--- a/goprofiles.xml	Sun Nov 26 19:19:39 2017 -0500
+++ b/goprofiles.xml	Fri Feb 16 03:40:36 2018 -0500
@@ -5,7 +5,7 @@
         <requirement type="package" version="3.4.1">R</requirement>
         <requirement type="package" version="3.3.0">bioconductor-org.hs.eg.db</requirement>
         <requirement type="package" version="1.38.0">bioconductor-annotationdbi</requirement>
-        <requirement type="package" version="2.34.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
         <requirement type="package" version="1.38.0">goprofiles</requirement>
     </requirements>
     <stdio>
@@ -14,29 +14,35 @@
     <command><![CDATA[
         Rscript $__tool_directory__/goprofiles.R
         #if $input.ids == "text"
-            "$input.text" "text"
-        #else 
-            "$input.file,$input.ncol,$input.header" "file"
+            --input_type="text"
+            --input="$input.text"
+        #else
+            --input_type="file"
+            --input="$input.file"
+            --ncol="$input.ncol"
+            --header="$input.header"
         #end if
         
-        $input.id_type
+        --id_type="$input.id_type"
+        
+        --onto_opt="$onto_opt"
         
-        $onto_opt
+        --plot_opt="$opt.plot_opt"
         
-        $opt.plot_opt
+        --level="$level"
         
-        $level
+        --per="$per"
         
-        $per
+        --title="$title"
         
-        "$title"
-        
-        $duplicate
+        --duplicate="$duplicate"
+
+        --text_output="$text_output"
 
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Provide your Entrez Gene or UniProt identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
+            <param name="ids" type="select" label="Enter your ID list (only Entrez Gene ID or UniProt accession number allowed" help="Copy/paste or ID list from a file (e.g. table)" >
                 <option value="text">Copy/paste your identifiers</option>
                 <option value="file">Input file containing your identifiers</option>
             </param>
@@ -53,7 +59,7 @@
                 </param>
                 <param name="id_type" type="select" label="Please select the type of your IDs list" >
                     <option value="Entrez">Entrez Gene ID</option>
-                    <option value="UniProt">UniProt protein ID</option>
+                    <option value="UniProt">UniProt protein acession number</option>
                 </param>
             </when>
             <when value="file" >
@@ -93,16 +99,18 @@
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+\.jpeg)" ext="jpg" />
 	        <discover_datasets pattern="(?P&lt;designation&gt;.+\.pdf)" ext="pdf" />
 	    </collection>
+        <data name="text_output" format="tabular" label="GO Profile text output" />
     </outputs>
     <tests>
         <test>
             <conditional name="input">
                 <param name="ids" value="file" />
-                <param name="file" value="UnipIDs.txt" />
+                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
                 <param name="ncol" value="c1" />
-                <param name="header" value="false" /> 
+                <param name="header" value="talse" /> 
                 <param name="id_type" value="UniProt" />              
             </conditional>
+            <param name="duplicate" value="false"/>
             <param name="onto_opt" value="CC,MF,BP" />
             <param name="level" value="2" />
             <param name="per" value="true" />
@@ -111,14 +119,15 @@
                 <param name="plot_opt" value="PDF" />
             </section>
             <output_collection name="output" type="list" >
-                <element name="profile.BP.pdf" file="profile.BP.pdf" ftype="pdf" />
-                <element name="profile.MF.pdf" file="profile.MF.pdf" ftype="pdf" />
-                <element name="profile.CC.pdf" file="profile.CC.pdf" ftype="pdf" />
+                <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" />
             </output_collection>
+            <output name="text_output" file="GO_Profile_text_output.txt"/>
         </test>
     </tests>
     <help><![CDATA[
-This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot ID) as input. 
+This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot accession number) as input. 
 
 You can choose one or more GO categories: 
 
@@ -126,11 +135,11 @@
 * Cellular Component (CC) 
 * Molecular Function (MF) 
 
-Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats.  
+Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats; textual output with GO terms and their computed frequencies is also provided.  
 
 For more details about GoProfiles, please read: Salicrú et al. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011;12:401.(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-401)  
 
-If your type of identifiers is not supported (i.e. different form Uniprot and Entrez), please use the **ID Converter** component in the ProteoRE section to convert your list of IDs first.
+If your type of identifiers is not supported (i.e. different from Uniprot and Entrez), please use the **ID Converter** tool in the ProteoRE section to convert your list of IDs first.
 
 -----