Trying to make batch runs with tool that takes single text entry

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tool-dev

#1

Myself and a colleague have developed a Galaxy tool that runs Picard for a specific purpose. It works fine with a single SAM/BAM input.

However, the issue arises when we wish to run a collection of files. The tool has been designed so that it takes a single sample/strain name as input which is required for running the Addreadgroups command. This, of course, would fail when attempting to run this on a collection because we would not be able to specify multiple sample names. We are limited to specifying one.

My question is: Is it possible to modify our tool so that it takes a text file input of strain names, or a list of some sort, and then runs those for the number of SAM/BAM files that it receives as input? I am not sure if this has been done in Galaxy or if it’s even possible. I’ve attached a screenshot of what our current tool looks like. You can see the “sample name” input box at the bottom that currently works with a single file input.

If anyone even has a tool that has been published in the toolshed that utilizes this functionality (ability to operate on a list of strains over a collection) that would be immensely helpful. Thank you.


#2

Cross-reference post and code example: https://gitter.im/galaxyproject/Lobby?at=5c814ca8b4b6ef7bc8701bdb