I wonder if it is possible to use a .txt file as input parameter for instrument which accepts text field parameter. I want to use this option in a workflow: 1) get user’s simple text input, 2) process this text with some instruments, 3) use the processed text as input parameter for the text field of other instrument. Can I do that?
Yes. Please see the functionality described in the tutorial below for the options.
Thank you! Now I cannot find the instrument “Parse parameter value” anywhere including Galaxy repositories. Could you help with this?
Are you looking for a text manipulation tool?
Many of the common utilities are explained here. More are in the tool panel and tend to have a similar name as the command-line that do the same. Data Manipulation Olympics
I cannot find the tool “Parse parameter value” that is mentioned in the tutorial Using Workflow Parameters. The common problem of galaxy tools is they are difficult to find by name. There different names for the same instrument in galaxy tool panel and galaxy tool shed. And the tutorial does not provide links for instruments it describes. Can you please give me the link for this tool or its name in galaxy tool shed? I need it in my workflow.
It was also tricky to find tool “Compose text parameter value” in galaxy tool shed. I found it by query “compose” and couldn’t find by its full name. It’s named “compose_text_param”. To make sure if it is the tool I needed I had to install the tool, there is no other way.
Some tools are specific to workflows. Find these in the tool panel within the workflow editor.
These screenshots of the two you mentioned seem to be coming up as a top hit at UseGalaxy.org. UseGalaxy.eu should be the same, and UseGalaxy.org.au might not have these yet (is pending an update for logistical reasons). Other public servers … I don’t know, but you could contact those admins to ask.
If you are working at a local Galaxy server, and these are not available, you also might just need to update your Galaxy server to the latest version. Some of this functionality is new-ish. Releases — Galaxy Project 23.0.1.dev0 documentation
Thank you very much! Now I found it.