# HG changeset patch
# User peterjc
# Date 1671442599 0
# Node ID cc1ab05a5588b8e9b655b3ff07c819264b17c40c
# Parent  fbff6786b2f6f6f8fa034196f9ff4c4540456536
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 716fba7fd96789c993382d1bebc593ad24f99f0a

diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/README.rst	Mon Dec 19 09:36:39 2022 +0000
@@ -136,6 +136,8 @@
 ============== ===============================================================
 Version        Changes
 -------------- ---------------------------------------------------------------
+2.10.1+galaxy3 - Silenced ``deltablast`` warning about using ``-num_threads``
+                 with ``--subject`` (i.e. FASTA file from your history).
 2.10.1+galaxy2 - Fixed ``dc-megablast`` option in ``ncbi_blastn_wrapper.xml`` 
                  wrapper from inserting ``-window_size`` twice when executing.
 2.10.1+galaxy1 - Add tool `NCBI get species taxids` that wraps NCBI's
diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Mon Dec 19 09:36:39 2022 +0000
@@ -46,7 +46,7 @@
     25 salltitles    All subject titles, separated by '<>'
 ====== ============= ===========================================
 
-Most of these fields are given explicitly in the XML file, others some like
+Most of these fields are given explicitly in the XML file, but some like
 the percentage identity and the number of gap openings must be calculated.
 
 Be aware that the sequence in the extended tabular output or XML direct from
@@ -60,13 +60,11 @@
 However, check this with "diff -b ..." since BLAST+ sometimes includes an extra
 space character (probably a bug).
 """
-
 from __future__ import print_function
 
 import os
 import re
 import sys
-
 from optparse import OptionParser
 
 if "-v" in sys.argv or "--version" in sys.argv:
diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Mon Dec 19 09:36:39 2022 +0000
@@ -152,7 +152,7 @@
             <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
             <param name="db_opts_selector" value="file" />
             <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="database value=" />
+            <param name="database" value="" />
             <param name="evalue_cutoff" value="1e-8"/>
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="6"/>
diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Mon Dec 19 09:36:39 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.10.1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">16.10</token>
     <xml name="parallelism">
         <!-- If job splitting is enabled, break up the query file into parts -->
diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Mon Dec 19 09:36:39 2022 +0000
@@ -92,7 +92,7 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
+ftp://ftp.jcvi.org/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see
diff -r fbff6786b2f6 -r cc1ab05a5588 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Jun 07 12:12:49 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Dec 19 09:36:39 2022 +0000
@@ -90,7 +90,7 @@
 http://smart.embl-heidelberg.de/
 
 *Tigr* - PSSMs from TIGRFAM database of protein families, see
-ftp://ftp.jcvi.org/pub/data/TIGRFAMs/
+ftp://ftp.jcvi.org/data/TIGRFAMs/
 
 *Prk* - PSSms from automatically aligned stable clusters in the
 Protein Clusters database, see