changeset 8:fb1305d0d1c6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 721504306833ba97c91f285e5bfd86efc04875ee

--- a/macros.xml	Mon Nov 06 20:24:33 2023 +0000
+++ b/macros.xml	Sun Feb 25 18:32:37 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@">

--- a/nhmmscan.xml	Mon Nov 06 20:24:33 2023 +0000
+++ b/nhmmscan.xml	Sun Feb 25 18:32:37 2024 +0000
@@ -1,13 +1,12 @@
 <?xml version="1.0"?>
-<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy1">
+<tool id="hmmer_nhmmscan" name="nhmmscan" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>search DNA sequence(s) against a DNA profile database</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@
 @INPUTHMMCHOICE@
 nhmmscan
@@ -54,7 +53,7 @@
       <param name="seqfile" value="dna_target.fa"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="MADE1.nhmmscan_out" lines_diff="12">
+      <output name="output" file="MADE1.nhmmscan_out" lines_diff="18">
           <expand macro="assert_out" tool="nhmmscan"/>
       </output>
       <output name="tblout" file="MADE1.nhmmscan_out.tblout" lines_diff="10">