So you don't want the multi-run options to appear next to these
inputs? There is currently no way for the tool author to disable this.
I will admit that I am skeptical this is a good idea, fundamentally is
feels like tool authors should not be able to prevent end users from
running the tool multiple times in parallel. Though I will also admit
in practice there are times this option leads to confusion for users
about what will actually happen and multiple people have requested an
option to disable it.

http://dev.list.galaxyproject.org/Tool-development-Selecting-a-single-item-from-input-dataset-td4666447.html
https://trello.com/c/qCtBBB8n

-John


On Tue, Jun 23, 2015 at 12:58 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:
> Hi all - I'm constructing a wrapper for a tool I have and the input to the
> tool can be:
>
> 1)  a single fastq file (single end sample)
> 2)  multiple singled-end fastq files
> 3)  a single paired-end sample
> 4)  multiple paired-end samples.
>
> I have cases #1 and #2 handled, however case #3 is presenting a problem.  If
> the user select "Paired-End" sample, I want to restrict them to selecting
> only a single fastq1 and fastq2 file.
>
> If they want to submit multiple paired-end samples I only want to allow them
> to submit them  as a list of dataset pairs.  I can get this part to work.
>
> I just need to restrict users to selecting only a single fastq1 and fastq2
> file when the input_type is Paired-End.
>
> My XML is as follows.  Any help would be appreciated
>
>     <!-- Input FastQ file(s) -->
>     <conditional name="input_type">
>       <param name="input_type_selector" type="select" label="Select input
> type" help="Select between single and paired fastq data">
>         <option value="single">Single-End</option>
>         <option value="paired">Paired-End</option>
>         <option value="paired_collection">Paired Collection</option>
>       </param>
>       <when value="single">
>         <param name="fastq_input1" type="data" format="fastq" label="Select
> fastq dataset" multiple="true" help="Specify dataset with single end reads"
> />
>       </when>
>       <when value="paired">
>         <param name="fastq_input1" type="data" format="fastq" label="Select
> fastq dataset" help="Specify dataset with 1st of paired-end reads" />
>         <param name="fastq_input2" type="data" format="fastq" label="Select
> fastq dataset" help="Specify dataset with 2nd of paired-end reads" />
>       </when>
>       <when value="paired_collection">
>         <param name="fastq_collection" type="data_collection"
> collection_type="list:paired" label="Select a paired collection" help="See
> help section for an explanation of dataset collections"/>
>       </when>
>     </conditional>
>
>
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