diff pangolin.xml @ 21:81804a978fc0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 35c4813d132f69036addcc447cc6c4ec7da04d92"

--- a/pangolin.xml	Tue May 03 19:27:06 2022 +0000
+++ b/pangolin.xml	Sat May 07 19:52:10 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
+<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="20.01">
     <description>Phylogenetic Assignment of Outbreak Lineages</description>
     <macros>
         <token name="@TOOL_VERSION@">4.0.5</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
-        <requirement type="package" version="0.3.16">scorpio</requirement>
+        <requirement type="package" version="0.3.17">scorpio</requirement>
         <requirement type="package" version="0.23.0">csvtk</requirement>
     </requirements>
     <version_command><![CDATA[pangolin --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
-      #if $engine.use_assignment_cache and str($db.source) != "download":
+      #if $str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache and str($db.source) != "download":
         ## This is no good. Better to fail immediately instead of downloading a lot of data first.
         echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1
       #else:
@@ -22,7 +22,7 @@
         #else if str($db.source) == "builtin"
             ln -s $db.db_release.fields.path datadir &&
         #end if
-        #if $engine.use_assignment_cache:
+        #if str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache:
             ## We need to install also the latest UShER assignment cache data.
             ## Pangolin has functionality to do so, but uses it incorrectly.
             ## We use the pangolin function to install into --datadir here,
@@ -217,6 +217,16 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test that use of latest assignment cache requires downloaded other data -->
+        <test expect_failure="true">
+            <param name="input1" value="multiple_alignment.fasta.gz"/>
+            <conditional name="engine">
+                <param name="use_assignment_cache" value="true" />
+            </conditional>
+            <conditional name="db">
+                <param name="source" value="default" />
+            </conditional>
+        </test>
         <!-- test with extra expanded_lineage column -->
         <test expect_num_outputs="1">
             <param name="input1" value="multiple_alignment.fasta.gz"/>