--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFToolsStats/vcfToolsStats.xml	Thu Feb 26 16:02:46 2015 -0500
@@ -0,0 +1,214 @@
+<tool id="sniplay_vcftoolsstats" name="VCF tools Stats" version="1.0.0">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> </description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+	<requirement type="package" version="0.1.13">VCFtools</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">
+	vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog
+    </command>
+     
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
+	<param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/>
+    </inputs>
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout_annot" format="txt" label="${fileout_label}.annotation" />
+	<data name="fileout_het" format="txt" label="${fileout_label}.het" />
+	<data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" />
+	<data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" />
+	<data name="filelog" format="txt" label="${fileout_label}.log" />
+    </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="sample.vcf" />
+         <output name="fileout_annot" file="result.annotation" />
+         <output name="fileout_het" file="result.het" />
+         <output name="fileout_imiss" file="result.imiss" />
+         <output name="fileout_sum" file="result.TsTv.summary" />
+         <output name="filelog" file="result.log" />
+        </test>
+    </tests>
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+.. class:: infomark
+
+**Authors** 
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep.
+
+---------------------------------------------------
+
+================
+VCF tools filter
+================
+
+-----------
+Description
+-----------
+
+  Compute statistics on VCF file 
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+=========== ========================== =======
+Name            output file(s)         format 
+=========== ========================== =======
+=========== ========================== =======
+
+
+**Downstream tools**
+
+=========== ========================== =======
+Name            output file(s)         format
+=========== ========================== =======
+=========== ========================== =======
+
+
+----------
+Input file
+----------
+
+VCF file
+	VCF file with all SNPs
+
+----------
+Parameters
+----------
+
+Output file basename
+	Prefix for the output VCF file
+
+------------
+Output files
+------------
+
+.annotation file
+	Statistics on annotation/location along genome
+
+.het file 
+	Statistics on heterozygosity of the individuals
+
+.imiss
+	Statistics on missing data of the inidividuals
+.TsTv.summary
+	Statistics on mutation types and transition/transvertion number
+
+.log file
+
+---------------------------------------------------
+
+---------------
+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
+==========
+
+Output name -> vcf_stat
+
+
+Output files
+============
+
+.annotation file
+----------------
+
+::
+
+	Genic	4489
+	Intergenic	466
+	========
+	Intron	960
+	Exon	3248
+	UTR	281
+	========
+	Non-syn	226
+	Synonym	3022
+        
+.het file
+---------
+
+::
+
+	INDV	O(HOM)	E(HOM)	N_SITES	F
+	CATB1	0	0.0	3616	0.00000
+
+.imiss file
+-----------
+
+::
+
+	INDV	N_DATA	N_GENOTYPES_FILTERED	N_MISS	F_MISS
+	CATB1	4813	0	0	0
+
+.TsTv.summary file
+------------------
+
+::
+
+	MODEL	COUNT
+	AC	371
+	AG	1467
+	AT	562
+	CG	330
+	CT	1659
+	GT	397
+	Ts	3126
+	Tv	1660
+
+
+    </help>
+    
+</tool>