# HG changeset patch
# User iuc
# Date 1708886000 0
# Node ID 71863d3bf72114935dcb7633a1d151d2d8d1a85b
# Parent  9319e9ed248bdbda3d54465e6532861acf356afd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee

diff -r 9319e9ed248b -r 71863d3bf721 hmmalign.xml
--- a/hmmalign.xml	Mon Nov 06 20:25:36 2023 +0000
+++ b/hmmalign.xml	Sun Feb 25 18:33:20 2024 +0000
@@ -1,13 +1,12 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmalign" name="hmmalign" version="@TOOL_VERSION@">
+<tool id="hmmer_hmmalign" name="hmmalign" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>align sequences to a profile HMM</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
 hmmalign
 
 $trim
diff -r 9319e9ed248b -r 71863d3bf721 macros.xml
--- a/macros.xml	Mon Nov 06 20:25:36 2023 +0000
+++ b/macros.xml	Sun Feb 25 18:33:20 2024 +0000
@@ -11,18 +11,8 @@
           <xref type="bio.tools">hmmer3</xref>
       </xrefs>
   </xml>
-  <token name="@TOOL_VERSION@">3.3.2</token>
-  <xml name="stdio">
-    <stdio>
-      <!-- Anything other than zero is an error -->
-      <exit_code range="1:"/>
-      <exit_code range=":-1"/>
-      <!-- In case the return code has not been set propery check stderr too -->
-      <regex match="Error:"/>
-      <regex match="Exception:"/>
-    </stdio>
-  </xml>
-
+  <token name="@TOOL_VERSION@">3.4</token>
+  <token name="@PROFILE@">22.05</token>
   <!-- command line for thresholds_* -->
   <token name="@THRESHOLDS@">
 #if $repopt.repopt_sel == "evalue"
@@ -363,17 +353,13 @@
         <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
         <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
       </param>
-      <when value="--wpb">
-      </when>
-      <when value="--wgsc">
-      </when>
+      <when value="--wpb"/>
+      <when value="--wgsc"/>
       <when value="--wblosum">
         <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
       </when>
-      <when value="--wnone">
-      </when>
-      <when value="--wgiven">
-      </when>
+      <when value="--wnone"/>
+      <when value="--wgiven"/>
     </conditional>
   </xml>
   <token name="@AEEWS@">