From 8c8bceb23396b8ec196f1501ef0af1e7781b2a8d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 16 Dec 2024 10:09:07 +0100
Subject: [PATCH] Fix fasttree tool

---
 tools/fasttree/.lint_skip   | 2 --
 tools/fasttree/fasttree.xml | 9 ++++++++-
 2 files changed, 8 insertions(+), 3 deletions(-)
 delete mode 100644 tools/fasttree/.lint_skip

diff --git a/tools/fasttree/.lint_skip b/tools/fasttree/.lint_skip
deleted file mode 100644
index 48f8d2ba903..00000000000
--- a/tools/fasttree/.lint_skip
+++ /dev/null
@@ -1,2 +0,0 @@
-# the bool is used in a filter and an if statement of the command block which works
-InputsBoolDistinctValues
diff --git a/tools/fasttree/fasttree.xml b/tools/fasttree/fasttree.xml
index ac00fd8bcf0..3352c7eb452 100644
--- a/tools/fasttree/fasttree.xml
+++ b/tools/fasttree/fasttree.xml
@@ -90,7 +90,7 @@ $model_selector.model
                 </conditional>
             </when>
         </conditional>
-        <param name="save_logfile" type="boolean" truevalue="" falsevalue="" checked="false" label="Save log file output" />
+        <param name="save_logfile" type="boolean" checked="false" label="Save log file output" />
         <conditional name="model_selector">
             <param name="format" type="select" label="Protein or nucleotide alignment" help="Specify if the aligned sequences are nucleotide or protein sequences">
                 <option value="-nt">Nucleotide</option>
@@ -154,6 +154,13 @@ $model_selector.model
             <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" />
             <output name="log" file="log.txt" ftype="txt" compare="contains" />
         </test>
+        <test expect_num_outputs="1">
+            <param name="select_format" value="fasta" />
+            <param name="model" value="" />
+            <param name="input" value="aligned.fasta" />
+            <param name="format" value="-nt" />
+            <output name="output" file="tree.nhx" ftype="nhx" lines_diff="2" />
+        </test>
     </tests>
     <help>
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