diff iqtree.xml @ 4:f97743d52b87 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"

--- a/iqtree.xml	Wed Jan 29 16:34:20 2020 -0500
+++ b/iqtree.xml	Fri Apr 03 09:04:30 2020 -0400
@@ -4,10 +4,14 @@
         <import>iqtree_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors='exit_code' ><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
 iqtree
     -pre PREF
-    -nt \${GALAXY_SLOTS:-10}
+    #if $general_options.short_alignments:
+        -nt 1
+    #else:
+        -nt \${GALAXY_SLOTS:-10}
+    #end if
     -redo
 
 ## file
@@ -268,12 +272,12 @@
 #if str($miscellaneous_options.fconst) != ''
     -fconst '$miscellaneous_options.fconst'
 #end if
-
 ]]>
     </command>
     <inputs>
-        <section name="general_options" expanded="True" title="General options">
+        <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="-st" 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 -st 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.
@@ -498,12 +502,12 @@
         </section>
     </inputs>
     <outputs>
-        <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
-        <data name='treefile' format='nhx' from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
-        <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
-        <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
-        <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
-        <data name='iqtree' format='iqtree' from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
+        <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
+        <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
+        <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
+        <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
+        <data name="splits.nex" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
+        <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
     </outputs>
     <tests>
         <test>
@@ -515,35 +519,35 @@
             <param name="madd" value="LG4M,LG4X" />
             <param name="merit" value="AICc" />
             <param name="bb" value="1000" />
-            <output name='bionj'>
+            <output name="bionj">
                 <assert_contents>
                     <has_text_matching expression=".*Human.*Whale.*" />
                 </assert_contents>
             </output>
-            <output name='iqtree'>
+            <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
                 </assert_contents>
             </output>
-            <output name='mldist'>
+            <output name="mldist">
                 <assert_contents>
                     <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
                     <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
                     <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
                 </assert_contents>
             </output>
-            <output name='treefile'>
+            <output name="treefile">
                 <assert_contents>
                     <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                 </assert_contents>
             </output>
-            <output name='contree' >
+            <output name="contree">
                 <assert_contents>
                     <has_line_matching
                         expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
                 </assert_contents>
             </output>
-            <output name='splits.nex'>
+            <output name="splits.nex">
                 <assert_contents>
                     <has_line line="BEGIN Splits;" />
                     <has_line line="END; [Splits]" />
@@ -573,12 +577,12 @@
             <param name="nstep" value="100" />
             <param name="beps" value="0.5" />
             <param name="b" value="2" />
-            <output name='iqtree'>
+            <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                 </assert_contents>
             </output>
-            <output name='treefile'>
+            <output name="treefile">
                 <assert_contents>
                     <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                 </assert_contents>
@@ -607,45 +611,49 @@
             <param name="nstep" value="100" />
             <param name="beps" value="0.5" />
             <!-- <param name="b" value="100" /> -->
-            <output name='iqtree'>
+            <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
                 </assert_contents>
             </output>
-            <output name='treefile'>
+            <output name="treefile">
                 <assert_contents>
                     <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name='s' value='example.phy' />
-            <output name='iqtree'>
+            <param name="s" value="example.phy" />
+            <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression=".*Human.*Whale.*" />
                 </assert_contents>
             </output>
-            <output name='treefile'>
+            <output name="treefile">
                 <assert_contents>
                     <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name='s' value='example.phy' />
-            <param name='opt_custommodel' value='true' />
-            <param name='m' value='GTR+G{0.9}' />
-            <output name='iqtree'>
+            <param name="s" value="example.phy" />
+            <param name="opt_custommodel" value="true" />
+            <param name="m" value="GTR+G{0.9}" />
+            <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression=".*Human.*Whale.*" />
                 </assert_contents>
             </output>
-            <output name='treefile'>
+            <output name="treefile">
                 <assert_contents>
                     <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="s" value="short.fasta" />
+            <param name="short_alignments" value="true" />
+        </test>
     </tests>
     <help><![CDATA[
 IQ-TREE