diff --git a/tools/unipept/unipept.xml b/tools/unipept/unipept.xml
index d0e5a7638..9744f0e73 100644
--- a/tools/unipept/unipept.xml
+++ b/tools/unipept/unipept.xml
@@ -1,4 +1,4 @@
-<tool id="unipept" name="Unipept" version="4.5.1">
+<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
@@ -17,10 +17,10 @@
             </param>
         </xml>
         <xml name="names">
-            <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
+            <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names">
                 <help>return the names in complete taxonomic lineage</help>
             </param>
-            <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
+            <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>
         </xml>
@@ -39,13 +39,13 @@
             </param>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">unipept</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="3">python</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
       python '$__tool_directory__/unipept.py' 
       ## --url 'http://morty.ugent.be/api/v1' -g -M 1  
       --api=$unipept.api
@@ -106,142 +106,142 @@
       #end if
     ]]></command>
     <inputs>
-      <conditional name="unipept">
-          <param name="api" type="select" label="Unipept application" >
-              <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
-              <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
-              <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>
-          <when value="pept2lca">
-              <expand macro="equate_il" />
-              <expand macro="extra">
-                  <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
-              </expand>
-              <expand macro="names" />
-          </when>
-          <when value="pept2taxa">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the complete lineage of each organism, and include ID fields.</help>
-              </expand>
-              <expand macro="names" />
-          </when>
-          <when value="pept2prot">
-              <expand macro="equate_il" />
-              <expand macro="extra">
-                  <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
+        <conditional name="unipept">
+            <param name="api" type="select" label="Unipept application">
+                <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
+                <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
+                <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>
+            <when value="pept2lca">
+                <expand macro="equate_il"/>
+                <expand macro="extra">
+                    <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
+                </expand>
+                <expand macro="names"/>
+            </when>
+            <when value="pept2taxa">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the complete lineage of each organism, and include ID fields.</help>
+                </expand>
+                <expand macro="names"/>
+            </when>
+            <when value="pept2prot">
+                <expand macro="equate_il"/>
+                <expand macro="extra">
+                    <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
                         WARNING: Huge perfomance penalty!  Only use for small number of peptides when the extra infomation is required.
                   </help>
-              </expand>
-          </when>
-          <when value="pept2ec">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the EC-number.
+                </expand>
+            </when>
+            <when value="pept2ec">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the EC-number.
                   </help>
-              </expand>
-          </when>
-          <when value="pept2go">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the GO-term.
+                </expand>
+            </when>
+            <when value="pept2go">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-          </when>
-          <when value="pept2interpro">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the GO-term.
+                </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">
-                  <help>Return the name of the  EC-number and GO-term.
+                </expand>
+                <expand macro="domains"/>
+            </when>
+            <when value="pept2funct">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the  EC-number and GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-          </when>
-          <when value="peptinfo">
-              <expand macro="equate_il" />
-              <expand macro="extra_true">
-                  <help>Return the name of the  EC-number and GO-term.
+                </expand>
+                <expand macro="domains"/>
+            </when>
+            <when value="peptinfo">
+                <expand macro="equate_il"/>
+                <expand macro="extra_true">
+                    <help>Return the name of the  EC-number and GO-term.
                   </help>
-              </expand>
-              <expand macro="domains" />
-              <expand macro="names" />
-          </when>
-      </conditional>
-      <conditional name="peptide_src">
-        <param name="fmt" type="select" label="Peptides input format" >
-          <option value="proteomic">proteomics formats:  mzid, pepxml, fasta</option>
-          <option value="tabular">tabular</option>
-          <option value="fasta">fasta</option>
-          <option value="mzid">mzid</option>
-          <option value="pepxml">pepxml</option>
+                </expand>
+                <expand macro="domains"/>
+                <expand macro="names"/>
+            </when>
+        </conditional>
+        <conditional name="peptide_src">
+            <param name="fmt" type="select" label="Peptides input format">
+                <option value="proteomic">proteomics formats:  mzid, pepxml, fasta</option>
+                <option value="tabular">tabular</option>
+                <option value="fasta">fasta</option>
+                <option value="mzid">mzid</option>
+                <option value="pepxml">pepxml</option>
+            </param>
+            <when value="proteomic">
+                <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input"/>
+            </when>
+            <when value="tabular">
+                <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column"/>
+                <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv"/>
+            </when>
+            <when value="fasta">
+                <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input"/>
+            </when>
+            <when value="mzid">
+                <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input"/>
+            </when>
+            <when value="pepxml">
+                <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>
-        <when value="proteomic">
-          <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
-        </when>
-        <when value="tabular">
-          <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
-          <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
-        </when>
-        <when value="fasta">
-          <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
-        </when>
-        <when value="mzid">
-          <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
-        </when>
-        <when value="pepxml">
-          <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>
-        <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>
-      </param>
-      <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
+        <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>
+            <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>
+        </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="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json"> 
-        <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
-        <change_format>
-            <when input="api" value="pept2prot" format="json" />
-        </change_format>
-      </data> 
-      <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
-        <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
-      </data>
-      <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv"> 
-        <filter>'tsv' in selected_outputs</filter>
-        <actions>
-            <action name="comment_lines" type="metadata" default="1" />
-            <!--
+        <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
+            <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
+            <change_format>
+                <when input="api" value="pept2prot" format="json"/>
+            </change_format>
+        </data>
+        <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
+            <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+        </data>
+        <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
+            <filter>'tsv' in selected_outputs</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1"/>
+                <!--
             <conditional name="unipept.api">
                 <when value="pept2funct">
                     <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
@@ -254,195 +254,194 @@
                 </when>
             </conditional>
             -->
-        </actions>
-      </data> 
-      <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv"> 
-        <filter>'csv' in selected_outputs</filter>
-      </data> 
-      <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv"> 
-        <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
-        </actions>
-      </data> 
-      <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv"> 
-        <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
-        </actions>
-      </data> 
-      <data name="output_ipr_tsv" format="tabular" label="${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 ${on_string} unmatched"> 
-        <filter>'unmatched' in selected_outputs</filter>
-        <actions>
-            <action name="column_names" type="metadata" default="Unmatched Peptide" />
-        </actions>
-      </data> 
+            </actions>
+        </data>
+        <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
+            <filter>'csv' in selected_outputs</filter>
+        </data>
+        <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
+            <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name"/>
+            </actions>
+        </data>
+        <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
+            <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name"/>
+            </actions>
+        </data>
+        <data name="output_ipr_tsv" format="tabular" label="${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>
+                <action name="column_names" type="metadata" default="Unmatched Peptide"/>
+            </actions>
+        </data>
     </outputs>
     <tests>
-      <!-- Test-1 -->
-      <test>
-        <param name="api" value="pept2lca"/>
-        <param name="fmt" value="tabular"/>
-        <param name="input_tsv" value="tryptic.tsv"/>
-        <param name="column" value="2"/>
-        <param name="extra" value="True"/>
-        <param name="names" value="True"/>
-        <param name="selected_outputs" value="tsv,unmatched"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="Homininae" />
-            </assert_contents>
-        </output>
-        <output name="output_unmatched">
-            <assert_contents>
-              <has_text text="QTAMAV" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-2 -->
-      <test>
-        <param name="api" value="pept2lca"/>
-        <param name="fmt" value="fasta"/>
-        <param name="input_fasta" value="peptide.fa"/>
-        <param name="equate_il" value="True"/>
-        <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" />
-            </assert_contents>
-        </output>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="9606" />
-              <has_text text="9596" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-3 -->
-      <test>
-        <param name="api" value="pept2taxa"/>
-        <param name="fmt" value="fasta"/>
-        <param name="input_fasta" value="peptide.fa"/>
-        <param name="equate_il" value="True"/>
-        <param name="extra" value="False"/>
-        <param name="names" value="False"/>
-        <param name="selected_outputs" value="tsv"/>
-        <output name="output_tsv">
-            <assert_contents>
-              <has_text text="sapiens" />
-              <has_text text="troglodytes" />
-            </assert_contents>
-        </output>
-      </test>
-      <!-- Test-4 -->
-      <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="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">
-            <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-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>
+        <!-- Test-1 -->
+        <test expect_num_outputs="2">
+            <param name="api" value="pept2lca"/>
+            <param name="fmt" value="tabular"/>
+            <param name="input_tsv" value="tryptic.tsv"/>
+            <param name="column" value="2"/>
+            <param name="extra" value="True"/>
+            <param name="names" value="True"/>
+            <param name="selected_outputs" value="tsv,unmatched"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="Homininae"/>
+                </assert_contents>
+            </output>
+            <output name="output_unmatched">
+                <assert_contents>
+                    <has_text text="QTAMAV"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-2 -->
+        <test expect_num_outputs="2">
+            <param name="api" value="pept2lca"/>
+            <param name="fmt" value="fasta"/>
+            <param name="input_fasta" value="peptide.fa"/>
+            <param name="equate_il" value="True"/>
+            <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"/>
+                </assert_contents>
+            </output>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="9606"/>
+                    <has_text text="9596"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-3 -->
+        <test expect_num_outputs="1">
+            <param name="api" value="pept2taxa"/>
+            <param name="fmt" value="fasta"/>
+            <param name="input_fasta" value="peptide.fa"/>
+            <param name="equate_il" value="True"/>
+            <param name="extra" value="False"/>
+            <param name="names" value="False"/>
+            <param name="selected_outputs" value="tsv"/>
+            <output name="output_tsv">
+                <assert_contents>
+                    <has_text text="sapiens"/>
+                    <has_text text="Cercocebus"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test-4 -->
+        <test expect_num_outputs="5">
+            <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="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">
+                <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-5 -->
+        <test expect_num_outputs="5">
+            <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 expect_num_outputs="5">
+            <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="AAEGGLSR\tAAEGGLSR\t6"/>
+                </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** 
@@ -637,8 +636,7 @@
     DOI: 10.1002/pmic.201400361
 
     ]]></help>
-  <citations>
-    <citation type="doi">doi:10.1002/pmic.201400361</citation>
-  </citations>
-
+    <citations>
+        <citation type="doi">doi:10.1002/pmic.201400361</citation>
+    </citations>
 </tool>