Re: [galaxy-dev] discover_datasets

[John Chilton]

Just reran this tool and it did indeed give me multiple outputs. I
think the problem is the files appear but the history needs to be
refreshed to see them. There is a little refresh icon at the top of
the history panel that is needed. This is a known limitation of the
multiple file output support currently. If the tool outputs pretty
regular homogeneous files, it is probably worth investigating
outputting a collection of files instead of individual files. This way
these files can be used in workflows for instance and operated on as a
group.

-John

On Thu, Sep 3, 2015 at 4:02 PM, srodriguez  wrote:
> Hi,
>
> I am developing a tool with unknown output dataset number;
> so, I am trying to use discover_datasets tag.
>
> I have tested the following code as explained in the galaxy project
> documentation:
>
> https://bitbucket.org/galaxy/galaxy-central/raw/d1f51ff3c495b52b621ea6562ef54ba62a9205ed/test/functional/tools/multi_output_configured.xml
>
> But, when I look at he result, I only obtain a single dataset corresponding
> to the "report".
>
> When I check in the job_working_directory, no "subdir(1,2 and 3)" folders
> have been created and no datasets displayed on galaxy as results.
>
> Can someone help me understand how discover_datasets work and why all the
> supposed multi datasets are not displayed in the galaxy interface?
>
> Thanks in advance.
>
> Best regards,
>
> Sabrina
> Sabrina LEGOUEIX RODRIGUEZ
> Responsable Plateau Bioinformatique
> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane •
> 31520 Ramonville Saint-Agne
> Tél. : +33 (0) 5 61 28 57 92
> sabrina.rodrig...@toulouse.inra.fr
> www.toulouse-white-biotechnology.com
>
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[galaxy-dev] discover_datasets

[srodriguez]

Hi,

I am developing a tool with unknown output dataset number;
so, I am trying to use discover_datasets tag.

I have tested the following code as explained in the galaxy project
documentation:

https://bitbucket.org/galaxy/galaxy-central/raw/d1f51ff3c495b52b621ea6562ef54ba62a9205ed/test/functional/tools/multi_output_configured.xml

But, when I look at he result, I only obtain a single dataset corresponding
to the "report".
 
When I check in the job_working_directory, no "subdir(1,2 and 3)" folders
have been created and no datasets displayed on galaxy as results.

Can someone help me understand how discover_datasets work and why all the
supposed multi datasets are not displayed in the galaxy interface?

Thanks in advance.

Best regards,

Sabrina


Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue  
Ariane • 31520 Ramonville Saint-Agne

Tél. : +33 (0) 5 61 28 57 92
sabrina.rodrig...@toulouse.inra.fr
www.toulouse-white-biotechnology.com
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[galaxy-dev] discover_datasets

[Sabrina Legoueix Rodriguez]

Hi,

I am developing a tool with unknown output dataset number;
so, I am trying to use discover_datasets tag.

I have tested the following code as explained in the galaxy project 
documentation:


  
echo "Hello" > $report;
mkdir subdir1;
echo "This" > subdir1/this.txt;
echo "That" > subdir1/that.txt;
mkdir subdir2;
echo "1" > subdir2/CUSTOM_1.txt;
echo "2" > subdir2/CUSTOM_2.tabular;
echo "3" > subdir2/CUSTOM_3.txt;
mkdir subdir3;
echo "Foo" > subdir3/Foo;
echo "mapped reads" > split_bam_.MAPPED.bam;
echo "unmapped reads" > split_bam_.UNMAPPED.bam;
echo "1" > sample1.report.tsv;
echo "2" > sample2.report.tsv;
echo "3" > sample3.report.tsv;
  
  


  
  

  directory="subdir1" visible="true" />
  pattern="CUSTOM_(?P.+)\.(?P.+)" 
directory="subdir2" visible="true" />
  ext="input" visible="true" />
  pattern="split_bam_\.(?P([A-Z-])\w+)\.bam" ext="txt" 
visible="true" />
  pattern="(?P.+)\.report\.tsv" ext="tabular" 
visible="true" />


  



But, when I look at he result, I only obtain a single dataset 
corresponding to the "report" and the following information:


Job Command-Line: 	echo "Hello" > 
/path/database/job_working_directory/002/2227/galaxy_dataset_5307.dat; 
mkdir subdir1; echo "This" > subdir1/this.txt; echo "That" > 
subdir1/that.txt; mkdir subdir2; echo "1" > subdir2/CUSTOM_1.txt; echo 
"2" > subdir2/CUSTOM_2.tabular; echo "3" > subdir2/CUSTOM_3.txt; mkdir 
subdir3; echo "Foo" > subdir3/Foo; echo "mapped reads" > 
split_bam_.MAPPED.bam; echo "unmapped reads" > split_bam_.UNMAPPED.bam; 
echo "1" > sample1.report.tsv; echo "2" > sample2.report.tsv; echo "3" > 
sample3.report.tsv;



and when I check in the job_working_directory, no "subdir(1,2 and 3)" 
folders have been created and no datasets displayed on galaxy as results.


Can someone help me understand how discover_datasets work and why all 
the supposed multi datasets are not displayed in the galaxy interface?


Thanks in advance.

Best regards,

--
Signature e-mail TWB
Sabrina



**Sabrina LEGOUEIX RODRIGUEZ**
Responsable Plateau Bioinformatique

Tél. : +33 (0) 5 61 28 57 92
sabrina.legou...@toulouse.inra.fr 
www.toulouse-white-biotechnology.com 



LinkedIn  Twitter 



TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue 
Ariane • 31520 Ramonville Saint-Agne



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