# HG changeset patch
# User iuc
# Date 1638006309 0
# Node ID 9b892d7f82cccb438ca3787bb3419e1712724048
# Parent  563c3aa769f2149d4ab64efaf19adcc5da93cfd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"

diff -r 563c3aa769f2 -r 9b892d7f82cc iqtree.xml
--- a/iqtree.xml	Mon Sep 27 15:55:35 2021 +0000
+++ b/iqtree.xml	Sat Nov 27 09:45:09 2021 +0000
@@ -1,7 +1,6 @@
-<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" >
+<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
     <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">galaxy2</token>
         <import>iqtree_macros.xml</import>
     </macros>
     <expand macro="requirements" />
@@ -23,7 +22,7 @@
 #if $general_options.o
     -o '$general_options.o'
 #end if
-
+--seqtype $general_options.seqtype
 ## file
 #if $general_options.t
     -t '$general_options.t'
@@ -545,22 +544,22 @@
                     </param>
                     <when value="none" />
                     <when value="p">
-                        <param argument="-p" type="data" format="nex" optional="true" label="Partition file" />
+                        <param argument="-p" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
                         <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
                         <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
                     </when>
                     <when value="q">
-                        <param argument="-q" type="data" format="nex" optional="true" label="Partition file" />
+                        <param argument="-q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
                         <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
                         <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
                     </when>
                     <when value="Q">
-                        <param argument="-Q" type="data" format="nex" optional="true" label="Partition file" />
+                        <param argument="-Q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
                         <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
                         <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
                     </when>
                     <when value="S">
-                        <param argument="-S" type="data" format="nex" optional="true" label="Partition file" />
+                        <param argument="-S" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
                         <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
                         <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
                     </when>
@@ -705,7 +704,7 @@
     <tests>
         <test expect_num_outputs="5">
             <param name="seed" value="1257" />
-            <param name="seqtype" value="AA" />
+            <param name="seqtype" value="DNA" />
             <param name="s" value="example.phy" />
             <param name="m" value="TEST" />
             <param name="msub" value="nuclear" />
@@ -751,7 +750,7 @@
         <test expect_num_outputs="5">
             <!-- bootstrap sans model -->
             <param name="seed" value="1257" />
-            <param name="seqtype" value="AA" />
+            <param name="seqtype" value="DNA" />
             <param name="s" value="example.phy" />
             <!-- <param name="m" value="TESTONLY" /> -->
             <param name="msub" value="nuclear" />
@@ -785,7 +784,7 @@
         <test expect_num_outputs="5">
             <!-- model sans bootstrap -->
             <param name="seed" value="1257" />
-            <param name="seqtype" value="AA" />
+            <param name="seqtype" value="DNA" />
             <param name="s" value="example.phy" />
             <param name="m" value="TESTONLY" />
             <param name="msub" value="nuclear" />
diff -r 563c3aa769f2 -r 9b892d7f82cc iqtree_macros.xml
--- a/iqtree_macros.xml	Mon Sep 27 15:55:35 2021 +0000
+++ b/iqtree_macros.xml	Sat Nov 27 09:45:09 2021 +0000
@@ -1,5 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.1.2</token>
+    <token name="@VERSION_SUFFIX@">2</token>
 
     <xml name="requirements">
         <requirements>