I’m annotation a set of protein sequences for presence or absence of signal peptide with SignalP through InterProScan. It is the first time I’m doing this. Everything seems to work ok, however in the output there is not column indicating whether a signal peptide was predicted or not. I would expect a column giving a YES/NO or SP/CYT to indicate signal peptide or not. Do anyone have some tips? Am I missing something?
The tool doesn’t provide a Y/N type of flag … just the results of the annotation it found along with metadata and statistics about the query, target, and match. The columns are defined in the tool form help. Scroll down on the form to review this section – most tool have something, including links to the tool source and any author documentation available. The notes included directly on the form are usually the most important parts to pay attention to as far as usage goes, since those tend to reflect the types of questions that have come up before (“translating” how to use the tool in Galaxy with the form, or just general help that applies wherever the tool is used).
This particular tool also has some optional outputs that might provide more insight (the author seems to think so…). Maybe rerun, output those, and see if any are helpful? You could also select more “Applications to run” to see what those produce: confirming or new evidence from other sources and the like.
And, as a general observation, I am wondering if the GO mappings might provide a class of information you could use to apply a custom Y/N type of filter against the raw output (as an extra action) when running this in batch. So, maybe try that as well if it seems interesting.
Once you come up with a process, you can save all those steps into a workflow. If you then “favorite” the workflow, it will be listed in the tool panel, and can be used just like any other tool.
Galaxy has many of the same of the text manipulation tools usually available on the command line (or, in spreadsheet programs), and this tutorial is a good overview if curious about the how-to whenever custom parsing results into summaries. Data Manipulation Olympics
Hope that helps!
Thanks a lot for the clarifying answer @jennaj. I’ll try what you suggest and see if that helps on the interpretation.