# HG changeset patch
# User crique
# Date 1462632715 14400
# Node ID a09846dcba83e0dd552111343d9487fd4026278b

Uploaded

diff -r 000000000000 -r a09846dcba83 phyml.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyml.xml	Sat May 07 10:51:55 2016 -0400
@@ -0,0 +1,127 @@
+<tool id="phyml" name="PhyML" version="0.1.0">
+  <description> Phylogeny software based on the maximum-likelihood principle </description>
+  <requirements> 
+	<package name="phyml" version="3.1"/>
+  </requirements>
+  <command><![CDATA[
+  ln -sf $input input_phy;
+ 
+  phyml -i input_phy
+	 $format
+
+	 -n $nb_data_set
+	 -d $type.type_of_seq
+
+	#if ($type.type_of_seq == "nt"):
+		-t $type.tstv
+	#end if
+	
+	-m $type.model
+
+	#if (str($bs.bootstrap) in ['0','-1','-2','-4']):
+                    -b $bs.bootstrap
+        #elif (str($bs.bootstrap) == '1'):
+                    -b $bs.bootstrap.replicate_num
+        #end if
+
+	-f $character_freq
+	-v $prop_invar
+	-c $nb_subst_cat
+	-a $gamma
+	-s $search_move
+	-o $optimisation_parameter
+
+	> ${stdout_output};
+  ]]>
+  </command>
+  <inputs>
+   	<param name="input" format="txt" type="data" label="Source file" help="Select the input file"/> 
+   	<param name="format" type="select" label="Choose between interleaved format or sequential format" display="radio">
+		<option value="">Interleaved</option>
+		<option value="--sequential">Sequential</option>
+   	</param> 
+   	<param name="nb_data_set" type="integer" value="1" label="Number of data sets"/>
+   
+	<conditional name="type">
+   		<param name="type_of_seq" type="select"  label="Data type" help="Select between nucleic acids or amino acids" display="radio">
+			<option value="nt">Nucleic acids</option>
+        		<option value="aa">Amino acids</option>
+   		</param>
+   		<when value="nt">
+   			<param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Can be a fixed positive value or type 'e' to get the maximum likelihood estimate"/>
+			<param name="model" type="select" label="Nucleotide-based models" display="radio">
+				<option value="HKY85">HKY85</option>
+               		 	<option value="JC69">JC69</option>
+                		<option value="K80">K80</option>
+                		<option value="F81">F81</option>
+                		<option value="F84">F84</option>
+                		<option value="TN93">TN93</option>
+                		<option value="GTR">GTR</option>
+        		</param>
+   		</when>
+
+   		<when value="aa">
+			<param name="model" type="select" label="Amino-acid based models" display="radio">
+				<option value="LG">LG</option>
+                		<option value="WAG">WAG</option>
+                		<option value="JTT">JTT</option>
+                		<option value="MtREV">MtREV</option>
+                		<option value="Dayhoff">Dayhoff</option>
+                		<option value="DCMut">DCMut</option>
+                		<option value="RtREV">RtREV</option>
+                		<option value="CpREV">CpREV</option>
+                		<option value="VT">VT</option>
+                		<option value="Blosum62">Blosum62</option>
+                		<option value="MtMam">MtMam</option>
+                		<option value="MtArt">MtArt</option>
+                		<option value="HIVw">HIVw</option>
+                		<option value="HIVb">HIVb</option>
+			</param>            
+   		</when>
+	</conditional>
+
+   	<conditional name="bs">
+   		<param name="bootstrap" type="select" min="1" value="100" label="Branch supports" display="radio"> 
+        		<option value="0">No bootstrap</option>
+        		<option value="1">Number of bootstrap</option>
+        		<option value="-1">Likelihood ratio test using aLRT statistics</option>
+        		<option value="-2">Likelihood ratio test using Chi2</option>
+        		<option value="-4" selected='true'>SH-like</option>
+   		</param>  
+   		<when value="1">
+        		<param name="replicate_num" type="integer" min="1" value="100" label="Number of bootstrap replicates"/>
+   		</when>
+	</conditional>
+
+	<param name="character_freq" type="select" label="Character frequencies" display="radio"> 
+            	<option value="e">Empirical</option> 
+            	<option value="m">ML/Model</option>
+   	</param>
+   	<param name="prop_invar" type="text" value="e" label="Proportion of invariable sites" help="Can be a fixed value in the [0,1] range or type 'e' to get the maximum likelihood estimate"/>
+   	<param name="nb_subst_cat" type="integer" min="1" value="4" label="Number of relative substitution rate categories" help="Must be a positive integer"/>
+   	<param name="gamma"  type="text" value="e" label="Value of the gamma shape parameter" help="Can be a fixed positive value or 'e' to get the maximum likelihood estimate"/>
+   	<param name="search_move" type="select" label="Tree topology search operation option" display="radio">
+		<option value="NNI">NNI</option>
+        	<option value="SPR">SPR</option>
+        	<option value="BEST">Best of NNI and SPR search</option>
+   	</param>
+   	<param name="optimisation_parameter" type="select" label="Optimise topology" display="radio">
+		<option value="tlr">Tree topology, branch length and substitution rate parameters</option>
+        	<option value="tl">Tree topology and branch lengths</option>
+        	<option value="lr">Branch lengths and substitution rate parameters</option>
+        	<option value="l">Branch lengths</option>
+        	<option value="r">Substitution rate parameters</option>
+        	<option value="n">No parameter is optimized</option>
+   	</param>
+  </inputs>
+
+  <outputs>
+   	<data name="output_tree" format="txt" label="Output_tree" from_work_dir="*_phyml_tree.txt"/>
+   	<data name="output_stats" format="txt" label="Output_stats" from_work_dir="*_phyml_stats.txt"/>
+   	<data name="stdout_output" label="Output_stdout" format="txt"/>
+  </outputs>
+
+</tool>
+
+
+