Hello!
I’m using the Select tool (Galaxy Version 1.0.4; link: Galaxy), My question is about whether this tool is case-sensitive.
In particular, I am filtering out contaminant and decoy peptides, so here is how I set the tool:
Select lines from Data input ‘input’ (txt)
that
NOT matching
the pattern
(con_)|(contam_)|(rev_)
Would exclude lines that have all upper-case (CON_, REV_) or capitalized first letter (Con_, Rev_)?
Thanks in advance!
I hope we can clarify this for you, and you can ask follow up questions!
Yes.
The select tool completes the search using regular expressions. However it will allow the search to occur without actually constructing a full regular expression. Meaning, a simple word can be entered, and that will work too! But for full control, constructing the full term is best.
For your example here:
Yes, you are correct, the expression will not find the other terms, so they would not be excluded.
If instead you do want to capture and exclude the variations, you can try using a character class with the [] notation.
Please let us know if this solves your problem or if you need more help! 
Hello @jennaj !
Thank you for your response. A separate issue arose where I realized I had more terms to capture than I thought, each with their own set of variations.–I might have misunderstood how to use [], but I didn’t think I could put whole terms inside the brackets.–I don’t use regex in my daily work, so I was pretty confused 
After trial and error, I ended up reaching out to the software developer on our team, and he put together this regex for me:
(\t(generic\|)?((?i)con_|contam_|rev_|decoy_)|((?i)_human\t))
I know the generic| is optional, but I wanted to include it for completeness in covering different prefixes.
Also I have a question about a different Galaxy tool, Unipept. Can I ask it in this thread, or should I make a new topic?
Thank you!
Glad you have this working, @katherine-d21 !!
My suggestion was [cC]at to match “cat” or "Cat’ but regular expressions can get more complicated of course, so getting help from someone was a good idea!
And, yes, a new topic is best if the tool is different. Thanks!