--- a/goprofiles.xml	Fri Mar 23 10:47:17 2018 -0400
+++ b/goprofiles.xml	Wed Sep 19 05:49:06 2018 -0400
@@ -1,11 +1,11 @@
-<tool id="goProfiles" name="goProfiles" version="0.1.0">
-    <description> Statistical analysis of functional profiles
-    </description>
-    <requirements>
+<tool id="goProfiles" name="goProfiles" version="2018.09.04">
+    <description>Statistical analysis of functional profiles</description>
+    <requirements> 
         <requirement type="package" version="3.4.1">R</requirement>
-        <requirement type="package" version="3.4.1">bioconductor-org.hs.eg.db</requirement>
-        <requirement type="package" version="1.38.2">bioconductor-annotationdbi</requirement>
-        <requirement type="package" version="2.36.2">bioconductor-biobase</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement>
+        <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
         <requirement type="package" version="1.38.0">goprofiles</requirement>
     </requirements>
     <stdio>
@@ -39,6 +39,8 @@
 
         --text_output="$text_output"
 
+        --species="$species"
+
     ]]></command>
     <inputs>
         <conditional name="input" >
@@ -73,6 +75,10 @@
             </when>            
         </conditional>
         <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
+        <param name="species" type="select" label="Select your species">
+            <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
+            <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
+        </param>
         <param type="select" name="onto_opt" label="Please select GO terms category" multiple="True" display="checkboxes" >
             <option value="CC">Cellular Component (CC)</option>
             <option value="MF">Molecular Function (MF)</option>
@@ -94,7 +100,7 @@
         </section>
     </inputs>
     <outputs>
-	    <collection type="list" label="GO Profile diagram outputs" name="output" >
+	    <collection type="list" label="GO Profile diagram output" name="output" >
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
@@ -105,9 +111,9 @@
         <test>
             <conditional name="input">
                 <param name="ids" value="file" />
-                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
+                <param name="file" value="ID_Converted_FKW_Lacombe_et_al_2017_OK.txt" />
                 <param name="ncol" value="c1" />
-                <param name="header" value="talse" /> 
+                <param name="header" value="true" /> 
                 <param name="id_type" value="UniProt" />              
             </conditional>
             <param name="duplicate" value="false"/>
@@ -119,9 +125,9 @@
                 <param name="plot_opt" value="PDF" />
             </section>
             <output_collection name="output" type="list" >
-                <element name="GO_Profile_diagram_outputs__profile.BP.pdf" file="GO_Profile_diagram_outputs__profile.BP.pdf" ftype="pdf" />
-                <element name="GO_Profile_diagram_outputs__profile.CC.pdf" file="GO_Profile_diagram_outputs__profile.CC.pdf" ftype="pdf" />
-                <element name="GO_Profile_diagram_outputs__profile.MF.pdf" file="GO_Profile_diagram_outputs__profile.MF.pdf" ftype="pdf" />
+                <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" compare="sim_size"/>
+                <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" compare="sim_size"/>
+                <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" compare="sim_size"/>
             </output_collection>
             <output name="text_output" file="GO_Profile_text_output.txt"/>
         </test>