--- a/kaks_analysis.xml	Thu Mar 02 10:03:03 2017 -0500
+++ b/kaks_analysis.xml	Thu Mar 02 10:23:21 2017 -0500
@@ -24,9 +24,15 @@
                 #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
+                #set set_lower_ks_limit_cond = $options_cond.set_lower_ks_limit_cond
+                #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
+                #set set_upper_ks_limit_cond = $options_cond.set_upper_ks_limit_cond
+                #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
             #else:
                 #set codeml_ctl_file_select = 'no'
                 #set fit_components = 'no'
+                #set set_lower_ks_limit = 'no'
+                #set set_upper_ks_limit = 'no'
             #end if
             KaKsAnalysis
             --config_dir '$scaffold.fields.path'
@@ -53,8 +59,12 @@
                 #if str($fit_components) == 'yes':
                     --fit_components
                     --num_of_components $fit_components_cond.num_of_components
-                    --min_ks $fit_components_cond.min_ks
-                    --max_ks $fit_components_cond.max_ks
+                #end if
+                #if str($set_lower_ks_limit) == 'yes':
+                    --min_ks $set_lower_ks_limit_cond.min_ks
+                #end if
+                #if str($set_upper_ks_limit) == 'yes':
+                    --max_ks $set_upper_ks_limit_cond.max_ks
                 #end if
             #end if
             >/dev/null
@@ -138,8 +148,26 @@
                     <when value="no" />
                     <when value="yes">
                         <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" />
-                        <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome" />
-                        <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" help="Excludes likey ancient paralogous pairs" />
+                    </when>
+                </conditional>
+                <conditional name="set_lower_ks_limit_cond">
+                    <param name="set_lower_ks_limit" type="select" label="Set lower limit of synonymous subsitutions (ks)?" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" />
+                    </when>
+                </conditional>
+                <conditional name="set_upper_ks_limit_cond">
+                    <param name="set_upper_ks_limit" type="select" label="Set upper limit of synonymous subsitutions (ks)?" help="Excludes likey ancient paralogous pairs">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" />
                     </when>
                 </conditional>
             </when>