--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml	Mon May 23 17:49:17 2016 -0400
@@ -0,0 +1,204 @@
+<tool id="sniplay_density" name="SNP density" version="2.0.0">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> Calculate SNP densities along chromosome from a VCF input</description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+	<requirement type="package" version="0.1.12b">vcftools</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>
+
+    <!-- [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="bash">
+	calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step
+    </command>
+
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
+	<param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
+	<param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
+    </inputs>
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout" type="data" format="txt" label="${fileout_label}" />
+	<data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" />
+    </outputs>
+
+    <tests>
+        <test> 
+         <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
+         <param name="step" value="20000" />
+         <output name="fileout" file="SNPden-result.txt" />
+         <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
+        </test>
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+<!--
+        <test>
+        </test>
+-->
+    </tests>
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+.. class:: infomark
+
+**Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform 
+
+ | **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).
+
+
+.. 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 support.abims@sb-roscoff.fr
+
+---------------------------------------------------
+
+
+
+=============
+SNP densities
+=============
+
+-----------
+Description
+-----------
+
+  Calculate SNP densities along chromosome from a VCF file
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tool**
+
+=============== ====================== ===========
+Name            output file(s)         format 
+=============== ====================== ===========
+=============== ====================== ===========
+
+
+----------
+Input file
+----------	
+
+VCF file
+	File with SNPs
+
+
+----------
+Parameters
+----------
+
+Step
+        Step in bp for the window to calculate SNP density
+
+Output name
+        Output base name for the two ouput files
+
+
+------------
+Output files
+------------
+
+Output_name
+	Tabular file with SNP density in each postion 
+
+Output_name.by_sample
+	Tabular file with SNP density for each sample
+
+	
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+vcf file
+-----------
+
+::
+
+	#fileformat=VCFv4.1
+	#FILTER=&lt;ID=LowQual,Description="Low quality">
+	#FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+	[...]
+	CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CATB1
+	chr1	2209	.	G	T	213.84	.	AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|)	GT:AD:DP:GQ:PL	1/1:0,7:7:18:242,18,0
+
+Parameters
+==========
+
+Step -> 200000
+
+Output name -> densities
+
+
+Output files
+============
+
+densities
+---------
+
+::
+
+	Chromosome Position SNPs
+	chr1       200000   355
+	chr1       400000   228
+	chr1       600000   63
+	chr1       800000   191
+
+
+densities.by_sample
+-------------------
+
+::
+
+	Chromosome BA58 BA59 BD54
+	chr1       220  197  225
+	chr1       130  119  133
+	chr1       43   43   40
+	chr1       139  167  141
+
+    </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>