From 92847ad78bf2ce18a2cff8c896bf38d0a7007d1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern.gruening@gmail.com>
Date: Sun, 27 Oct 2024 15:16:33 +0100
Subject: [PATCH 1/3] change reviewed to true/false

---
 tools/uniprotxml_downloader/uniprotxml_downloader.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/uniprotxml_downloader/uniprotxml_downloader.xml b/tools/uniprotxml_downloader/uniprotxml_downloader.xml
index 288ba25c2..2277fdb6e 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="21.01">
+<tool id="uniprotxml_downloader" name="UniProt" version="2.4.1" profile="23.0">
     <description>download proteome as XML or fasta</description>
     <macros>
         <import>macros.xml</import>
@@ -55,8 +55,8 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                     less of a chance peptides will be identified but less sequence redundancy
                     ]]>
                     </help>
-                    <option value="yes">UniProtKB/Swiss-Prot (reviewed only)</option>
-                    <option value="no">UniProtKB/TrEMBL (unreviewed only)</option>
+                    <option value="true">UniProtKB/Swiss-Prot (reviewed only)</option>
+                    <option value="false">UniProtKB/TrEMBL (unreviewed only)</option>
                 </param>
             </when>
             <when value="enter_ids">

From 6126cccc13caa109f1aec73dfdf6d2542edddf8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern.gruening@gmail.com>
Date: Sun, 27 Oct 2024 15:32:56 +0100
Subject: [PATCH 2/3] Update .shed.yml

---
 tools/uniprotxml_downloader/.shed.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/uniprotxml_downloader/.shed.yml b/tools/uniprotxml_downloader/.shed.yml
index e174328a5..b0f6778fc 100644
--- a/tools/uniprotxml_downloader/.shed.yml
+++ b/tools/uniprotxml_downloader/.shed.yml
@@ -12,5 +12,6 @@ long_description: |
 name: uniprotxml_downloader
 owner: galaxyp
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
+homepage_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader
 type: unrestricted
 

From c564d0e2eb8e0db85e4e642e3241c62ba5c90b89 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern.gruening@gmail.com>
Date: Sun, 27 Oct 2024 15:37:04 +0100
Subject: [PATCH 3/3] Update uniprotxml_downloader.xml

---
 tools/uniprotxml_downloader/uniprotxml_downloader.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/tools/uniprotxml_downloader/uniprotxml_downloader.xml b/tools/uniprotxml_downloader/uniprotxml_downloader.xml
index 2277fdb6e..ffa2147d4 100644
--- a/tools/uniprotxml_downloader/uniprotxml_downloader.xml
+++ b/tools/uniprotxml_downloader/uniprotxml_downloader.xml
@@ -170,6 +170,17 @@ python '$__tool_directory__/uniprotxml_downloader.py'
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="input_choice" value="common"/>
+            <param name="reviewed" value="true"/>
+            <param name="format" value="fasta"/>
+            <output name="proteome">
+                <assert_contents>
+                    <has_text text="E1Q2I0" />
+                    <has_text text="E1Q3C4" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
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