<?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>