--- a/unipept.xml	Wed Jan 23 09:16:38 2019 -0500
+++ b/unipept.xml	Thu Apr 30 07:39:28 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="unipept" name="Unipept" version="4.0.0">
+<tool id="unipept" name="Unipept" version="4.3.0">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
@@ -40,7 +40,7 @@
         </xml>
     </macros>
     <requirements>
-        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="3">python</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -94,6 +94,9 @@
       #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
         --go_tsv $output_go_tsv
       #end if
+      #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
+        --ipr_tsv $output_ipr_tsv
+      #end if
       #if 'unmatched' in str($selected_outputs).split(','):
         --unmatched $output_unmatched
       #end if
@@ -106,6 +109,7 @@
               <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
               <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
               <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
+              <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
               <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
               <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
           </param>
@@ -146,6 +150,14 @@
               </expand>
               <expand macro="domains" />
           </when>
+          <when value="pept2interpro">
+              <expand macro="equate_il" />
+              <expand macro="extra_true">
+                  <help>Return the name of the GO-term.
+                  </help>
+              </expand>
+              <expand macro="domains" />
+          </when>
           <when value="pept2funct">
               <expand macro="equate_il" />
               <expand macro="extra_true">
@@ -194,6 +206,7 @@
        <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
         <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
         <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
+        <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
         <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
         <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
         <option value="unmatched">Unmatched peptides</option>
@@ -244,6 +257,13 @@
             <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
         </actions>
       </data> 
+      <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv"> 
+        <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
+        <actions>
+            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
+        </actions>
+      </data> 
+
       <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 
         <filter>'unmatched' in selected_outputs</filter>
         <actions>
@@ -279,6 +299,8 @@
         <param name="extra" value="True"/>
         <param name="names" value="True"/>
         <param name="selected_outputs" value="json,tsv"/>
+<!--
+-->
         <output name="output_json">
             <assert_contents>
               <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
@@ -303,7 +325,6 @@
             <assert_contents>
               <has_text text="sapiens" />
               <has_text text="paniscus" />
-              <has_text text="Gorilla" />
             </assert_contents>
         </output>
       </test>
@@ -314,11 +335,12 @@
         <param name="column" value="2"/>
         <param name="extra" value="True"/>
         <param name="names" value="True"/>
-        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,unmatched"/>
+        <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
         <output name="output_tsv">
             <assert_contents>
               <has_text text="GO:0004802" />
               <has_text text="2.2.1.1" />
+              <has_text text="IPR005475" />
             </assert_contents>
         </output>
         <output name="output_ec_tsv">
@@ -331,6 +353,11 @@
               <has_text text="GO:0004802" />
             </assert_contents>
         </output>
+        <output name="output_ipr_tsv">
+            <assert_contents>
+              <has_text text="IPR005475" />
+            </assert_contents>
+        </output>
       </test>
     </tests>
     <help><![CDATA[
@@ -485,6 +512,19 @@
         name: Optional, name of the GO-term. Included when the extra parameter is set to true.
 
 
+    **pept2interpro**  - http://unipept.ugent.be/apidocs/pept2interpro
+
+    Returns the functional InterPro entries associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
+
+    By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
+
+        peptide: the peptide that matched this record
+        total_protein_count: Total amount of proteins matched with the given peptide
+        code: InterPro entry code associated with the current tryptic peptide
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
+        type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
+        name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
+
     **pept2funct**  - http://unipept.ugent.be/apidocs/pept2funct
 
     Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
@@ -499,6 +539,10 @@
         go_term: The GO-term associated with the current tryptic peptide.
         protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
         name: Optional, name of the GO-term. Included when the extra parameter is set to true.
+        code: InterPro entry code associated with the current tryptic peptide
+        protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
+        type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
+        name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
 
 
     **Attributions**