changeset 6:224c75ad0518 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"

--- a/iqtree.xml	Wed Aug 11 13:42:01 2021 +0000
+++ b/iqtree.xml	Thu Aug 12 07:52:10 2021 +0000
@@ -294,9 +294,9 @@
     -r '$tree_parameters.generating_random.r'
 #end if
 
-$tree_parameters.generating_random.r
-$tree_parameters.generating_random.rand
-
+#if $tree_parameters.generating_random.rand
+    $tree_parameters.generating_random.rand
+#end if
 
 #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
     --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
@@ -426,6 +426,29 @@
                     </when>
                     <when value="false">
                         <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
+                            <help><![CDATA[
+<b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/>
+IQ-TREE also works for codon, binary and morphogical data.
+<table>
+    <tr>
+        <td><i>TESTONLY</i></td>
+        <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td>
+    </tr>
+    <tr>
+        <td><i>TEST</i></td>
+        <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td>
+    </tr>
+    <tr>
+        <td><i>MF</i></td>
+        <td>Best-fit model selection without tree reconstruction.</td>
+    </tr>
+    <tr>
+        <td><i>MFP</i></td>
+        <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
+    </tr>
+</table>
+]]>
+                            </help>
                             <option value="" selected="true">(None)</option>
                             <option value="TESTONLY">Standard model selection</option>
                             <option value="TEST">Standard model selection followed by tree inference</option>
@@ -586,9 +609,11 @@
             </section>
             <section name="generating_random" expanded="False" title="Generating random trees">
                 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
-                <param argument="--rand" type="boolean" truevalue="--rand UNI" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/>
-                <param argument="--rand" type="boolean" truevalue="--rand CAT" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/>
-                <param argument="--rand" type="boolean" truevalue="--rand BAL" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/>
+                <param argument="--rand" type="select" optional="true" label="Random tree creation">
+                    <option value="--rand UNI">Uniform model</option>
+                    <option value="--rand CAT">Random caterpillar tree</option>
+                    <option value="--rand BAL">Random balanced tree</option>
+                </param>
                 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
                 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
                 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
@@ -662,7 +687,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="6">
             <param name="seed" value="1257" />
             <param name="seqtype" value="AA" />
             <param name="s" value="example.phy" />
@@ -707,7 +732,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="6">
             <!-- bootstrap sans model -->
             <param name="seed" value="1257" />
             <param name="seqtype" value="AA" />
@@ -741,7 +766,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="6">
             <!-- model sans bootstrap -->
             <param name="seed" value="1257" />
             <param name="seqtype" value="AA" />
@@ -775,7 +800,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="6">
             <param name="s" value="example.phy" />
             <output name="iqtree">
                 <assert_contents>
@@ -788,7 +813,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="6">
             <param name="s" value="example.phy" />
             <param name="opt_custommodel" value="true" />
             <param name="m" value="GTR+G{0.9}" />
@@ -803,7 +828,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="6">
             <param name="s" value="short.fasta" />
             <param name="short_alignments" value="true" />
             <output name="treefile">