Ok, Great. I think I have part of this figured out. I have a conditional
input as specified:
<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 paired-end reads" />
<param name="fastq_input2" type="data" format="fastq" label="Select
fastq dataset" help="Specify dataset with 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>
In my <command> section, I want to test how this is passed to the tool, so
I have:
<command>
#if str( $input_type.input_type_selector ) == "single":
echo "Input Type: Single"
echo "Input File: $input_type.fastq_input1"
#elif str( $input_type.input_type_selector ) == "paired":
echo "Input Type: Paired"
echo "FastQ1: $input_type.fastq_input1\nFastQ2:
$input_type.fastq_input2"
#elif str( $input_type.input_type_selector ) == "paired_collection":
print "Input Type: Collection\n"
#for $element in $input_type.$fastq_collection:
echo "FastQ1: $element.fastq_input1"
#end for
#end if
</command>
The "single" and "paired" works as expected, however I can select multiple
input for "paired" which I don't want to allow. A user should only be able
to select a single pair of fastq files. To select multiple pairs, I have
"paired_collection".
The second problem is in the command section, I'm trying to iterated
through the pair of inputs, however my echo statement is causing a Cheetah
error. I tried different incarnations of it as well. My latest (and what
I thought correct) is shown above. It generates the error:
Traceback (most recent call last):
File
"/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/runners/__init__.py",
line 163, in prepare_job
job_wrapper.prepare()
File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/__init__.py",
line 858, in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py",
line 411, in build
self.__build_command_line( )
File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py",
line 427, in __build_command_line
command_line = fill_template( command, context=param_dict )
File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/util/template.py",
line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
"/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1434732603_97_56713.py",
line 107, in respond
AttributeError: 'dict' object has no attribute 'VFFSL'
How do I iterate through the fastq inputs when they are passed as a list:paired?
On Fri, Jun 19, 2015 at 11:31 AM, John Chilton <jmchil...@gmail.com> wrote:
> The option in the GUI for selecting multiple datasets for a single
> data parameter - causes multiple jobs to be created as you noted. If
> you just place multiple="true" on your data input parameter - that
> button will go away and all the datasets will be used for a single
> job.
>
> If your tool consumes pairs of datasets - you will want to expose an
> option where you are using a parameter like:
>
> <input name="input_pairs" type="data_collection"
> collection_type="list:paired" format="fastq" />
>
> and then your users will have to use the data collection creator to
> pair off the datasets into a big list before using your tool - but the
> creator is actually really nice - I think it makes it very easy to
> build large lists of pairs.
>
> Hope this helps - happy to provide more details,
> -John
>
> On Fri, Jun 19, 2015 at 11:24 AM, Ryan G <ngsbioinformat...@gmail.com>
> wrote:
> > Hi all - I have a tool which is essentially an entire NGS pipeline
> bundled
> > into a perl script and associated modules. I'd like to offer this tool
> to
> > users via Galaxy.
> >
> > I'm trying to pass a bunch of fastq files to the tool, but noticed that
> > operating on multiple datasets creates a separate job for each dataset.
> I
> > want to pass all the datasets to the tool so only one galaxy job is
> actually
> > created. Is this possible, and if so, how do I go about doing this?
> >
> > Ryan
> >
> >
> > ___________________________________________________________
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>
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