Mercurial > repos > iuc > pangolin

changeset 16:ca0d8cf80567 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
author iuc
date Wed, 15 Dec 2021 19:39:45 +0000
parents 36912871ccdc
children 5f8727ff21e7
files pangolin.xml
diffstat 1 files changed, 8 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/pangolin.xml	Mon Dec 13 11:02:29 2021 +0000
+++ b/pangolin.xml	Wed Dec 15 19:39:45 2021 +0000
@@ -1,10 +1,11 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
         <token name="@TOOL_VERSION@">3.1.17</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
+        <requirement type="package" version="0.3.16">scorpio</requirement>
         <requirement type="package" version="0.23.0">csvtk</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -45,7 +46,7 @@
         <param name="include_header" type="boolean" label="Include header line in output file" 
             truevalue="true" falsevalue="false" />
         <conditional name="db">
-            <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
+            <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database. While 'Download latest from web' is recommended, if errors occur see the warning in the main help text below.">
                 <option value="download">Download latest from web</option>
                 <option value="builtin">Use database from Galaxy server</option>
                 <option value="default">Use default database built in to pangolin (not recommended)</option>
@@ -162,6 +163,11 @@
 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
 default model rapidly becomes out of date.
 
+.. class:: warningmark
+
+	The "Download latest from web" updates the pangolin database but not the pangolin (and scorpio) software. If
+	the database format changes this can cause the pangolin job and the tool to fail. The solution to this kind of
+	failure is to update the pangolin tool installed in the Galaxy server.
     ]]></help>
     <citations>
       <citation type="doi">10.1093/ve/veab064</citation>