Mercurial > repos > iuc > pangolin

diff pangolin.xml @ 29:f0fc9c4f00fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin commit 89a03f607cc5f9862ebc6f6e1f3111c9dbc6ccdf
author iuc
date Mon, 27 Oct 2025 09:30:25 +0000
parents 3ccccf6c08cd
children 5f736365108b
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--- a/pangolin.xml	Thu Jul 20 05:39:30 2023 +0000
+++ b/pangolin.xml	Mon Oct 27 09:30:25 2025 +0000
@@ -1,8 +1,8 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.3</token>
-        <token name="@PANGOLIN_DATA_VERSION@">1.21</token>
+        <token name="@TOOL_VERSION@">4.3.2</token>
+        <token name="@PANGOLIN_DATA_VERSION@">1.26</token>
         <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>
         <!-- a regex describing the pangolin-data versions that this wrapper version
         is backwards-compatible with; can be used with the min_pangolin_version
@@ -31,6 +31,9 @@
             </param>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">pangolin_cov-lineages</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
         <!-- Pin also the versions of all core dependencies - the ones
@@ -45,18 +48,18 @@
         Wrapper updates are **explicitly encouraged** when new dependency
         versions become available. Also, please check for updated dependencies
         when updating the wrapper for other reasons. -->
-        <requirement type="package" version="0.3.17">scorpio</requirement>
-        <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
-        <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
-        <requirement type="package" version="0.6.2">usher</requirement>
-        <requirement type="package" version="1.2.0">gofasta</requirement>
-        <requirement type="package" version="448">ucsc-fatovcf</requirement>
-        <requirement type="package" version="2.26">minimap2</requirement>
+        <requirement type="package" version="0.3.19">scorpio</requirement>
+        <requirement type="package" version="1.35">pangolin-data</requirement>
+        <requirement type="package" version="0.1.12">constellations</requirement>
+        <requirement type="package" version="0.6.6">usher</requirement>
+        <requirement type="package" version="1.2.3">gofasta</requirement>
+        <requirement type="package" version="482">ucsc-fatovcf</requirement>
+        <requirement type="package" version="2.30">minimap2</requirement>
         <!-- wrapper-specific requirements to turn pangolin's native
         comma-separated output into tab-separated one and to truncate
         pangolin's all-versions output. -->
-        <requirement type="package" version="0.26.0">csvtk</requirement>
-        <requirement type="package" version="3.11">grep</requirement>
+        <requirement type="package" version="0.35.0">csvtk</requirement>
+        <requirement type="package" version="3.12">grep</requirement>
     </requirements>
     <version_command><![CDATA[pangolin --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[