# HG changeset patch # User q2d2 # Date 1714080137 0 # Node ID 16ca8c90aba4ecc4c97d8b90011f7a76638ebae1 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e diff -r 000000000000 -r 16ca8c90aba4 qiime2__rescript__parse_silva_taxonomy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__parse_silva_taxonomy.xml Thu Apr 25 21:22:17 2024 +0000 @@ -0,0 +1,121 @@ + + + + + Generates a SILVA fixed-rank taxonomy. + + quay.io/qiime2/amplicon:2024.2 + + q2galaxy version rescript + q2galaxy run rescript parse_silva_taxonomy '$inputs' + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]'] + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[SILVATaxidMap]'] + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[SILVATaxonomy]'] + +
+ + + + + + + + + + + + + + + + + + + + + + + + value != '__q2galaxy__::literal::None' + + + +
+
+ + + + + +QIIME 2: rescript parse-silva-taxonomy +====================================== +Generates a SILVA fixed-rank taxonomy. + + +Outputs: +-------- +:taxonomy.qza: The resulting fixed-rank formatted SILVA taxonomy. + +| + +Description: +------------ +Parses several files from the SILVA reference database to produce a GreenGenes-like fixed rank taxonomy that is 6 or 7 ranks deep, depending on whether or not `include_species_labels` is applied. The generated ranks (and the rank handles used to label these ranks in the resulting taxonomy) are: domain (d__), phylum (p__), class (c__), order (o__), family (f__), genus (g__), and species (s__). NOTE: THIS ACTION ACQUIRES DATA FROM THE SILVA DATABASE. SEE https://www.arb-silva.de/silva-license-information/ FOR MORE INFORMATION and be aware that earlier versions may be released under a different license. + + +| + + + + @article{cite1, + author = {Pruesse, Elmar and Quast, Christian and Knittel, Katrin and Fuchs, Bernhard M and Ludwig, Wolfgang and Peplies, Jorg and Glockner, Frank Oliver}, + journal = {Nucleic Acids Res}, + number = {21}, + pages = {7188-7196}, + title = {SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB}, + volume = {35}, + year = {2007} +} + + @article{cite2, + author = {Quast, Christian and Pruesse, Elmar and Yilmaz, Pelin and Gerken, Jan and Schweer, Timmy and Yarza, Pablo and Peplies, Jorg and Glockner, Frank Oliver}, + journal = {Nucleic Acids Res}, + number = {Database issue}, + pages = {D590-6}, + publisher = {Oxford University Press}, + title = {The SILVA ribosomal RNA gene database project: improved data processing and web-based tools}, + volume = {41}, + year = {2013} +} + + 10.1371/journal.pcbi.1009581 + 10.1038/s41587-019-0209-9 + +
diff -r 000000000000 -r 16ca8c90aba4 test-data/.gitkeep