changeset 58:cc1ab05a5588 draft default tip

planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 716fba7fd96789c993382d1bebc593ad24f99f0a

--- 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

--- 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:

--- 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"/>

--- 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 -->

--- 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

--- 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