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>
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-f... https://trello.com/c/qCtBBB8n -John On Tue, Jun 23, 2015 at 12:58 PM, Ryan G <ngsbioinformatics@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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If the user selects mulitple pairs of paired-end data, I want that submitted the same way as a list of paired-end data. I don't want a separate job for each paired-end data. Rather, I want a single job to consume the entire list. It seems to be easier to disable the ability to select multiple fastq1s and fastq2s, and only allow the user to specify a list of paired-end reads. This way, I can guarantee the pairs of fastq files match up correctly. On Thu, Jun 25, 2015 at 10:41 AM, John Chilton <jmchilton@gmail.com> wrote:
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-f... https://trello.com/c/qCtBBB8n
-John
Hi all - I'm constructing a wrapper for a tool I have and the input to
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
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
On Tue, Jun 23, 2015 at 12:58 PM, Ryan G <ngsbioinformatics@gmail.com> wrote: the problem. If 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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Ryan G