diff Rooting/rooting.xml @ 1:420b57c3c185 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Rooting/rooting.xml	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,193 @@
+<tool id="sniplay_rooting" name="Rooting" version="1.0.2">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> Midpoint rooting of newick tree </description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+	<requirement type="package">Rootings_54.jar</requirement>
+    </requirements>
+    
+    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
+    <version_command>
+<!--
+        tool_binary -v
+-->
+    </version_command>
+    
+    <!-- [REQUIRED] The command to execute -->
+    <command interpreter="perl">
+	Rooting.pl -i $filein -o $fileout &amp;&amp; mv ${filein}.rooting.log $fileout_log
+    </command>
+   
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" />
+	<param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
+    </inputs> 
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+    </outputs>
+    
+    <!-- [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 -->
+
+        <test>
+         <param name="filein" value="newick" />
+         <output name="fileout" file="out_tree" />
+	 <output name="fileout_log" file="out_tree.log" />
+        </test>
+
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+<!--
+        <test>
+        </test>
+-->
+    </tests>
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+
+.. class:: infomark
+
+**Authors** Jean-François Dufayard, CIRAD, South Green platform
+
+
+.. 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]
+
+.. class:: infomark
+
+**Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
+
+---------------------------------------------------
+
+
+
+
+=======
+Rooting
+=======
+
+-----------
+Description
+-----------
+
+  Compute a midpoint newick rooted tree.
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tool**
+
+=========== ========================== =======
+Name            output file(s)         format 
+=========== ========================== =======
+fastme      Newick tree                Newick 
+=========== ========================== =======
+
+
+
+----------
+Input file
+----------
+
+Newick file
+	
+
+----------
+Parameters
+----------
+
+Output name
+        Output base name for the ouput files
+
+
+------------
+Output files
+------------
+
+Output_name
+	Resulting tree rooted in newick format
+
+Output_name.log
+	Log file
+
+------------
+Dependencies
+------------
+Rooting
+	CIRAD tool. Contact [e-mail]
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Newick file
+-----------
+
+::
+	
+	(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
+
+
+Parameters
+==========
+
+Output name -> out tree
+
+
+Output files
+============
+
+out tree
+--------
+
+::
+
+	(ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
+	
+
+    </help>
+    <citations>
+        <!-- [HELP] As DOI or BibTex entry -->
+    	<citation type="bibtex">@article{Dereeper03062015,
+author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 
+title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
+year = {2015}, 
+doi = {10.1093/nar/gkv351}, 
+abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, 
+URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, 
+eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, 
+journal = {Nucleic Acids Research} 
+}
+
+    	</citation>
+
+    </citations>
+    
+</tool>