Galaxy: using format_source on output collection elements not working

[shiltemann]

I have the following in my tool xml:

<inputs>
    <param name="infile" type="data" format="someformat" label="lab"/>
</inputs>
<outputs>
    <collection name="coll" type="list" label="lab">            
        <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.suffix" format_source="infile"/>
    </collection>
</outputs>

but the format of the collection elements gets set to None instead of the desired someformat

i.e. in planemo I get:
Dataset metadata verification for [file_ext] failed, expected [someformat] but found [None].

same results if I put format_source on the collection tag instead.

ping @jmchilton

edit: on a related note, it would also be handy if change_format tags worked for collection elements

[nsoranzo]

By looking at test/functional/tools/multi_output_configured.xml it seems that adding format="infile" or ext="infile" to <discover_datasets> may work, but this still needs to be honed.

[shiltemann]

format="someformat"works fine there, but format="infile" just gets me

Dataset metadata verification for [file_ext] failed, expected [someformat] but found [infile].

this isn't a big deal, but would be nice to have for input dataset parameters that allow multiple input formats or for subclass datatypes etc :)

[nsoranzo]

Ok, sorry, it was worth a try!

[shiltemann]

yeah it definitely was, thank you, hadn't tried that yet, would have been a nice workaround, but alas :)

[jmchilton]

Mostly for my only record keeping since I have so many branches - but very initial WIP at https://github.com/jmchilton/galaxy/tree/format_source_discovery.

[bernt-matthias]

Would really be nice :)