annotateMyIDs (several versions) is not really ignoring header line when option set

[jennaj]

Test history usegalaxy.eu: https://usegalaxy.eu:/u/jenj/h/test-hisat2-featurecounts-annotatemyids

Test history usegalaxy.org: https://usegalaxy.org:/u/jen/h/test-hisat2-featurecounts-annotatemyids

If the header is removed first, the tool works fine, across servers and tool versions.

[jennaj]

For reference, this was first reported at Galaxy Help here: https://help.galaxyproject.org/t/annotatemyids-fatal-error/701

[mblue9]

@jennaj it's due to the spaces in the column name ("HISAT on data N"), this should fix it #2320. Actually no, the spaces are causing the issue but the header should be handed better regardless and the fix should do that.

[jennaj]

@mblue9 Thank you!

[jennaj]

Looks like this was in the 3/8/19 tool update in the MTS. Only EU appears to have v 3.7.0 installed (yet). But is it really the latest version with this changeset included? GUI has 3.7.0 -- same as MTS -- but the issue doesn't seem to be fixed.

The test fails when the input has a header (single Featurecounts count file, two columns, contains spaces and tabs) + form marked "yes" the input has a header. See dataset 38 in the original test history:

Test history usegalaxy.eu: https://usegalaxy.eu:/u/jenj/h/test-hisat2-featurecounts-annotatemyids

Seems to still be splitting by header whitespace, not tabs, to create labels for data columns, even though sep="\t" is specified. @mblue9 what do you think?

[mblue9]

@jennaj it works fine for me locally with your input file and settings, see screenshot below

So maybe it just needs to be updated at EU? ping @bgruening

[bgruening]

Updated on usegalaxy.eu

[jennaj]

Great, works now at EU. I'll ping to get ORG updated, too. Going to close this out, thanks all!!

[jennaj]

@Slugger70 ping that you will probably want to update the tool at AU as well

[Slugger70]

Thanks @jennaj I'm updating tools today so will add the update for this in.