Dear Marius and all,

thanks a lot for your answer, it is indeed very interesting.

I'm following this one
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
to create an output list, starting from an input list.


The command section of my script_wrapper.xml looks like this:

  <command interpreter="python">
    <![CDATA[
      #for $key in $input_1.keys()#

        script_wrapper.py

        ## Input list BAM file
        -i $input_1[$key]

        ## Reference file
        -f "${reference}"

        ## Output file
        -1 "$output[$key]"

        ## Set number of threads
        -t "\${GALAXY_SLOTS:-4}";

      #end for#
    ]]>
  </command>


Once I've run the tool in galaxy the job command line looks like:

python /home/galaxy/galaxy/tools/script-collection/script_wrapper.py -i
/home/galaxy/galaxy/database/files/000/dataset_269.dat -f
"/home/galaxy/galaxy/database/files/000/dataset_256.dat" -1
"/home/galaxy/galaxy/database/files/000/dataset_312.dat" -t
"${GALAXY_SLOTS:-4}"; script_wrapper.py -i
/home/galaxy/galaxy/database/files/000/dataset_254.dat -f
"/home/galaxy/galaxy/database/files/000/dataset_256.dat" -1
"/home/galaxy/galaxy/database/files/000/dataset_313.dat" -t
"${GALAXY_SLOTS:-4}";

And the output looks fine only for the first command in the job comman
line, becasue "python" is called only at the first iteration of the for
cycle.

Is there a way to prevent this behaviour or some "best practices" ?

Thanks a lot,
Marco.

2016-06-07 14:05 GMT+02:00 Marius van den Beek <m.vandenb...@gmail.com>:

> Hi Marco,
>
> you've got an interesting use-case there.
> You may want to use either a dataset list (if you only supply rna_n.bam),
> or a paired dataset list (rna_n.bam and dna_n.bam).
> I would probably implement a conditional, where the user selects either a
> dataset list or a paired dataset list.
> The output would then be another collection of output files.
> Have a look at the test tool folder, and see if any of the tools named
> collection_*.xml fits what you would like to do
> https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
> These two may be a good basis for what you want to achieve:
>
> https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
> [this one creates an output collection]
>
> https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
> [this one has a conditional to either select a list or a paired list as
> input]
>
> Let us know if you need more help!
>
> Cheers,
> Marius
>
> On 7 June 2016 at 09:50, Marco Tangaro <ma.tang...@gmail.com> wrote:
>
>> Dear experts,
>> my name is Marco and I'm working to port our python tool to the Galaxy
>> framework.
>> The main script needs a rna.bam file as input, a reference fasta file,
>> both mandatory. Finally, you can add a dna.bam file, but this is optional.
>> Therefore an example command is:
>>
>> script.py -i rna.bam -f reference.fa -j dna.bam
>>
>> The outout is a tabular.
>> Again the -j dna.bam option is completely optional.
>> So quite soon it turned out that I had to use a python wrapper to parse
>> our script. Now the wrapper works fine.
>>
>>
>> The next step is to run the tool over multiple input file and we would
>> like to avoid to use a workflow.
>>
>> The idea is that to each input file corresponds an output file. The
>> reference is still the same.
>> For instance, we have:
>>
>> rna_1.bam + dna_1.bam -> output_1.txt
>> rna_2.bam + dna_2.bam -> output_2.txt
>> rna_3.bam + dna_3.bam -> output_3.txt
>> ...
>> and so on.
>>
>>
>> But I don't know the best strategy to give to my wrapper multiple input
>> files.
>> Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that
>> they correspond to the right rna_xyz.bam file.
>>
>> I would like to have as output a page which is showing as results the
>> link to the single output files as suggested here.
>> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
>> planning to integrate a javascript interface.
>>
>> I've browsed a lot, but on multiple input file the posts are old.
>> I'm using the last galaxy release (16_04).
>>
>> I'm quite new to the galaxy world...
>> Thanks a lot for your suggestions,
>> Marco
>>
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