--- a/cmsearch.xml	Thu Sep 23 19:38:58 2021 +0000
+++ b/cmsearch.xml	Mon Nov 11 10:27:19 2024 +0000
@@ -4,9 +4,9 @@
         <import>macros.xml</import>
     </macros>
     <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -39,6 +39,8 @@
             #if $A:
                 $A '$multiple_alignment_output'
             #end if
+            $noali
+            $verbose
             #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
                 --incE $inclusion_thresholds_opts.incE
             #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
@@ -79,25 +81,7 @@
     <inputs>
 
         <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
-
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models">
-              <option value="db" selected="True">Locally installed covariance models</option>
-              <option value="histdb">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
+        <expand macro="DB" />
 
         <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
             label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
@@ -241,7 +225,7 @@
 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="cm_opts">
                 <param name="cm_opts_selector" value="histdb"/>
                 <param name="cmfile" value="cmsearch_input1.cm"/>
@@ -249,6 +233,14 @@
             <param name="seqdb" value="cmsearch_input2.fa"/>
             <output name="outfile" file="cmsearch_result.tabular"/>
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmsearch_input1.cm"/>
+            </conditional>
+            <param name="seqdb" value="cmsearch_input2.fa"/>
+            <output name="outfile" file="cmsearch_result.tabular"/>
+        </test>
     </tests>
 
     <help>