--- a/uniprotxml_downloader.xml	Tue Jun 01 11:54:47 2021 +0000
+++ b/uniprotxml_downloader.xml	Fri Nov 04 15:08:37 2022 +0000
@@ -1,5 +1,8 @@
-<tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01">
+<tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01">
     <description>download proteome as XML or fasta</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="2.25.1">requests</requirement>
     </requirements>
@@ -11,14 +14,17 @@
 python '$__tool_directory__/uniprotxml_downloader.py'
 #if $taxid.input_choice == 'common':
     --taxon $taxid.organism
+    --field taxonomy_id
     #if $taxid.reviewed:
         --reviewed=$taxid.reviewed
     #end if
 #elif $taxid.input_choice == 'taxids':
+    --field $taxid.field
     #for $id in $taxid.taxons.split(','):
         -t '$id'
     #end for
 #elif $taxid.input_choice == 'history':
+    --field $taxid.field
     --input='${taxid.taxon_file}'
     --column=#echo int(str($taxid.column)) - 1#
 #end if
@@ -58,10 +64,12 @@
                        help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/">
                     <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator>
                 </param>
+                <expand macro="query_field"/>
             </when>
             <when value="history">
                 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/>
                 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/>
+                <expand macro="query_field"/>
             </when>
         </conditional>
         <param name="format" type="select" label="uniprot output format">
@@ -89,7 +97,20 @@
         </test>
         <test>
             <param name="input_choice" value="taxids"/>
+            <param name="taxons" value="765963,512562"/>
+            <param name="field" value="taxonomy_id"/>
+            <param name="format" value="fasta"/>
+            <output name="proteome">
+                <assert_contents>
+                    <has_text text="Shi470" />
+                    <has_text text="PeCan4" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_choice" value="taxids"/>
             <param name="taxons" value="Shi470,PeCan4"/>
+            <param name="field" value="taxonomy_name"/>
             <param name="format" value="fasta"/>
             <output name="proteome">
                 <assert_contents>
@@ -102,6 +123,7 @@
             <param name="input_choice" value="history"/>
             <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/>
             <param name="column" value="1"/>
+            <param name="field" value="taxonomy_name"/>
             <param name="format" value="fasta"/>
             <output name="proteome">
                 <assert_contents>
@@ -114,6 +136,7 @@
             <param name="input_choice" value="history"/>
             <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/>
             <param name="column" value="2"/>
+            <param name="field" value="taxonomy_id"/>
             <param name="format" value="fasta"/>
             <output name="proteome">
                 <assert_contents>