# HG changeset patch
# User iuc
# Date 1658155835 0
# Node ID 77402759b86643897988ffa8d15d9eb09c64cdc9
# Parent  a2099fb98cdb10c544ccc1bbff23eb30680e8ce7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d7751920c666de56e21cf48ffe19191b2d19d534

diff -r a2099fb98cdb -r 77402759b866 pangolin.xml
--- a/pangolin.xml	Fri Jul 08 08:33:57 2022 +0000
+++ b/pangolin.xml	Mon Jul 18 14:50:35 2022 +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@">4.1.1</token>
-        <token name="@PANGOLIN_DATA_VERSION@">1.11</token>
+        <token name="@TOOL_VERSION@">4.1.2</token>
+        <token name="@PANGOLIN_DATA_VERSION@">1.12</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
@@ -153,6 +153,14 @@
     echo "Running pangolin with the following possibly updated data packages:" &&
     pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" &&
 #end if
+## Since v4.0.6 pangolin can handle compressed fasta as input,
+## but recognizes file type by suffix.
+#if $input1.is_of_type('fasta.gz'):
+    #set $query = 'query.fa.gz'
+#else:
+    #set $query = 'query.fa'
+#end if
+ln -s '$input1' $query &&
 ## Finally run the pangolin analysis
 pangolin
 --threads \${GALAXY_SLOTS:-1}
@@ -177,7 +185,7 @@
 --max-ambig $max_ambig
 --min-length $min_length
 $expanded_lineage
-'$input1'
+$query
 && csvtk csv2tab report.csv
 #if not $include_header:
     | tail -n+2
@@ -185,7 +193,7 @@
 > '$output1'
     ]]></command>
     <inputs>
-        <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
+        <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">