diff fastme.xml @ 2:40200a22dba3 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastme.xml	Fri Dec 11 09:16:34 2015 -0500
@@ -0,0 +1,252 @@
+<tool id="sniplay_fastme" name="Fassqa" version="1.1.0">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> Calculate distance tree for an alignment file</description>
+    
+    <!-- [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>
+    </requirements>
+    
+    <!-- [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>
+	fastme --input_data=$input_data --dna=$model --output_tree=$fileout 
+	#if str( $distance ) == "SPR":
+	--spr
+	#elif str( $distance )[:3] == "NNI"  :
+	  #if str( $distance ) == "NNI_B" :
+           --nni=B
+          #else :
+           --nni=O
+          #end if
+
+	#else :
+	--method=$distance
+	#end if
+	> $fileout_log
+    </command>
+   
+
+
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />
+	<param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />
+	<param name="model" type="select" label="Evolutionary model" >
+	    <option value="p">p-distance</option>
+	    <option value="Y">RY symetric</option>
+	    <option value="R">RY</option>
+	    <option value="J">JC69</option>
+	    <option value="K">K2P</option>
+	    <option value="1">F81</option>
+	    <option value="4" selected="true">F84</option>
+	    <option value="T">TN93</option>
+	    <option value="L">LogDet</option>
+        </param>
+	<param name="distance" type="select" label="Distance methode" >
+	    <option value="B">TaxAdd_BalME</option>
+	    <option value="O">TaxAdd_OLSME</option>
+	    <option value="I" selected="true">BIONJ</option>
+	    <option value="N">NJ</option>
+	    <option value="U">UNJ</option>
+	    <option value="NNI_B">NNI_BalME</option>
+	    <option value="NNI_O">NNI_OLS</option>
+	    <option value="SPR">SPR</option>
+        </param>
+    </inputs> 
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+    </outputs>
+    
+    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
+    <tests>
+        <!-- [HELP] Test files have to be in the ~/test-data directory -->
+
+        <test>
+         <param name="input_data" value="phylip" />
+	 <param name="model" value="4"/>
+	 <param name="distance" value="I"/>
+         <output name="fileout" file="newick" />
+        </test>
+
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+<!--
+        <test>
+        </test>
+-->
+    </tests>
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+.. class:: infomark
+
+**Authors** 
+
+ | Richard Desper and Olivier Gascuel,
+ |	Journal of Computational Biology 19(5), 687-705, 2002.
+ |	Molecular Biology and Evolution 21(3), 587-598, 2004.
+ |	Please cite these papers if you use this software in your publications.
+
+
+.. class:: infomark
+
+**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]
+
+---------------------------------------------------
+
+
+======
+FastMe
+======
+
+-----------
+Description
+-----------
+
+
+  	FastME - A distance based phylogeny reconstruction algorithm.
+
+	FastME showed better topological accuracy than NJ,
+	BIONJ, WEIGHBOR and FITCH, in all evolutionary
+	conditions we tested, which include large range
+	deviations from molecular clock and substitution rates.
+
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+=========== ========================== =======
+Name            output file(s)         format 
+=========== ========================== =======
+Readseq     phylip conversion          phylip 
+=========== ========================== =======
+
+
+**Downstream tools**
+
+=========== ========================== =======
+Name            output file(s)         format
+=========== ========================== =======
+Rooting     out tree                   Newick 
+=========== ========================== =======
+
+
+----------
+Input file
+----------
+
+Phylip file 
+	Phylip file with sequence alignments
+	
+
+----------
+Parameters
+----------
+
+Output name
+        Output base name for the ouput files
+
+Evolutionary model
+	Indicate the evolutionary [model] which can be choosen from:p-distance, RY symmetric, RY, JC69, K2P, F81, F84 (default), TN93, LogDet.
+
+Distance methode
+	FastME computes a tree using a distance algorithm. You may choose this method/topologie from: TaxAdd_BalME, TaxAdd_OLSME, BIONJ (default), NJ, UNJ, NNI_BalME, NNI_OLS or SPR
+
+------------
+Output files
+------------
+
+Output_name
+	Resulting tree at Newick format 
+
+Output_name.log
+	Log file
+
+------------
+Dependencies
+------------
+FastME
+	http://www.atgc-montpellier.fr/fastme
+ 	
+
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Philip file
+-----------
+
+::
+
+	168 5125
+	IRAT112      GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AGTAATAAAG TAATACTAAT
+	KARASUKARA   GAGAACCGTC CTGTAAGTAC TCTTGCTTTA AATACGAAAG TAATACTAAT
+
+Parameters
+==========
+
+Output name -> Newick tree
+
+Evolutionary model -> F84
+
+Distance methode -> BIONJ
+
+Output files
+============
+
+Newick tree
+-----------
+
+::
+
+	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
+	
+
+    </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>