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

On 3/5/12 7:32 AM, Daniel Sobral wrote:

Hi,

I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool.

Is there a way to define the number of inputs at runtime? E.g. a series-like input?

Thanks, Daniel ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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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

On 3/6/12 1:01 AM, Daniel Sobral wrote:

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

On Mon 05 Mar 2012 05:56:16 PM WET, Jennifer Jackson 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

On 3/5/12 7:32 AM, Daniel Sobral wrote:

...

Hi,

I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool.

Is there a way to define the number of inputs at runtime? E.g. a series-like input?

Thanks, Daniel ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/