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 jmchil...@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-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=singleSingle-End/option
option value=pairedPaired-End/option
option value=paired_collectionPaired 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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