--- a/mob_typer.xml	Thu Jul 26 14:50:59 2018 -0400
+++ b/mob_typer.xml	Fri Aug 17 11:12:08 2018 -0400
@@ -1,70 +1,36 @@
-<tool id="mob_typer" name="MOB-Typer" version="1.4.5">
+<tool id="mob_typer" name="MOB-Typer" version="1.4.8">
   <description>Get the plasmid type and mobility given its sequence</description>
   <requirements>
-     <requirement type="package" version="1.4.5">mob_suite</requirement>
+     <requirement type="package" version="1.4.8">mob_suite</requirement>
   </requirements>   
   <command detect_errors="exit_code">
   <![CDATA[
     ln -s "${input}" "${input.name}";
     mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
-    #if str($adv_param.min_rep_evalue_condition.min_rep_evalue_param) == "True":
-      --min_rep_evalue $adv_param.min_rep_evalue_condition.min_rep_evalue_value
-    #end if 
-    #if str($adv_param.min_mob_evalue_condition.min_mob_evalue_param) == "True":
-      --min_mob_evalue $adv_param.min_mob_evalue_condition.min_mob_evalue_value
-    #end if 
-    #if str($adv_param.min_con_evalue_condition.min_con_evalue_param) == "True":
-      --min_con_evalue $adv_param.min_con_evalue_condition.min_con_evalue_value
-    #end if 
-    #if str($adv_param.min_ori_evalue_condition.min_ori_evalue_param) == "True":
-      --min_ori_evalue $adv_param.min_ori_evalue_condition.min_ori_evalue_value
-    #end if 
+   --min_rep_evalue '$adv_param.min_rep_evalue_value'
+   --min_mob_evalue '$adv_param.min_mob_evalue_value'
+   --min_con_evalue '$adv_param.min_con_evalue_value'
+   --min_ori_evalue '$adv_param.min_ori_evalue_value'
+   --min_mpf_evalue '$adv_param.min_mpf_evalue'
+   --min_rep_ident '$adv_param.min_rep_ident'
+   --min_mob_ident '$adv_param.min_mob_ident'
+   --min_ori_ident '$adv_param.min_ori_ident'
+   --min_mpf_ident '$adv_param.min_mpf_ident'
     --outdir '.';
   ]]>
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
     <section name="adv_param" title="Advanced parameters" expanded="False">
-      <conditional name="min_rep_evalue_condition">
-        <param name="min_rep_evalue_param" label="Minimum evalue threshold for replicon blastn" type="select" value="False">
-          <option value="False">No</option>
-          <option value="True">Yes</option>
-       </param>   
-        <when value="True">
-          <param name="min_rep_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
-        </when>  
-        <when value="False"/>
-      </conditional>
-      <conditional name="min_mob_evalue_condition">
-        <param name="min_mob_evalue_param" label="Minimum evalue threshold for relaxase tblastn" type="select" value="False">
-          <option value="False">No</option>
-          <option value="True">Yes</option>
-       </param>   
-        <when value="True">
-          <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="e-value (default: 0.00001)"/> 
-        </when>  
-        <when value="False"/>
-      </conditional>
-      <conditional name="min_con_evalue_condition">
-        <param name="min_con_evalue_param" label="Minimum evalue threshold for contig blastn" type="select" value="False">
-          <option value="False">No</option>
-          <option value="True">Yes</option>
-       </param>   
-        <when value="True">
-          <param name="min_con_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
-        </when>  
-        <when value="False"/>
-      </conditional>
-      <conditional name="min_ori_evalue_condition">
-        <param name="min_ori_evalue_param" label="Minimum evalue threshold for oriT elements blastn" type="select" value="False">
-          <option value="False">No</option>
-          <option value="True">Yes</option>
-       </param>   
-        <when value="True">
-          <param name="min_ori_evalue_value" type="float" value="0.00001" min="0" max="1" label="e-value (default: 0.00001)"/> 
-        </when>  
-        <when value="False"/>
-      </conditional>
+      <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> 
+      <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> 
+      <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> 
+      <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/>
+      <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/>
+      <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer"  min="0" max="100" value="80"/>
+      <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer"  min="0" max="100" value="90"/>
+      <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer"  min="0" max="100" value="80"/>
     </section>  
   </inputs>
   <outputs>