--- 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>