--- a/hmmsearch.xml	Wed Jul 21 14:14:52 2021 +0000
+++ b/hmmsearch.xml	Mon Nov 06 20:22:49 2023 +0000
@@ -1,9 +1,10 @@
 <?xml version="1.0"?>
-<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy0">
+<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1">
   <description>search profile(s) against a sequence database</description>
-  <macros>
+    <macros>
     <import>macros.xml</import>
   </macros>
+  <expand macro="bio_tools"/>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
   <command><![CDATA[
@@ -12,7 +13,7 @@
 
 @OFORMAT_WITH_OPTS@
 @THRESHOLDS@
-@CUT@
+@THRESHOLDS_DOM@
 @ACCEL_HEUR@
 @ADV_OPTS@
 @CPU@
@@ -27,8 +28,7 @@
     <!-- todo use Galaxy features like data libraries/data tables/??? -->
     <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/>
     <expand macro="oformat_with_opts_dom_pfam"/>
-    <expand macro="thresholds_xml"/>
-    <expand macro="cut"/>
+    <expand macro="thresholds_cut_dom_xml"/>
     <expand macro="accel_heur_xml"/>
     <expand macro="adv_opts"/>
     <expand macro="seed"/>
@@ -65,6 +65,41 @@
           <expand macro="assert_out" tool="hmmsearch"/>
       </output>
     </test>
+    <test expect_num_outputs="1"><!-- test with additional evalue threshold options  set -->
+      <param name="hmmfile" value="fn3.hmm"/>
+      <param name="seqdb" value="uniprot_matches.fasta"/>
+      <conditional name="repopt">
+        <param name="incE" value="0.00001"/>
+        <param name="incdomE" value="0.0001"/>
+      </conditional>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output">
+          <expand macro="assert_out" tool="hmmsearch"/>
+      </output>
+      <assert_command>
+        <has_text text="-E 10"/>
+        <has_text text="--incE 1e-05"/>
+        <has_text text="--domE 10"/>
+        <has_text text="--incdomE 0.0001"/>
+      </assert_command>
+    </test>
+    <test expect_num_outputs="1"><!-- test with cut_ga set -->
+      <param name="hmmfile" value="fn3.hmm"/>
+      <param name="seqdb" value="uniprot_matches.fasta"/>
+      <conditional name="repopt">
+        <param name="repopt_sel" value="--cut_ga"/>
+      </conditional>
+      <expand macro="oformat_test" />
+      <param name="oformat" value=""/>
+      <expand macro="seed_test" />
+      <output name="output" file="cut_ga_test.out" lines_diff="10">
+          <expand macro="assert_out" tool="hmmsearch"/>
+      </output>
+    </test>
+
+
   </tests>
   <help><![CDATA[
 @HELP_PRE@