# HG changeset patch
# User iuc
# Date 1610639065 0
# Node ID 24a67ef302dd578119e0229215c07740d14edd09
# Parent  2d406da5d34e6c7b22ebb68af6e794dbbfeade0c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"

diff -r 2d406da5d34e -r 24a67ef302dd macros.xml
--- a/macros.xml	Tue Jun 16 05:31:13 2020 -0400
+++ b/macros.xml	Thu Jan 14 15:44:25 2021 +0000
@@ -226,8 +226,12 @@
       <!-- -mxfile <f>  : read substitution score matrix from file <f> (with -singlemx)-->
     </conditional>
   </xml>
+  <token name="@ADDTHREADS@"><![CDATA[
+        ##compute the number of ADDITIONAL threads to be used (--cpu)
+        addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
+    ]]></token>
   <token name="@CPU@">
-      --cpu \${GALAXY_SLOTS:-2}
+      --cpu \$addthreads
   </token>
   <token name="@SEED@">
       --seed $seed
@@ -562,10 +566,9 @@
 **Advanced Documentation**
 
 A more detailed look at the internals of the various filter pipelines was
-posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
+posted on the `developer's blog <http://cryptogenomicon.org/hmmer3-is-stubborn.html>`__.
 The information posted there may be useful to those who are struggling with
 poor-scoring sequences.
-
 ]]></token>
   <token name="@ADV_OPTS_HELP@"><![CDATA[
 Advanced Options
diff -r 2d406da5d34e -r 24a67ef302dd nhmmscan.xml
--- a/nhmmscan.xml	Tue Jun 16 05:31:13 2020 -0400
+++ b/nhmmscan.xml	Thu Jan 14 15:44:25 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@">
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1">
   <description>search DNA sequence(s) against a DNA profile database</description>
   <macros>
     <import>macros.xml</import>
@@ -7,6 +7,7 @@
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
+@ADDTHREADS@
 @INPUTHMMCHOICE@
 nhmmscan