--- a/cmbuild.xml	Thu Sep 23 19:38:58 2021 +0000
+++ b/cmbuild.xml	Mon Nov 11 10:27:19 2024 +0000
@@ -4,9 +4,9 @@
         <import>macros.xml</import>
     </macros>
     <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
     cmbuild
@@ -196,19 +196,22 @@
                         <option value="--cyk">align with the CYK algorithm</option>
                     </param>
 
-                    <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
+                    <param name="refine_output" truevalue="--refine" falsevalue="" checked="False" type="boolean"
                         label="Output the refined alignment file as it is used to build the covariance model" help=""/>
 
                 </when>
             </conditional>
 
-            <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
+            <param name="is_summery_output" truevalue="-o" falsevalue="" checked="False" type="boolean"
                 label="Output a summery file?" help=""/>
 
             <!-- calibrate options -->
             <conditional name="Calibrate">
-                <param name="selector" type="boolean" checked="true" label="Calibrate the covariance model"
-                    help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU"/>
+                <param name="selector" type="select" label="Calibrate the covariance model"
+                    help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU">
+                    <option value="true">Yes</option>
+                    <option value="false">No</option>
+                </param>
                 <when value="false"/>
                 <when value="true">
                     <param argument="-L" type="float" value="1.6" min="0.01" max="160" label="Total length of random sequences to search" help="Set random seq length to search in Mb (megabases)"/>
@@ -325,7 +328,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
             <conditional name="Calibrate">
                 <param name="selector" value="true"/>
@@ -338,7 +341,7 @@
             </output>
         </test>
         <!-- Test emax seq parameter -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
             <conditional name="Calibrate">
                 <param name="selector" value="true"/>
@@ -422,8 +425,7 @@
 
 cmbuild uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight distantly related ones. This has the effect of making models less biased by uneven phylogenetic representation. For example, two identical sequences would typically each receive half the weight that one sequence would. These options control which algorithm gets used.
 
-  - *--wgb*: Use the Henikoff position-based sequence weighting scheme [Henikoff
-and Henikoff, J. Mol. Biol. 243:574, 1994].  This is the default.
+  - *--wgb*: Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994].  This is the default.
   - *--wgsc*: Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067, 1994].
   - *--wnone*: Turn sequence weighting off; e.g. explicitly set all sequence weights to 1.0.
   - *--wgiven*: Use sequence weights as given in annotation in the input alignment file. If no weights were given, assume they are all 1.0. The default is to determine new sequence weights by the Gerstein/Sonnhammer/Chothia algorithm, ignoring any annotated weights.