<tool id="snpSift_filter" name="SnpSift Filter" version="3.2">
	<options sanitize="False" />
	<description>Filter variants using arbitrary expressions</description>
	<requirements>
                <requirement type="package" version="3.2">snpEff</requirement>
	</requirements>
	<command>
		java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass 
                #if $filterId and len($filterId.__str__.strip()) > 0:
			--filterId = "$filterId"
                #end if
                #if $addFilter and len($addFilter.__str__.strip()) > 0:
			--addFilter = "$addFilter"
                #end if
                #if $rmFilter and len($rmFilter.__str__.strip()) > 0:
			--rmFilter = "$rmFilter"
                #end if
 		> $output
	</command>
	<inputs>
		<param format="vcf" name="input" type="data" label="VCF input"/>
		<param name="expr" type="text" label="Expression" size="120"/>
		<param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/>
		<param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/>
		<param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/>
		<param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
		<param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
	</inputs>
	<configfiles>
		<configfile name="exprFile">
		$expr
		</configfile> 
	</configfiles>

	<outputs>
		<data format="vcf" name="output" />
	</outputs>
        <stdio>
          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
          <exit_code range="1:"  level="fatal"   description="Error" />
        </stdio>

        <tests>

            <test>
                <param name="input" ftype="vcf" value="test01.vcf"/>
                <param name="expr" value="QUAL >= 50"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="28837706" />
                        <not_has_text text="NT_166464" />
                    </assert_contents>
                </output>
            </test>

            <test>
                <param name="input" ftype="vcf" value="test01.vcf"/>
                <param name="expr" value="(CHROM = '19')"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="3205820" />
                        <not_has_text text="NT_16" />
                    </assert_contents>
                </output>
            </test>

            <test>
                <param name="input" ftype="vcf" value="test01.vcf"/>
                <param name="expr" value="(POS >= 20175) &amp; (POS &lt;= 35549)"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="20175" />
                        <has_text text="35549" />
                        <has_text text="22256" />
                        <not_has_text text="18933" />
                        <not_has_text text="37567" />
                    </assert_contents>
                </output>
            </test>

            <test>
                <param name="input" ftype="vcf" value="test01.vcf"/>
                <param name="expr" value="( DP >= 5 )"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="DP=5;" />
                        <has_text text="DP=6;" />
                        <not_has_text text="DP=1;" />
                    </assert_contents>
                </output>
            </test>

        </tests>

	<help>

**SnpSift filter**

You can filter ia vcf file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.

Some examples:

  - *I want to filter out samples with quality less than 30*:

    * **( QUAL &gt; 30 )**

  - *...but we also want InDels that have quality 20 or more*:

    * **(( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**

  - *...or any homozygous variant present in more than 3 samples*:

    * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**

  - *...or any heterozygous sample with coverage 25 or more*:

    * **((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**

  - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:

    * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**


For complete details about this tool and epressions that can be used, please go to http://snpeff.sourceforge.net/SnpSift.html#filter

	</help>
</tool>