changeset 1:6362669c440a draft

planemo upload

--- a/fastMe_main/fastme.xml	Wed Jul 01 10:43:05 2015 -0400
+++ b/fastMe_main/fastme.xml	Fri Oct 02 10:55:52 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="sniplay_fastme" name="FastME" version="1.0.2">
+<tool id="sniplay_fastme" name="FastME" version="1.1.0">
     
     <!-- [REQUIRED] Tool description displayed after the tool name -->
     <description> Calculate distance tree for an alignment file</description>
@@ -6,15 +6,16 @@
     <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
     <requirements>
         <requirement type="binary">perl</requirement>
-	<requirement type="package" version="2.1.4">fastme</requirement>
+	<requirement type="package" version="2.1.4">fastme
+	</requirement>
     </requirements>
     
-    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
-    <version_command>
-<!--
-        tool_binary -v
--->
-    </version_command>
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
     
     <!-- [REQUIRED] The command to execute -->
     <command>
@@ -34,10 +35,13 @@
 	> $fileout_log
     </command>
    
+
+
     <!-- [REQUIRED] Input files and tool parameters -->
     <inputs>
 	<param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
 	<param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
+	<param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" />
 	<param name="model" type="select" label="Evolutionary model" >
 	    <option value="p">p-distance</option>
 	    <option value="Y">RY symetric</option>
@@ -67,12 +71,6 @@
 	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
     </outputs>
     
-    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
-    <stdio>
-        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-    
     <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
     <tests>
         <!-- [HELP] Test files have to be in the ~/test-data directory -->
@@ -124,6 +122,7 @@
 Description
 -----------
 
+
   	FastME - A distance based phylogeny reconstruction algorithm.
 
 	FastME showed better topological accuracy than NJ,
@@ -234,4 +233,23 @@
 
     </help>
     
+    <citations>
+            <!-- [HELP] As DOI or BibTex entry -->
+        <citation type="bibtex">    
+@article{Lefort30062015,
+author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, 
+title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},
+year = {2015}, 
+doi = {10.1093/molbev/msv150}, 
+abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, 
+URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract}, 
+eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html}, 
+journal = {Molecular Biology and Evolution} 
+}
+
+	</citation>
+
+    </citations>
+
+
 </tool>