# HG changeset patch
# User iuc
# Date 1749562363 0
# Node ID 46a0e11a76070880d0edda4fe0fa0c88f0b65e3d
# Parent  f793ae405fd14490defb843f4918a40d95eaa20f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5

diff -r f793ae405fd1 -r 46a0e11a7607 macros.xml
--- a/macros.xml	Tue Mar 11 09:14:19 2025 +0000
+++ b/macros.xml	Tue Jun 10 13:32:43 2025 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
   <token name="@TOOL_VERSION@">1.0.13</token>
-  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@VERSION_SUFFIX@">1</token>
   <xml name="requirements">
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">squirrel</requirement>
@@ -29,4 +29,4 @@
         </citation>
     </citations>
   </xml>
-</macros>
\ No newline at end of file
+</macros>
diff -r f793ae405fd1 -r 46a0e11a7607 squirrel-phylo.xml
--- a/squirrel-phylo.xml	Tue Mar 11 09:14:19 2025 +0000
+++ b/squirrel-phylo.xml	Tue Jun 10 13:32:43 2025 +0000
@@ -130,7 +130,7 @@
 
     <outputs>
       <!-- standard outputs-->
-      <data name="tree" format="newick" label="${tool.name} - phylogenetic tree" />
+      <data name="tree" format="nexus" label="${tool.name} - phylogenetic tree" />
       <data name="alignment" format="fasta" label="${tool.name} - aligned sequences" />
       <!-- apobec3 outputs-->
       <data name="svg" format="svg" label="${tool.name} - phylotree svg image">
@@ -139,10 +139,10 @@
       <data name="png" format="png" label="${tool.name} - phylotree png image"> 
         <filter>apobec3</filter>
       </data>
-      <data name="aa_recon" format="png" label="${tool.name} - aa mutations ancestral reconstruction">
+      <data name="aa_recon" format="csv" label="${tool.name} - aa mutations ancestral reconstruction">
         <filter>apobec3</filter>
       </data>
-      <data name="branch_snps" format="png" label="${tool.name} - apobec3 nt mutations">
+      <data name="branch_snps" format="csv" label="${tool.name} - apobec3 nt mutations">
         <filter>apobec3</filter>
       </data>
     </outputs>