I know this is sort of a controversial topic so I will try to tread lightly. It seems that for a couple of years the idea of a password parameter for Galaxy tools has come up a lot but has also been rejected a lot although I believe there is a lot of merit to it. I have found at least two other times where people have tried to implement this and it was rejected, but there must have been a reason why they needed that parameter. My situation currently is that I have created two tools in Galaxy which communicate with another software called iRODS which needs authentication from the user. In my own department, there is another tool that was created which needed authentication from the user but the developer had to create some other workaround for this problem. 

In terms of the work I have done for this so far, I have been working off the latest release version of Galaxy. I have implemented the field so that it is obfuscated in the tool form view as well as on the tool info page. I will next be looking into storing the parameter in an environment variable so it doesn't get passed through the command line and encrypting the password before it enters the database. Speaking with a co-worker of mine, we discussed the possibility of implementing two option, irreversible encryption of the password as it gets entered into the database but then making the tool not workflow compatible, or using regular encryption and making the tool workflow compatible. I look forward to hearing your opinions and ideas.

Katherine