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. 2020 Feb;17(2):123-124.
doi: 10.1038/s41592-019-0727-x.

Galaxy External Display Applications: closing a dataflow interoperability loop

Daniel Blankenberg  1 , John Chilton  2 , Nate Coraor  2
Affiliations

Galaxy External Display Applications: closing a dataflow interoperability loop

Daniel Blankenberg et al. Nat Methods. 2020 Feb.
No abstract available

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Figures

Figure 1:
Figure 1:. Anatomy of a basic Galaxy External Display Application.
(A) The user-experience of accessing a GEDA is shown through the automatic availability of a link (A.I) “display at bam.iobio bam.iobio.io”. that will send the user to the (A.II) external resource along with a URL to the Galaxy dataset content. The external resource can then load the data using its standard process. In this basic example, paired-end reads, accession ERR091571, were mapped to human genome build hg38 using BWA-MEM and examined within bam.iobio. (B) A GEDA definition contains several elements that describe how to interoperate across external resources, with (B.I) defining the entire application, shown to the user here as “display at bam.iobio”. (B.II) GEDAs have one or more “link” elements which contain a user actionable item. (B.III) A URL template is designed that can utilize placeholders (e.g. bam_file) that will be populated by the GEDA framework and used as the target resource URL. Here, query string encoding is applied using a qp (quote_plus) method to the URL that will contain the BAM file data. (B.IV) A parameter of type “data” is created from the Galaxy dataset that can be referenced within the URL or in subsequent parameters (figure S2). The value specified within the “url” attribute (here: “galaxy.bam”) will be used as the terminal “filename” being passed to the external resource. (B.V) BAM files within Galaxy have a “bam_index” metadata element that is made available to the external resource as a file named “galaxy.bam.bai” (internally: “bai_file”). (C) To instruct Galaxy to load the GEDA defined in (B) for the BAM datatype (C.I), a “display” tagset (C.II) is added that references the GEDA XML file within the datatypes_conf.xml file.
See this image and copyright information in PMC

References

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