# HG changeset patch # User peterjc # Date 1648565508 0 # Node ID 4ffaf58c9791f321919cbebbfde5bc7b11f5d27a # Parent 673539b0f1550809e764d196f4d786bc7a417cb1 "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 7eaaba230e124ac12114584e7ee5ff3b8aeda859" diff -r 673539b0f155 -r 4ffaf58c9791 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Mar 17 19:17:18 2021 +0000 +++ b/tools/ncbi_blast_plus/README.rst Tue Mar 29 14:51:48 2022 +0000 @@ -136,7 +136,15 @@ ============== =============================================================== Version Changes -------------- --------------------------------------------------------------- -2.10.1+galaxy1 - Make locally installed database selector non-optional. +2.10.1+galaxy1 - Add tool `NCBI get species taxids` that wraps NCBI's + `get_species_taxids.sh` script + (https://www.ncbi.nlm.nih.gov/books/NBK546209/). + It allows to determine all species taxids below a certain + Taxon. + - Add the possibility to restrict BLAST searches taxonomically + by species taxids given in a file. + - Properly quote cached databases + - Make locally installed database selector non-optional. 2.10.1+galaxy0 - Updated for NCBI BLAST+ 2.10.1 release. - Supports locally installed v4 or v5 format BLAST databases (listed in the ``blastdb*.loc`` files). diff -r 673539b0f155 -r 4ffaf58c9791 tools/ncbi_blast_plus/get_species_taxids.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/get_species_taxids.xml Tue Mar 29 14:51:48 2022 +0000 @@ -0,0 +1,106 @@ + + + + ncbi_macros.xml + + + &2 echo "could not find taxid for $name" && exit 1; + else + echo " $name -> \$taxid"; + fi && + get_species_taxids.sh -t \$taxid >> species_ids.txt && + #end for +#else + #for taxid in $type_cond.ids.split(',') + get_species_taxids.sh -t $taxid >> species_ids.txt && + #end for +#end if +sort -n -u species_ids.txt > '$output' + ]]> + + + + + + + + + [a-zA-Z ,]+$ + + + + + [0-9,]+$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Returns a list of species taxids for a taxon. It relies on the get_species_taxids.sh script of the BLAST+ package https://www.ncbi.nlm.nih.gov/books/NBK546209/ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 673539b0f155 -r 4ffaf58c9791 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Mar 17 19:17:18 2021 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Tue Mar 29 14:51:48 2022 +0000 @@ -558,6 +558,8 @@ + + @@ -572,8 +574,17 @@ + + + + + + +