--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_gwas_inputs/CheckGWASInputs.xml	Wed Feb 07 22:08:47 2018 -0500
@@ -0,0 +1,194 @@
+<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1">
+	<description>checks concordance between input files for GWAS analysis</description>
+
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</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>
+
+	<command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
+    </command>
+	<inputs>
+		<param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
+		<param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
+	</inputs>
+	<outputs>
+		<data format="txt" name="out_hapmap" label="Hapmap output"/>
+		<data format="txt" name="out_trait" label="Trait output"/>
+		<data format="txt" name="stats" label="Logfile and statistics"/>
+	</outputs>
+    
+    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
+    <tests>
+        <!-- [HELP] Test files have to be in the ~/test-data directory -->
+        <!-- [HELP] Multiple tests can be defined with different parameters -->
+        <test>
+         <param name="hapmap" value="gwas-hapmap" />
+         <param name="trait" value="gwas-trait" />
+         <output name="out_hapmap" file="gwas-result.hapmap" />
+         <output name="out_trait" file="gwas-result.trait" />
+         <output name="stats" file="gwas-result.stats" />
+        </test>
+    </tests>
+	<help>
+	
+        <![CDATA[
+
+
+.. class:: infomark
+
+**Authors** South Green
+
+  | **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** South Green.
+
+---------------------------------------------------
+
+
+===============
+CheckGWASInputs
+===============
+
+-----------
+Description
+-----------
+
+  | CheckGWASInputs checks concordance between input files for GWAS analysis.
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tool**
+
+=============== ====================== ===========
+Name            output file(s)         format 
+=============== ====================== ===========
+VCF to Hapmap   Hapmap file	       hapmap
+=============== ====================== ===========
+
+
+
+
+----------
+Input file
+----------
+
+Hapmap file
+	Allelic file in Hapmap format
+
+Trait file
+	Phenotypic file
+
+------------
+Output files
+------------
+
+Hapmap output
+
+Trait output
+
+Logfile and statistics
+
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+Input files
+===========
+
+Hapmap file
+-----------
+
+::
+	
+	rs#	alleles	chrom	pos	strand	assembly#	center	protLSID	assayLSID	panel	QCcode	Ind1	Ind2
+	SNP1	A/T	1	3102	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
+	SNP2	A/T	1	4648	+	assembly	NA	NA	NA	speciesname	NA	AA	AA	AA
+
+Trait file
+----------
+
+::
+	
+	<Trait>	Test
+	Ind1	-2.9985936006411
+	Ind2	-2.68669426456267
+
+Output files
+============
+
+Hapmap output
+-------------
+
+::
+
+        rs#     alleles chrom   pos     strand  assembly#       center  protLSID        assayLSID       panel   QCcode  Ind1    Ind2    Ind3    Ind4
+        SNP1    A/T     1       3102    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      AA
+        SNP2    A/T     1       4648    +       assembly        NA      NA      NA      speciesname     NA      AA      AA      AA      AA      TT
+	
+
+Trait output
+------------
+
+::
+
+        <Trait> Test
+        Ind429  -26.2142525264157
+        Ind373  12.0306115988504
+        Ind81   1.98118654229534
+
+Logfile and statistics
+----------------------
+
+::
+
+
+        ==============================================
+        Individuals
+        ==============================================
+        Individuals in hapmap file: 500
+        Individuals in trait file: 500
+        Individuals found in both files: 500
+        ==============================================
+        Markers
+        ==============================================
+        Discarded markers:
+        Monomorphic: 0
+        Not biallelic: 0
+        Modified markers:
+        Difference in variation: 0
+
+        ]]>
+
+	
+	</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>