--- a/kaks_analysis.xml	Wed Mar 01 14:04:23 2017 -0500
+++ b/kaks_analysis.xml	Wed Mar 01 14:17:43 2017 -0500
@@ -20,6 +20,10 @@
                 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
                 #set fit_components_cond = $options_type.fit_components_cond
                 #set fit_components = $fit_components_cond.fit_components
+                #set recalibrate_cond = $options_type.recalibrate_cond
+                #set recalibrate = $recalibrate_cond.recalibrate
+                #set set_min_coverage_cond = $options_type.set_min_coverage_cond
+                #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
             #else:
                 #set codeml_ctl_file_select = 'no'
                 #set fit_components = 'no'
@@ -35,8 +39,12 @@
                 --proteins_species_2 '$comparison_cond.proteins_species_2'
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
-                --min_coverage $options_type.min_coverage
-                --recalibration_rate $options_type.recalibration_rate
+                #if str($set_min_coverage) == 'yes':
+                    --min_coverage $set_min_coverage_cond.min_coverage
+                #end if
+                #if str($recalibrate) == 'yes':
+                    --recalibration_rate $recalibrate_cond.recalibration_rate
+                #end if
                 #if str($codeml_ctl_file_select) == 'yes':
                     --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
                     # No else block needed here because the default codeml_ctl config
@@ -92,8 +100,26 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" />
-                <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Predetermined evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
+                <conditional name="set_min_coverage_cond">
+                    <param name="set_min_coverage" type="select" label="Specify minimum sequence pairwise coverage length between homologous pairs?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" />
+                    </when>
+                </conditional>
+                <conditional name="recalibrate_cond">
+                    <param name="recalibrate" type="select" label="Specify evolutionary rate for recalibrating synonymous subsitutions (ks) of species?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
+                    </when>
+                </conditional>
                 <conditional name="codeml_ctl_file_cond">
                     <param name="codeml_ctl_file_select" type="select" label="Select PAML codeml control file?" help="Used for ML analysis of protein-coding DNA sequences using codon substitution models, select No to use the default control file">
                         <option value="no" selected="true">No</option>