# HG changeset patch # User q2d2 # Date 1714080099 0 # Node ID 31dca1855f5fdf500b4639935bc6db08595413b5 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e diff -r 000000000000 -r 31dca1855f5f qiime2__rescript__get_ncbi_data_protein.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__rescript__get_ncbi_data_protein.xml Thu Apr 25 21:21:39 2024 +0000 @@ -0,0 +1,149 @@ + + + + + Download, parse, and import NCBI protein sequences and taxonomies + + quay.io/qiime2/amplicon:2024.2 + + q2galaxy version rescript + q2galaxy run rescript get_ncbi_data_protein '$inputs' + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value != '__q2galaxy__::literal::None' + + + + + + + + + + + + +
+
+ + + + + + +QIIME 2: rescript get-ncbi-data-protein +======================================= +Download, parse, and import NCBI protein sequences and taxonomies + + +Outputs: +-------- +:sequences.qza: Sequences from the NCBI Protein database +:taxonomy.qza: Taxonomies from the NCBI Taxonomy database + +| + +Description: +------------ +Download and import sequences from the NCBI Protein database and download, parse, and import the corresponding taxonomies from the NCBI Taxonomy database. + +Please be aware of the NCBI Disclaimer and Copyright notice (https://www.ncbi.nlm.nih.gov/home/about/policies/), particularly "run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests". As a rough guide, if you are downloading more than 125,000 sequences, only run this method at those times. + +The NCBI servers can be capricious but reward polite persistence. If the download fails and gives you a message that contains the words "Last exception was ReadTimeout", you should probably try again, maybe with more connections. If it fails for any other reason, please create an issue at https://github.com/bokulich-lab/RESCRIPt. + + +| + + + + 10.1093/nar/gkx1095 + @article{cite2, + author = {Benson, Dennis A and Cavanaugh, Mark and Clark, Karen and Karsch-Mizrachi, Ilene and Lipman, David J and Ostell, James and Sayers, Eric W}, + journal = {Nucleic acids research}, + number = {D1}, + pages = {D36--D42}, + publisher = {Oxford University Press}, + title = {GenBank}, + volume = {41}, + year = {2012} +} + + 10.1371/journal.pcbi.1009581 + 10.1038/s41587-019-0209-9 + +
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