Variable Number Of Inputs In Workflow (Or Optional Inputs)

6.7 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Daniel, Examining existing tools that have multiple/optional inputs can be a good way to see how this is done. One example is the tool: "NGS: QC and manipulation -> Manipulate FASTQ". The 'Manipulate FASTQ' tool source is here: http://bitbucket.org/galaxy/galaxy- central/src/e58a87c91bc4/tools/fastq/ fastq_manipulation.py fastq_manipulation.xml The tool tag set is defined in this wiki; http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax See <repeat>, <conditional>, and <when> for more details and examples. Questions about tools are best sent to the galaxy-dev@bx.psu.edu mailing list (the galaxy-user list is primarily for questions about data/tools usages on the main public instance). I am going to forward your question over there so that the development community can add to my reply in case they have a simpler way of doing this or other advice. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number of inputs, it seems that I have to define the number of inputs during workflow creation and not when I run the workflow. I was just asking if it would be feasible to have a variable number of inputs (only defined when a running instance of a workflow is created). It feels to me that the answer is no. Thanks again, Daniel

ADD REPLY • link written 6.7 years ago by Daniel Sobral • 30

Hi Daniel, My apologies! I misunderstood what your question was about. You are correct, the required inputs are defined when the workflow is created. For tools that accept a variable number of inputs, when that tool is added to a workflow, the run-time parameters, including expected inputs, are defined. Did you have a particular tool in mind? We can ask Dannon for some suggestions/comments if you want to share your ideas about how this sort of processing would flow. I am glad you wrote back. Please send more details if you want and we can try to offer more (better!) help, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD REPLY • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k

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