diff iqtree.xml @ 7:524d31add34a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"

--- a/iqtree.xml	Thu Aug 12 07:52:10 2021 +0000
+++ b/iqtree.xml	Fri Aug 13 21:35:49 2021 +0000
@@ -20,6 +20,10 @@
     -s '$general_options.s'
 #end if
 
+#if $general_options.o
+    -o '$general_options.o'
+#end if
+
 ## file
 #if $general_options.t
     -t '$general_options.t'
@@ -363,7 +367,11 @@
     <inputs>
         <section name="general_options" expanded="true" title="General options">
             <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
-            <param type="boolean" name="short_alignments" truevalue="true" falsevalue="false" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />
+            <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
+                <expand macro="sanitize_query" />
+            </param>
+
+            <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />
             <param argument="--seqtype" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
                 <help><![CDATA[
 Note that --seqtype CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
@@ -682,9 +690,12 @@
         <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
         <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
         <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
-        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="">
+        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
             <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
         </data>
+        <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
+            <filter>time_tree['date_source']['select_source'] != 'none'</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="6">
@@ -837,6 +848,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="7">
+            <param name="s" value="dates.fa" />
+            <param name="n" value="100" />
+            <param name="seed" value="122125" />
+            <param name="select_source" value="dataset" />
+            <param name="date" value="dates.tabular" />
+            <output name="timetree">
+                <assert_contents>
+                    <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 IQ-TREE