--- a/unipept.xml	Wed Dec 07 16:44:07 2016 -0500
+++ b/unipept.xml	Mon Feb 20 10:32:03 2017 -0500
@@ -1,33 +1,38 @@
-<tool id="unipept" name="Unipept" version="1.1.0">
+<tool id="unipept" name="Unipept" version="2.0.1">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
             <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
                 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
-            </param >
+            </param>
         </xml>
         <xml name="extra">
             <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
                 <yield/>
-            </param >
+            </param>
+        </xml>
+        <xml name="extra_true">
+            <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
+                <yield/>
+            </param>
         </xml>
         <xml name="names">
             <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
                 <help>return the names in complete taxonomic lineage</help>
-            </param >
+            </param>
             <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
                 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
-            </param >
+            </param>
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="2.7.12">python</requirement>
+        <requirement type="package" version="2.7">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
-    <command interpreter="python"><![CDATA[
-      unipept.py 
+    <command><![CDATA[
+      python '$__tool_directory__/unipept.py' 
       --api=$unipept.api
       $unipept.equate_il $unipept.extra 
       #if $unipept.api != 'pept2prot':
@@ -53,7 +58,7 @@
       #elif str($peptide_src.fmt) == 'pepxml':
         --pepxml="$peptide_src.input_pepxml"
       #end if
-      #if 'json' in str($outputs).split(','):
+      #if 'json' in str($outputs).split(',') and str($unipept.api) != 'pept2prot':
         --json $output_json
       #end if
       #if 'tsv' in str($outputs).split(','):
@@ -82,8 +87,7 @@
           </when>
           <when value="pept2taxa">
               <expand macro="equate_il" />
-              <expand macro="extra">
-                  <checked>true</checked>
+              <expand macro="extra_true">
                   <help>Return the complete lineage of each organism, and include ID fields.</help>
               </expand>
               <expand macro="names" />
@@ -125,14 +129,17 @@
       <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
         <option value="tsv" selected="true">tabular</option>
         <option value="csv">Comma Separated Values (.csv)</option>
-        <option value="json">JSON</option>
+        <option value="json">JSON Taxomony Tree (ignored for pept2prot)</option>
         <option value="unmatched">Unmatched peptides</option>
       </param>
       <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
     </inputs>
     <outputs>
-      <data name="output_json" format="json" label="${tool.name} ${unipept.api} on ${on_string} json"> 
-        <filter>'json' in outputs</filter>
+      <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} json"> 
+        <filter>'json' in outputs and unipept['api'] != 'pept2prot'</filter>
+        <change_format>
+            <when input="api" value="pept2prot" format="json" />
+        </change_format>
       </data> 
       <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 
         <filter>'tsv' in outputs</filter>