--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jvarkit/vcffilterso.xml	Fri Feb 27 09:52:06 2015 -0500
@@ -0,0 +1,84 @@
+<?xml version="1.0"?>
+<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterso">
+  <!--Date: 2015-02-27T15:54:06+01:00-->
+  <description>Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology</description>
+  <requirements>
+    <requirement type="binary">java</requirement>
+  </requirements>
+  <command>(gunzip -c ${input} || cat ${input}) | java -cp  $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcffilterso.jar com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology 
+#for  s in $accessions 
+ -A '$s'
+#end for
+$inverse $noreason -o ${output}.vcf.gz  &amp;&amp; mv  ${output}.vcf.gz ${output} </command>
+  <inputs>
+		 <param format="vcf" name="input" type="data" label="VCF input"/> 
+		<repeat name="accessions" title="accessions">
+			 <param name="acn" type="text" label="SO Accession Number">
+			 	<validator type="regex" message="must match with SO:(number)">SO\:[0-9]+</validator>
+			 </param>
+		</repeat>
+		 <param name="inverse" type="boolean" checked="false" label="inverse selection" truevalue="-v" falsevalue=""/>
+		 <param name="noreason" type="boolean" checked="false" label="disable reasoning" truevalue="-d" falsevalue=""/>
+	</inputs>
+  <outputs>
+    <data format="vcf" name="output"/>
+  </outputs>
+  <stdio>
+    <exit_code range="1:"/>
+    <exit_code range=":-1"/>
+  </stdio>
+  <help>
+
+
+**Examples**
+
+
+	
+
+**Inputs**
+
+
+- **VCF input** :  VCF input
+
+- **inverse selection** :  inverse selection
+
+- **disable reasoning** :  disable reasoning
+
+
+**Outputs**
+
+
+- **output** :  output
+
+
+**Wiki**
+
+https://github.com/lindenb/jvarkit/wiki/VcfFilterSequenceOntology
+
+-----
+
+
+**Author**
+
+Pierre Lindenbaum PhD @yokofakun
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite: Pierre Lindenbaum PhD  https://github.com/lindenb/jvarkit
+
+**Contribute**
+
+- Issue Tracker: http://github.com/lindenb/jvarkit/issues`
+- Source Code: http://github.com/lindenb/jvarkit
+
+**License**
+
+The project is licensed under the MIT license.
+
+**Compilation**
+
+Date: 2015-02-27T15:54:06+01:00
+Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
+</help>
+</tool>