# HG changeset patch
# User iuc
# Date 1708885979 0
# Node ID 9fdeca68a6b5272ee303f1b1c8f5ac02bbcd6e12
# Parent  5cbef50c0c635367b0bace9bd4536403af9d7b64
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee

diff -r 5cbef50c0c63 -r 9fdeca68a6b5 jackhmmer.xml
--- a/jackhmmer.xml	Mon Nov 06 20:26:42 2023 +0000
+++ b/jackhmmer.xml	Sun Feb 25 18:32:59 2024 +0000
@@ -1,13 +1,12 @@
 <?xml version="1.0"?>
-<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0">
+<tool id="hmmer_jackhmmer" name="jackhmmer" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="bio_tools"/>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[
+  <command detect_errors="aggressive"><![CDATA[
 @ADDTHREADS@
 jackhmmer
 -N $N
@@ -31,7 +30,7 @@
   <inputs>
     <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
-    <param name="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
+    <param argument="-N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
     <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
     <expand macro="oformat_with_opts_dom"/>
     <expand macro="hssi"/>
@@ -56,10 +55,10 @@
       <output name="output" file="jackhmmer.out" lines_diff="180">
           <expand macro="assert_out" tool="jackhmmer"/>
       </output>
-      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10">
+      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="12">
           <expand macro="assert_tblout" tool="jackhmmer"/>
       </output>
-      <output name="tblout" file="jackhmmer.tblout" lines_diff="10">
+      <output name="tblout" file="jackhmmer.tblout" lines_diff="12">
           <expand macro="assert_tblout" tool="jackhmmer"/>
       </output>
     </test>
diff -r 5cbef50c0c63 -r 9fdeca68a6b5 macros.xml
--- a/macros.xml	Mon Nov 06 20:26:42 2023 +0000
+++ b/macros.xml	Sun Feb 25 18:32:59 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@">