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Stortebecker / training-material

A collection of training material from offered Galaxy courses
http://stortebecker.github.io/training-material
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OpenMS tool issues #6

Closed Stortebecker closed 6 years ago

Stortebecker commented 7 years ago

As there are still so many bugs in OMS tools, I wanted to post them separately, not in issues dedicated to a tutorial / workflow.

Stortebecker commented 7 years ago

Ach ja, beim FeatureFinderMultiplex könnte man tickboxen für optionalen Output hinzufügen, ähnlich wie bei PS. Er macht jetzt standardmäßig drei outputs: consensusXML, featureXML, mgf. Man braucht sicher selten alle drei.

Stortebecker commented 7 years ago

IDFileConverter kann keine mzid files in idXML umschreiben. Error: Warning: Could not determine format of input file '/data/1/galaxy_db/files/003/823/dataset_3823757.dat'! Progress of 'Loading...': Error: Unknown input file type given. Aborting!

Stortebecker commented 7 years ago

@blankclemens TextExporter creates four tabular output files, only the first contains data, the other are empty.

Stortebecker commented 7 years ago

Bei FileConverter v.2.2.0 ist der Wrapper defekt, man kann nix einstellen, v.a. nicht den Output File Type. Deshalb crasht das Tool.

blankclemens commented 7 years ago

Regarding the TextExporter: The output files will contain data if the input is a consensusXML. Sadly, out of the tool information it is not possible to tell automatically when these outputs are needed - I'll check if we can fix this, otherwise I might do a manual fix. For the time being, let's enjoy these empty files!

blankclemens commented 7 years ago

FileConverter: It works just fine for me, for some reason all settings are hidden in the advanced options. Kek.

Stortebecker commented 7 years ago

FileConverter: Jep, sorry. It works now, but I had to modify the old workflow I used...

blankclemens commented 7 years ago

Oh, did it change?

Edit: Yes indeed, all the options where made advanced in OpenMS 2.2.

Stortebecker commented 7 years ago

yep, in v 2.1.0, this option was not hidden in the Advanced section