--- a/unipept.xml	Tue Jun 02 10:30:01 2020 -0400
+++ b/unipept.xml	Tue Apr 06 16:13:57 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="unipept" name="Unipept" version="4.3.0">
+<tool id="unipept" name="Unipept" version="4.5.0">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
@@ -76,6 +76,10 @@
       #elif str($peptide_src.fmt) == 'pepxml':
         --pepxml="$peptide_src.input_pepxml"
       #end if
+      --peptide_match $peptide_match
+      #if $peptide_match == 'report' and $unmatched_aa != 'default':
+          --unmatched_aa $unmatched_aa
+      #end if
       #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
         --json $output_json
       #end if
@@ -201,6 +205,16 @@
           <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
         </when>
       </conditional>
+      <param name="peptide_match" type="select" label="Match input peptides by">
+          <option value="full">Match to the full input peptide</option>
+          <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
+          <option value="report">Best match to tryptic parts, add tryptic_match column</option>
+      </param> 
+      <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
+          <option value="default">List of matched tryptic parts</option>
+          <option value=".">peptide with unmatched AAs as .</option>
+          <option value="x">peptide with unmatched AAs as x</option>
+      </param> 
       <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
        <option value="tsv" selected="true">Tabular with one line per peptide</option>
        <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
@@ -272,6 +286,7 @@
       </data> 
     </outputs>
     <tests>
+      <!-- Test-1 -->
       <test>
         <param name="api" value="pept2lca"/>
         <param name="fmt" value="tabular"/>
@@ -291,6 +306,7 @@
             </assert_contents>
         </output>
       </test>
+      <!-- Test-2 -->
       <test>
         <param name="api" value="pept2lca"/>
         <param name="fmt" value="fasta"/>
@@ -299,8 +315,6 @@
         <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" />
@@ -313,6 +327,7 @@
             </assert_contents>
         </output>
       </test>
+      <!-- Test-3 -->
       <test>
         <param name="api" value="pept2taxa"/>
         <param name="fmt" value="fasta"/>
@@ -328,6 +343,7 @@
             </assert_contents>
         </output>
       </test>
+      <!-- Test-4 -->
       <test>
         <param name="api" value="pept2funct"/>
         <param name="fmt" value="tabular"/>
@@ -359,6 +375,74 @@
             </assert_contents>
         </output>
       </test>
+      <!-- Test-5 -->
+      <test>
+        <param name="api" value="pept2funct"/>
+        <param name="fmt" value="tabular"/>
+        <param name="input_tsv" value="input.tsv"/>
+        <param name="column" value="2"/>
+        <param name="extra" value="True"/>
+        <param name="names" value="True"/>
+        <param name="peptide_match" value="full"/>
+        <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" />
+              <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" />
+            </assert_contents>
+        </output>
+        <output name="output_ec_tsv">
+            <assert_contents>
+              <has_text text="2.2.1.1" />
+            </assert_contents>
+        </output>
+        <output name="output_go_tsv">
+            <assert_contents>
+              <has_text text="GO:0004802" />
+            </assert_contents>
+        </output>
+        <output name="output_ipr_tsv">
+            <assert_contents>
+              <has_text text="IPR005475" />
+            </assert_contents>
+        </output>
+      </test>
+      <!-- Test-6 -->
+      <test>
+        <param name="api" value="pept2funct"/>
+        <param name="fmt" value="tabular"/>
+        <param name="input_tsv" value="input.tsv"/>
+        <param name="column" value="2"/>
+        <param name="extra" value="True"/>
+        <param name="names" value="True"/>
+        <param name="peptide_match" value="report"/>
+        <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" />
+              <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" />
+            </assert_contents>
+        </output>
+        <output name="output_ec_tsv">
+            <assert_contents>
+              <has_text text="2.2.1.1" />
+            </assert_contents>
+        </output>
+        <output name="output_go_tsv">
+            <assert_contents>
+              <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[
     **Unipept**