# HG changeset patch
# User iuc
# Date 1610639034 0
# Node ID d92dd2f040cdb44aa17c725ef2a483cbb9f112b8
# Parent  be7097d6e3ffd35ed5b7c9cd6dc7b53e6e6cf83d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit db615ae8a189ad988ec08090051a128355a4be70"

diff -r be7097d6e3ff -r d92dd2f040cd hmmscan.xml
--- a/hmmscan.xml	Tue Jun 16 05:34:25 2020 -0400
+++ b/hmmscan.xml	Thu Jan 14 15:43:54 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@">
+<tool id="hmmer_hmmscan" name="hmmscan" version="@TOOL_VERSION@+galaxy1">
   <description>search protein sequence(s) against a protein profile database</description>
   <macros>
     <import>macros.xml</import>
@@ -7,6 +7,7 @@
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
+@ADDTHREADS@
 @INPUTHMMCHOICE@
 hmmscan
 
diff -r be7097d6e3ff -r d92dd2f040cd macros.xml
--- a/macros.xml	Tue Jun 16 05:34:25 2020 -0400
+++ b/macros.xml	Thu Jan 14 15:43:54 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