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<designation>.+).(?P<ext>.+)" directory="subdir2" visible="true" /> <discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" /> <discover_datasets pattern="split_bam_.(?P<designation>([A-Z-])\w+).bam" ext="txt" visible="true" /> <discover_datasets pattern="(?P<designation>.+).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,
galaxy-dev@lists.galaxyproject.org