changeset 8:3a656a4a43ed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"

--- a/pangolin.xml	Tue Jul 20 12:23:51 2021 +0000
+++ b/pangolin.xml	Fri Aug 13 19:53:03 2021 +0000
@@ -1,7 +1,7 @@
 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.1.7</token>
+        <token name="@TOOL_VERSION@">3.1.11</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
@@ -9,7 +9,7 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($db.source) == "download"
-            python '$__tool_directory__/fetch_latest_pangolearn.py' --max_retries=$db.max_retries --timeout=$db.timeout &&
+            pangolin --update-data --datadir datadir &&
         #else if str($db.source) == "builtin"
             ln -s $db.db_release.fields.path datadir &&
         #end if
@@ -51,8 +51,9 @@
                 <option value="default">Use default database built in to pangolin (not recommended)</option>
             </param>
             <when value="download">
-                <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" />
-                <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" />
+                <!-- these are currently not supported by the pangolin downloader -->
+                <!-- <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> -->
+                <!-- <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> -->
             </when>
             <when value="builtin">
                 <param name="db_release" label="pangoLEARN release" type="select">
@@ -173,17 +174,6 @@
                 </assert_contents>
             </output>
         </test>
-        <test expect_failure="true">
-            <param name="input1" value="test1.fasta" />
-            <conditional name="db">
-                <param name="source" value="download" />
-                <param name="timeout" value="0.00001" />
-                <param name="max_retries" value="1" />
-            </conditional>
-            <assert_stderr>
-                <has_text text="timed out" />
-            </assert_stderr>
-        </test>
     </tests>
     <help><![CDATA[
 
@@ -201,14 +191,6 @@
 
     ]]></help>
     <citations>
-      <citation type="bibtex">
-      @misc{githubpangolin,
-        author = {O'Toole, Áine},
-        year = {2020},
-        title = {pangolin},
-        publisher = {GitHub},
-        journal = {GitHub repository},
-        url = {https://github.com/cov-lineages/pangolin},
-      }</citation>
+      <citation type="doi">10.1093/ve/veab064</citation>
     </citations>
 </tool>