# HG changeset patch
# User diodupima
# Date 1626367886 0
# Node ID fb0ce7937a85450f880a290a0f9c2ff804f49e1b
"planemo upload commit 50c5525c05d834545335e0273352b1aff79e5702"
diff -r 000000000000 -r fb0ce7937a85 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Jul 15 16:51:26 2021 +0000
@@ -0,0 +1,11 @@
+COAST's suite of Galaxy Tools
+________________________________________
+
+COAST is tool designed to identify close proteomes for a user provided query, particulary for virus, using conventional alignment tools.
+The close proteomes are provided at NCBI's taxonomy node level.
+
+This suite includes:
+
+- Tools for COAST Search (BLAST and diamond)
+- Tools for COAST Report
+- PhageCOAST tool for the Phage Toolkit
\ No newline at end of file
diff -r 000000000000 -r fb0ce7937a85 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jul 15 16:51:26 2021 +0000
@@ -0,0 +1,402 @@
+
+ 0.1.2
+
+ coast
+
+
+ @misc{noauthor_coast_nodate,
+ title = {{COAST} - {Compartive} {Ominc} {Alignment} {Search} {Tool}},
+ url = {https://gitlab.com/coast_tool/COAST},
+ abstract = {Alignment search tool that identifies similar proteomes},
+ language = {en},
+ urldate = {2021-06-22},
+ }
+
+
+
+ @article{shen_taxonkit_2021,
+ abstract = {The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility could facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.},
+ author = {Shen, Wei and Ren, Hong},
+ doi = {10.1016/j.jgg.2021.03.006},
+ file = {ScienceDirect Snapshot:/home/dm/Zotero/storage/Q3KYT6QS/S1673852721000837.html:text/html},
+ issn = {1673-8527},
+ journal = {Journal of Genetics and Genomics},
+ keywords = {Lineage; NCBI Taxonomy; TaxId; TaxId changelog; TaxonKit},
+ language = {en},
+ month = apr,
+ shorttitle = {{TaxonKit}},
+ title = {{TaxonKit}: {A} practical and efficient {NCBI} taxonomy toolkit},
+ url = {https://www.sciencedirect.com/science/article/pii/S1673852721000837},
+ urldate = {2021-06-21},
+ year = {2021}
+ }
+
+
+
+ @article{buchfink_sensitive_2021,
+ title = {Sensitive protein alignments at tree-of-life scale using {DIAMOND}},
+ volume = {18},
+ issn = {1548-7091, 1548-7105},
+ url = {http://www.nature.com/articles/s41592-021-01101-x},
+ doi = {10.1038/s41592-021-01101-x},
+ abstract = {Abstract
+ We are at the beginning of a genomic revolution in which all known species are planned to be sequenced. Accessing such data for comparative analyses is crucial in this new age of data-driven biology. Here, we introduce an improved version of DIAMOND that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard BLASTP.},
+ language = {en},
+ number = {4},
+ urldate = {2021-04-14},
+ journal = {Nature Methods},
+ author = {Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg},
+ month = apr,
+ year = {2021},
+ pages = {366--368},
+ file = {Full Text:/home/dm/Zotero/storage/6HKCWF6S/Buchfink et al. - 2021 - Sensitive protein alignments at tree-of-life scale.pdf:application/pdf},
+ }
+
+
+
+ @article{camacho_blast_2009,
+ title = {{BLAST}+: architecture and applications},
+ volume = {10},
+ issn = {1471-2105},
+ shorttitle = {{BLAST}+},
+ url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803857/},
+ doi = {10.1186/1471-2105-10-421},
+ abstract = {Background
+ Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications.
+
+ Results
+ We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site.
+
+ Conclusion
+ The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.},
+ urldate = {2021-04-14},
+ journal = {BMC Bioinformatics},
+ author = {Camacho, Christiam and Coulouris, George and Avagyan, Vahram and Ma, Ning and Papadopoulos, Jason and Bealer, Kevin and Madden, Thomas L},
+ month = dec,
+ year = {2009},
+ pmid = {20003500},
+ pmcid = {PMC2803857},
+ pages = {421},
+ file = {PubMed Central Full Text PDF:/home/dm/Zotero/storage/5FCYSMW5/Camacho et al. - 2009 - BLAST+ architecture and applications.pdf:application/pdf},
+ }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ "r" in outfmt
+
+
+ "b" in outfmt
+
+
+ "a" in outfmt
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r fb0ce7937a85 phage_coast_search.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phage_coast_search.xml Thu Jul 15 16:51:26 2021 +0000
@@ -0,0 +1,62 @@
+
+ Run a new job, and identify the closest proteomes
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@TIME_WARNING@
+
+PhageCOAST
+==========
+
+@GENERAL_DESC@
+
+PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.
+
+@AAI_DESC@
+@TAX_FILTER_WARNING@
+@OUT_DESC@
+
+
+
+
+
+
+