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:
<tool id="sr_discover1" name="Discover">
  <command>
    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;
  </command>
  <inputs>
    <param name="num_param" type="integer" value="7" />
    <param name="input" type="data" />
  </inputs>
  <outputs>
    <data format="txt" name="report">
      <discover_datasets pattern="__designation_and_ext__" directory="subdir1" visible="true" />
      <discover_datasets pattern="CUSTOM_(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="subdir2" visible="true" />
      <discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" />
      <discover_datasets pattern="split_bam_\.(?P&lt;designation&gt;([A-Z-])\w+)\.bam" ext="txt" visible="true" />
      <discover_datasets pattern="(?P&lt;designation&gt;.+)\.report\.tsv" ext="tabular" visible="true" />
    </data>
  </outputs>
</tool>


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,

--
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Sabrina

Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique

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

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