diff --git a/tools/uniprotxml_downloader/uniprotxml_downloader.py b/tools/uniprotxml_downloader/uniprotxml_downloader.py
index 6d9da40e9..12ae261fa 100755
--- a/tools/uniprotxml_downloader/uniprotxml_downloader.py
+++ b/tools/uniprotxml_downloader/uniprotxml_downloader.py
@@ -27,9 +27,10 @@ def __main__():
     parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains search search_ids')
     parser.add_option('-s', '--search-id', dest='search_id', action='append', default=[], help='ID to search in Uniprot')
     parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
-    parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format')
+    parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta', 'tsv'], default='xml', help='output format')
     parser.add_option('-k', '--field', dest='field', choices=['taxonomy_name', 'taxonomy_id', 'accession'], default='taxonomy_name', help='query field')
     parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
+    parser.add_option('--output_columns', dest='output_columns', help='Columns to include in output (tsv)')
     parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
     (options, args) = parser.parse_args()
     search_ids = set(options.search_id)
@@ -66,13 +67,14 @@ def get_batch(batch_url):
             while batch_url:
                 response = session.get(batch_url)
                 response.raise_for_status()
-                print(response.headers)
                 total = response.headers["x-total-results"]
                 release = response.headers["x-uniprot-release"]
                 yield response, total, release
                 batch_url = get_next_link(response.headers)
 
         params = {'size': 500, 'format': options.format, 'query': search_query + reviewed}
+        if options.output_columns:
+            params['fields'] = options.output_columns
         url = f'https://rest.uniprot.org/uniprotkb/search?{parse.urlencode(params)}'
         print(f"Downloading from:{url}")
 
diff --git a/tools/uniprotxml_downloader/uniprotxml_downloader.xml b/tools/uniprotxml_downloader/uniprotxml_downloader.xml
index cb56bb8d7..7ed1ac740 100644
--- a/tools/uniprotxml_downloader/uniprotxml_downloader.xml
+++ b/tools/uniprotxml_downloader/uniprotxml_downloader.xml
@@ -1,4 +1,4 @@
-<tool id="uniprotxml_downloader" name="UniProt" version="2.4.0" profile="23.1">
+<tool id="uniprotxml_downloader" name="UniProt" version="2.5.0" profile="23.1">
     <description>download proteome as XML or fasta</description>
     <macros>
         <xml name="query_field">
@@ -34,7 +34,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
     --input='${input_method.id_file}'
     --column=#echo int(str($input_method.column)) - 1#
 #end if
---format $format
+--format $format_cond.format
+#if $format_cond.format == "tsv"
+    --output_columns #echo ','.join($format_cond.columns)
+#end if
 --output '${proteome}'
 ]]>
     </command>
@@ -42,8 +45,8 @@ python '$__tool_directory__/uniprotxml_downloader.py'
         <conditional name="input_method">
             <param name="input_choice" type="select" label="Select">
                 <option value="common">A Common Organism</option>
-                <option value="enter_ids">A manually entered list of IDs</option>
-                <option value="history">A history dataset with a column containing IDs</option>
+                <option value="enter_ids">A manually entered list of accessions or taxonomy IDs/names</option>
+                <option value="history">A history dataset with a column containing accessions or taxonomy IDs/names</option>
             </param>
             <when value="common">
                 <param name="organism" type="select" label="Common Organisms"
@@ -78,15 +81,39 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <expand macro="query_field"/>
             </when>
         </conditional>
-        <param name="format" type="select" label="uniprot output format">
-            <option value="xml">xml</option>
-            <option value="fasta">fasta</option>
-        </param>
+        <conditional name="format_cond">
+            <param name="format" type="select" label="uniprot output format">
+                <option value="fasta">fasta</option>
+                <option value="tsv">TSV</option>
+                <option value="xml">xml</option>
+            </param>
+            <when value="fasta"/>
+            <when value="xml"/>
+            <when value="tsv">
+                <param name="columns" type="select" multiple="true">
+                    <options from_url="https://rest.uniprot.org/configure/uniprotkb/result-fields">
+                        <postprocess_expression type="ecma5.1"><![CDATA[${
+                            var options = [];
+                            inputs.forEach(function(group) {
+                                var groupName = group.groupName;
+                                group.fields.forEach(function(field) {
+                                    var D = ["accession", "id", "reviewed", "protein_name", "gene_names", "organism_name", "length"];
+                                    var selected = D.includes(field.name);
+                                    options.push([group.groupName + " - " + field.label, field.name, selected]);
+                                });
+                            });
+                            return options;
+                        }]]></postprocess_expression>
+                    </options>
+                </param>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data format="uniprotxml" name="proteome" label="UniProt.${format}">
+        <data format="uniprotxml" name="proteome">
             <change_format>
-                <when input="format" value="fasta" format="fasta" />
+                <when input="format_cond.format" value="fasta" format="fasta" />
+                <when input="format_cond.format" value="tsv" format="tsv" />
             </change_format>
         </data>
     </outputs>
@@ -96,8 +123,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="input_choice" value="enter_ids"/>
                 <param name="ids" value="1566990"/>
             </conditional>
-            <param name="format" value="xml"/>
-            <output name="proteome">
+            <conditional name="format_cond">
+                <param name="format" value="xml"/>
+            </conditional>
+            <output name="proteome" ftype="uniprotxml">
                 <assert_contents>
                     <has_text text="&lt;/uniprot&gt;" />
                 </assert_contents>
@@ -113,8 +142,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="ids" value="765963,512562"/>
                 <param name="field" value="taxonomy_id"/>
             </conditional>
-            <param name="format" value="fasta"/>
-            <output name="proteome">
+            <conditional name="format_cond">
+                <param name="format" value="fasta"/>
+            </conditional>
+            <output name="proteome" ftype="fasta">
                 <assert_contents>
                     <has_text text="Shi470" />
                     <has_text text="PeCan4" />
@@ -132,7 +163,9 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="ids" value="Shi470,PeCan4"/>
                 <param name="field" value="taxonomy_name"/>
             </conditional>
-            <param name="format" value="fasta"/>
+            <conditional name="format_cond">
+                <param name="format" value="fasta" ftype="fasta"/>
+            </conditional>
             <output name="proteome">
                 <assert_contents>
                     <has_text text="Shi470" />
@@ -146,8 +179,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="ids" value="E1Q2I0,E1Q3C4"/>
                 <param name="field" value="accession"/>
             </conditional>
-            <param name="format" value="fasta"/>
-            <output name="proteome">
+            <conditional name="format_cond">
+                <param name="format" value="fasta"/>
+            </conditional>
+            <output name="proteome" ftype="fasta">
                 <assert_contents>
                     <has_text text="E1Q2I0" />
                     <has_text text="E1Q3C4" />
@@ -166,8 +201,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="column" value="1"/>
                 <param name="field" value="taxonomy_name"/>
             </conditional>
-            <param name="format" value="fasta"/>
-            <output name="proteome">
+            <conditional name="format_cond">
+                <param name="format" value="fasta"/>
+            </conditional>
+            <output name="proteome" ftype="fasta">
                 <assert_contents>
                     <has_text text="Shi470" />
                     <has_text text="PeCan4" />
@@ -186,8 +223,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="column" value="2"/>
                 <param name="field" value="taxonomy_id"/>
             </conditional>
+                <conditional name="format_cond">
             <param name="format" value="fasta"/>
-            <output name="proteome">
+            </conditional>
+            <output name="proteome" ftype="fasta">
                 <assert_contents>
                     <has_text text="Shi470" />
                     <has_text text="PeCan4" />
@@ -206,8 +245,10 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <param name="column" value="1"/>
                 <param name="field" value="accession"/>
             </conditional>
-            <param name="format" value="fasta"/>
-            <output name="proteome">
+            <conditional name="format_cond">
+                <param name="format" value="fasta"/>
+            </conditional>
+            <output name="proteome" ftype="fasta">
                 <assert_contents>
                     <has_text text="E1Q2I0" />
                     <has_text text="E1Q3C4" />
@@ -219,6 +260,53 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 <has_line line="Entries:0" negate="true"/>
             </assert_stdout>
         </test>
+        <!-- tsv output -->
+        <test>
+            <conditional name="input_method">
+                <param name="input_choice" value="enter_ids"/>
+                <param name="ids" value="765963,512562"/>
+                <param name="field" value="taxonomy_id"/>
+            </conditional>
+            <conditional name="format_cond">
+                <param name="format" value="tsv"/>
+            </conditional>
+            <output name="proteome" ftype="tsv">
+                <assert_contents>
+                    <has_n_columns n="7" />
+                    <has_text text="Shi470" />
+                    <has_text text="PeCan4" />
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
+                <has_text_matching expression="Entries:\d+"/>
+                <has_line line="Entries:0" negate="true"/>
+            </assert_stdout>
+        </test>
+        <!-- tsv output non default columns-->
+        <test>
+            <conditional name="input_method">
+                <param name="input_choice" value="enter_ids"/>
+                <param name="ids" value="765963,512562"/>
+                <param name="field" value="taxonomy_id"/>
+            </conditional>
+            <conditional name="format_cond">
+                <param name="format" value="tsv"/>
+                <param name="columns" value="accession,sequence"/>
+            </conditional>
+            <output name="proteome" ftype="tsv">
+                <assert_contents>
+                    <has_n_columns n="2" />
+                    <has_text text="Shi470" negate="true"/>
+                    <has_text text="B2US14" />
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="UniProt-Release:\d{4}_\d{2}"/>
+                <has_text_matching expression="Entries:\d+"/>
+                <has_line line="Entries:0" negate="true"/>
+            </assert_stdout>
+        </test>
     </tests>
     <help>
 <![CDATA[