

#for $t in $dataset.tags:
    #if $t.user_tname == 'name':
        #set taglist = taglist + [t.user_value]
    #else:
        #set taglist = taglist + [t.user_tname]
    #end if
#end for
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#6

The way you’re looping you don’t maintain the tags as they are stored in Galaxy.
I think the correct way would be

#set tags = ','.join(["%s:%s" % (t.user_tname, t.user_value) if t.user_tname else str(t.user_value) for t in $dataset.tags])

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#7

And we could also make that the __str__ method of the ItemTagAssociation class so that you only have to do $set tags = ",".join($dataset.tags)

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