# HG changeset patch
# User peterjc
# Date 1654604144 0
# Node ID 0e3cf9594bb78d58d2f955a8388bd82b3b7b1d6c
# Parent  acf4e47b734cea8cd712535a152837fcb8a29823
Update with window size fix

diff -r acf4e47b734c -r 0e3cf9594bb7 tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Tue Mar 29 14:54:02 2022 +0000
+++ b/tools/ncbi_blast_plus/README.rst	Tue Jun 07 12:15:44 2022 +0000
@@ -136,6 +136,8 @@
 ============== ===============================================================
 Version        Changes
 -------------- ---------------------------------------------------------------
+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
                  `get_species_taxids.sh` script
                  (https://www.ncbi.nlm.nih.gov/books/NBK546209/).
diff -r acf4e47b734c -r 0e3cf9594bb7 tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Mar 29 14:54:02 2022 +0000
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Tue Jun 07 12:15:44 2022 +0000
@@ -3,6 +3,9 @@
     <macros>
         <import>ncbi_macros.xml</import>
     </macros>
+    <requirements>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
     <version_command>python $__tool_directory__/blastxml_to_tabular.py --version</version_command>
     <command detect_errors="aggressive">
 python $__tool_directory__/blastxml_to_tabular.py -o '$tabular_file'
diff -r acf4e47b734c -r 0e3cf9594bb7 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Mar 29 14:54:02 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Jun 07 12:15:44 2022 +0000
@@ -30,7 +30,7 @@
 @ADV_QCOV_HSP_PERC@
 ## only use window size if dc-megablast mode is used
 #if ($blast_type == "dc-megablast"):
--window_size @ADV_WINDOW_SIZE@
+   @ADV_WINDOW_SIZE@
 #end if
 @ADV_GAPOPEN@
 @ADV_GAPEXTEND@
diff -r acf4e47b734c -r 0e3cf9594bb7 tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Mar 29 14:54:02 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Jun 07 12:15:44 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.10.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">16.10</token>
     <xml name="parallelism">
         <!-- If job splitting is enabled, break up the query file into parts -->
@@ -10,6 +10,7 @@
     <xml name="preamble">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">blast</requirement>
+            <yield />
         </requirements>
         <version_command>@BINARY@ -version</version_command>
     </xml>
diff -r acf4e47b734c -r 0e3cf9594bb7 tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Mar 29 14:54:02 2022 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Jun 07 12:15:44 2022 +0000
@@ -4,7 +4,9 @@
         <token name="@BINARY@">makeblastdb</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="preamble" />
+    <expand macro="preamble">
+        <requirement type="package" version="3.9">python</requirement>
+    </expand>
     <command detect_errors="aggressive" strict="true"><![CDATA[
 python $__tool_directory__/check_no_duplicates.py
 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)