--- a/fasttree.xml	Tue Aug 31 08:07:18 2021 +0000
+++ b/fasttree.xml	Sat Oct 05 10:02:31 2024 +0000
@@ -1,12 +1,11 @@
-<?xml version="1.0"?>
-<tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy2" profile="18.01">
+<tool id="fasttree" name="FASTTREE" version="@VERSION@+galaxy3" profile="23.1">
     <description>build maximum-likelihood phylogenetic trees</description>
+    <macros>
+        <token name="@VERSION@">2.1.10</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">fasttree</xref>
     </xrefs>
-    <macros>
-        <token name="@VERSION@">2.1.10</token>
-    </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">fasttree</requirement>
     </requirements>
@@ -48,7 +47,6 @@
 #if $save_logfile:
     2> '$log'
 #end if
-
 ]]>
     </command>
     <inputs>
@@ -59,7 +57,7 @@
             </param>
             <when value="fasta">
                 <param format="fasta" name="input" type="data" multiple="false" label="FASTA file"/>
-                <param name="quote" argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." />
+                <param argument="-quote" type="boolean" truevalue="-quote" falsevalue="" checked="false" label="Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree." help="This tool is only available for fasta input only; FastTree will not be able to read these trees back in." />
                 <conditional name="intree_selector">
                     <param name="intree_format" type="select" label="Set starting tree(s)">
                         <option value="none" selected="true">No starting trees</option>
@@ -134,9 +132,9 @@
                 <param value="gamma" argument="-gamma" type="boolean" truevalue="-gamma" falsevalue="" checked="false" label="Use Gamma20" help="After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood." />
                 <param value="nosupport" argument="-nosupport" type="boolean" truevalue="-nosupport" falsevalue="" checked="false" label="Eliminates the support value computation. Support value computation is not recommended for wide alignments."/>
                 <param name="likelihood" argument="-noml" type="boolean" truevalue="-noml" falsevalue="" checked="false" label = "Turn off maximum-likelihood." />
-                <param name="fastest" argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" />
-                <param name="pseudo" argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." />
-                <param name="mllen" argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." />
+                <param argument="-fastest" type="boolean" truevalue="-fastest" falsevalue="" checked="false" label="Speed up the neighbor joining phase and reduce memory usage (recommended for >50,000 sequences)" />
+                <param argument="-pseudo" type="boolean" truevalue="-pseudo" falsevalue="" checked="false" label="Use pseudocounts" help="Recommended for highly gapped/fragmentary sequences." />
+                <param argument="-mllen" type="boolean" truevalue="-mllen" falsevalue="" checked="false" label="Optimize branch lengths without ML NNIs." />
             </when>
         </conditional>
     </inputs>
@@ -147,7 +145,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="select_format" value="fasta" />
             <param name="model" value="" />
             <param name="input" value="aligned.fasta" />