# HG changeset patch
# User iuc
# Date 1673778849 0
# Node ID 007ffbb118815e629cfe7c934d46c776c3c4313c
# Parent  ca337cce388886ffd55cffb17dea54d91aa0d9f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739

diff -r ca337cce3888 -r 007ffbb11881 pangolin.xml
--- a/pangolin.xml	Fri Oct 14 23:50:44 2022 +0000
+++ b/pangolin.xml	Sun Jan 15 10:34:09 2023 +0000
@@ -1,8 +1,8 @@
 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.1.2</token>
-        <token name="@PANGOLIN_DATA_VERSION@">1.12</token>
+        <token name="@TOOL_VERSION@">4.1.3</token>
+        <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
         <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
         <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
         <!-- a regex describing the scorpio versions that this wrapper version
@@ -73,14 +73,14 @@
         <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="0.5.6">usher</requirement>
+        <requirement type="package" version="0.6.2">usher</requirement>
         <requirement type="package" version="1.1.0">gofasta</requirement>
         <requirement type="package" version="426">ucsc-fatovcf</requirement>
         <requirement type="package" version="2.24">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="0.23.0">csvtk</requirement>
+        <requirement type="package" version="0.25.0">csvtk</requirement>
         <requirement type="package" version="3.4">grep</requirement>
     </requirements>
     <version_command><![CDATA[pangolin --version]]></version_command>
@@ -196,7 +196,7 @@
         <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
         <conditional name="engine">
             <param argument="--analysis-mode" type="select" label="Analysis mode"
-            help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">
+            help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases.">
                 <option value="usher">UShER</option>
                 <option value="pangolearn">pangoLEARN</option>
             </param>
@@ -262,14 +262,13 @@
         </data>
     </outputs>
     <tests>
+        <!-- Test only the default UShER mode for now since the
+        pangolearn random forest model uses too much memory
+        see https://github.com/cov-lineages/pangolin/issues/395
         <test expect_num_outputs="1">
             <param name="input1" value="test1.fasta"/>
             <conditional name="engine">
-                <!-- Test only the default UShER mode for now since the
-                pangolearn random forest model uses too much memory
-                see https://github.com/cov-lineages/pangolin/issues/395
                 <param name="analysis_mode" value="pangolearn" />
-                -->
                 <conditional name="pangolin_data">
                     <param name="source" value="default" />
                 </conditional>
@@ -282,21 +281,23 @@
                 </assert_contents>
             </output>
         </test>
+        -->
         <test expect_num_outputs="1">
             <param name="input1" value="test1.fasta"/>
             <conditional name="engine">
                 <conditional name="pangolin_data">
-                    <param name="source" value="download" />
+                    <param name="source" value="default" />
                 </conditional>
             </conditional>
             <output name="output1" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" />
+                    <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" />
                     <has_text text="pass" />
                     <has_n_lines n="1" />
                 </assert_contents>
             </output>
         </test>
+        <!-- test download and alignment options -->
         <test expect_num_outputs="2">
             <param name="input1" value="test1.fasta" />
             <conditional name="engine">