Describe tabular output column names in Galaxy metadata

[peterjc]

Ideally the tabular files from BLAST tools would result in datasets in Galaxy with the column names in the Galaxy metadata. We know the column names from the command line options used... the trick is how to tell Galaxy this.

There is an open Galaxy issue for using the column data in the interface (e.g. the column selector), https://trello.com/c/kwL8zzSR/436-554-show-column-names-headers-or-first-entry-in-column-select-parameters

See also https://trello.com/c/YlADVbkI which does some clever stuff with metadata which might be helpful.

[bgruening]

@peterjc this is working with recent Galaxy versions. Please have a look at this wrapper: https://github.com/galaxyproject/tools-iuc/blob/master/tools/featurecounts/featurecounts.xml#L356

[peterjc]

Thanks for that example setting column names @bgruening:

<actions>
    <action name="column_names" type="metadata" default="Status,${','.join([ a.name for a in $alignments  ])}" />
</actions>

I see @yhoogstrate worked on this as part of galaxyproject/tools-iuc#588 using the galaxyproject/galaxy#961 addition to Galaxy merged on 11 Feb 2016 by @jmchilton

[update: meaning it should work with the two most recent Galaxy releases, v16.04 and v16.07].

Is there any other documentation (e.g. galaxy-dev emails) I should look at? There is an <actions> example on https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set but not setting column names. I'll give this a try, and if it works update that wiki page a little.

[bgruening]

Hi Peter,

Am 20.09.2016 um 15:35 schrieb Peter Cock:

Thanks for that example setting column names @bgruening
https://github.com/bgruening:

I see @yhoogstrate https://github.com/yhoogstrate worked on this as
part of galaxyproject/tools-iuc#588
galaxyproject/tools-iuc#588 using the
galaxyproject/galaxy#961
galaxyproject/galaxy#961 addition to Galaxy
merged on 11 Feb 2016 by @jmchilton https://github.com/jmchilton.

Is there any other documentation (e.g. galaxy-dev emails) I should look
at?

Not that I now of, sorry.

There is an || example on
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_tag_set
but not setting column names. I'll give this a try, and if it works
update that wiki page a little.

The wiki is deprecated, please look at this awesome work from John:
galaxyproject/galaxy#2923

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[peterjc]

Doing this for the main BLAST tools might be tricky as they already change the output format dynamically. Therefore I started with the BLAST XML to tabular tool. First hurdle is testing the column names worked, see galaxyproject/galaxy#2941