# HG changeset patch
# User iuc
# Date 1531244140 14400
# Node ID 72b8ce355fae778e9154814fdd19e820e0e5d247

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797

diff -r 000000000000 -r 72b8ce355fae macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,57 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">varscan</requirement>
+            <requirement type="package" version="4.2.1">gawk</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@VERSION@">2.4.3</token>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
+            <regex match=".*" source="both" level="log" description="tool progress"/>
+        </stdio>
+        <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/gr.129684.111</citation>
+        </citations>
+    </xml>
+
+    <xml name="min_coverage">
+        <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
+            label="Minimum read depth" help="Minimum depth at a position to make a call"/>
+    </xml>
+    <xml name="min_reads2">
+        <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
+            label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
+    </xml>
+    <xml name="min_avg_qual">
+        <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
+            label="Minimum base quality at a position to count a read"/>
+    </xml>
+    <xml name="min_var_freq" token_value="0.01">
+        <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
+            label="Minimum variant allele frequency threshold"/>
+    </xml>
+    <xml name="min_freq_for_hom">
+        <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
+            label="Minimum frequency to call homozygote"/>
+    </xml>
+    <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01">
+        <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0"
+            label="@LABEL@"/>
+    </xml>
+    <xml name="strand_filter">
+        <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
+            <option value="no" selected="True">no</option>
+            <option value="yes">yes</option>
+        </param>
+    </xml>
+
+</macros>
diff -r 000000000000 -r 72b8ce355fae test-data/N_Region_Chr1_CDKN2C.pileup.gz
Binary file test-data/N_Region_Chr1_CDKN2C.pileup.gz has changed
diff -r 000000000000 -r 72b8ce355fae test-data/T_Region_Chr1_CDKN2C.pileup.gz
Binary file test-data/T_Region_Chr1_CDKN2C.pileup.gz has changed
diff -r 000000000000 -r 72b8ce355fae test-data/test_in1.pileup
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_in1.pileup	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,13 @@
+chr1	10087	a	41	..+1C...........,,,,,.....C..C,...,..,,..c,.+1C	A9D<<#C#<(C9ACAFF<?D>=(#;D#;AF=7898.GJ'6I
+chr1	10088	c	41	.......T.....,,,,,.........,..A,..,,..,,.	2BBB<#B#A5?5?GJ;JD?@A?;#6B#HEG)GBBIB>IEE!
+chr1	10089	c	41	.............,,,,,.........,...,..,,..,,.	8BBB<#D#?5A9AHJ;IFBBB??#6A#FEG8C=>H?FJ@C$
+chr1	10090	c	41	.............,,,,,.........,...,..,,..,,.	2#AB(#9#9(A<<GJEHEBBDA?#;;#D?H@5=CF1HJ;D'
+chr1	10091	t	41	.............,,,,,A........,...,..,,..,,.	(#(?5#,#<(?<?FIAF;(D=B9#;@#?#G8-=F=<CJ6BI
+chr1	10092	a	41	.............,,,,,.........,...,..,,..,,.	9#9C<#5#9,5(<FH:GE9C?<?#3A#:#A@B8CC5EI=?J
+chr1	10093	a	41	.............,,,,,.........,...c..,c..,,.	?#<DC#9#99?39CFEFC?D<(C#,C#1#HE'7G8'>I);J
+chr1	10094	c	41	.............,,,,,.....G...,...,..,,..,,T	?#?B?#?#<8A8ABJBIG9D?9<#,?#F#IHH(AIGEHGH6
+chr1	10095	c	41	A............,,,,,.........,...,..,,..,,.	##8B<#A#??B8<EJCJB7BAAA#5B#>#>=F(@HHCIBH6
+chr1	10096	c	41	.............,,,,,........A,...,..,,..,,.	##ADA#B#18B?AHI<IE<AA?D#<;#C#E6B=FGCCIBE9
+chr1	10097	t	41	.............,,,,,.........,..C,..,,..-1A,,-1a.	##(B8#B#8(BB?AFAH:(B2??#<?#8#E'6;;B6@J8@J
+chr1	10098	a	41	.............,,,,,.........,...,..,,.*,*.	##3C9#3#9999AFH2H;9D<C?#C3#?#E5?DAD@D!=$J
+chr1	10099	a	41	.............,,,,,.........,...c..,,..,,.	##<D<#9#<9?<9FD+DF9CAA?#39#1#H?)C>9.D!.$J
diff -r 000000000000 -r 72b8ce355fae test-data/varscan_copynumber_result1.interval
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/varscan_copynumber_result1.interval	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,9 @@
+chrom	chr_start	chr_stop	num_positions	normal_depth	tumor_depth	log2_ratio	gc_content
+chr1	51436045	51436144	100	26.9	25.9	-0.052	51.0
+chr1	51436145	51436214	70	27.6	30.3	0.134	45.7
+chr1	51439427	51439526	100	31.1	29.3	-0.086	36.0
+chr1	51439527	51439626	100	85.3	86.0	0.012	44.0
+chr1	51439627	51439726	100	107.2	108.0	0.011	46.0
+chr1	51439727	51439826	100	70.8	80.3	0.183	58.0
+chr1	51439827	51439926	100	46.3	53.3	0.202	60.0
+chr1	51439927	51439960	34	27.5	35.9	0.383	52.9
diff -r 000000000000 -r 72b8ce355fae test-data/varscan_mpileup_result1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/varscan_mpileup_result1.vcf	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,26 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
+##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
+##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
+##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
+##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
+##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
+##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
+chr1	10087	.	A	AC	.	PASS	ADP=33;WT=0;HET=1;HOM=0;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:41:33:31:2:6.06%:9.8E-1:30:32:22:9:2:0
+chr1	10097	.	TA	T	.	PASS	ADP=30;WT=0;HET=1;HOM=0;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	0/1:0:41:30:28:2:6.67%:9.8E-1:29:36:18:10:1:1
diff -r 000000000000 -r 72b8ce355fae test-data/varscan_somatic_indel_result1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/varscan_somatic_indel_result1.vcf	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,18 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
diff -r 000000000000 -r 72b8ce355fae test-data/varscan_somatic_snp_result1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/varscan_somatic_snp_result1.vcf	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,41 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr1	51436072	.	C	A	.	PASS	DP=47;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.4681E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:26:26:0:0%:23,3,0,0	0/1:.:21:20:1:4.76%:19,1,1,0
+chr1	51436311	.	T	C	.	PASS	DP=16;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.375E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:9:9:0:0%:1,8,0,0	0/1:.:7:6:1:14.29%:0,6,0,1
+chr1	51436320	.	G	A	.	PASS	DP=19;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2632E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:9:9:0:0%:1,8,0,0	0/1:.:10:9:1:10%:0,9,0,1
+chr1	51439628	.	T	C	.	str10	DP=237;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.8101E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:123:123:0:0%:77,46,0,0	0/1:.:114:113:1:0.88%:74,39,0,1
+chr1	51439638	.	G	A	.	str10	DP=234;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9145E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:119:119:0:0%:72,47,0,0	0/1:.:115:114:1:0.87%:75,39,0,1
+chr1	51439665	.	C	T	.	PASS	DP=226;SOMATIC;SS=2;SSC=9;GPV=1E0;SPV=1.2006E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:114:114:0:0%:56,58,0,0	0/1:.:112:109:3:2.68%:63,46,2,1
+chr1	51439671	.	G	A	.	str10	DP=222;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.045E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:110:110:0:0%:53,57,0,0	0/1:.:112:111:1:0.89%:59,52,1,0
+chr1	51439684	.	G	T	.	str10	DP=210;SOMATIC;SS=2;SSC=3;GPV=1E0;SPV=4.9524E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:106:106:0:0%:51,55,0,0	0/1:.:104:103:1:0.96%:53,50,1,0
+chr1	51439703	.	C	T	.	str10	DP=202;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.099E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:99:99:0:0%:46,53,0,0	0/1:.:103:102:1:0.97%:48,54,0,1
+chr1	51439705	.	G	T	.	str10	DP=204;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1961E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:98:98:0:0%:42,56,0,0	0/1:.:106:105:1:0.94%:48,57,0,1
+chr1	51439706	.	G	T	.	str10	DP=201;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1741E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:97:97:0:0%:41,56,0,0	0/1:.:104:103:1:0.96%:46,57,1,0
+chr1	51439726	.	C	G	.	str10	DP=187;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1872E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:90:90:0:0%:37,53,0,0	0/1:.:97:96:1:1.03%:44,52,1,0
+chr1	51439751	.	C	G	.	str10	DP=168;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.3293E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:79:78:0:0%:28,50,0,0	0/1:.:89:88:1:1.12%:35,53,0,1
+chr1	51439763	.	G	A	.	PASS	DP=159;SOMATIC;SS=2;SSC=5;GPV=1E0;SPV=2.7092E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:76:76:0:0%:34,42,0,0	0/1:.:83:81:2:2.41%:32,49,1,1
+chr1	51439766	.	G	T	.	str10	DP=154;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1299E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:75:75:0:0%:34,41,0,0	0/1:.:79:78:1:1.27%:30,48,0,1
+chr1	51439788	.	T	C	.	str10	DP=136;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1471E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:66:66:0:0%:21,45,0,0	0/1:.:70:69:1:1.43%:24,45,1,0
+chr1	51439828	.	G	A	.	str10	DP=122;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.7377E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:52:52:0:0%:14,38,0,0	0/1:.:70:69:1:1.43%:27,42,0,1
+chr1	51439832	.	C	G	.	str10	DP=125;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.52E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:56:56:0:0%:14,42,0,0	0/1:.:69:68:1:1.45%:25,43,0,1
+chr1	51439876	.	T	G	.	str10	DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.619E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:46:46:0:0%:10,36,0,0	0/1:.:59:58:1:1.69%:23,35,0,1
+chr1	51439882	.	G	T	.	str10	DP=105;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.2381E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:50:50:0:0%:13,37,0,0	0/1:.:55:54:1:1.82%:22,32,0,1
+chr1	51439889	.	G	T	.	str10	DP=97;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.1546E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:47:47:0:0%:14,33,0,0	0/1:.:50:49:1:2%:21,28,0,1
+chr1	51439953	.	G	T	.	str10	DP=59;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=5.9322E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:24:24:0:0%:5,19,0,0	0/1:.:35:34:1:2.86%:7,27,0,1
+chr1	51440035	.	G	T	.	PASS	DP=21;SOMATIC;SS=2;SSC=2;GPV=1E0;SPV=6.1905E-1	GT:GQ:DP:RD:AD:FREQ:DP4	0/0:.:8:8:0:0%:1,7,0,0	0/1:.:13:12:1:7.69%:1,11,0,1
diff -r 000000000000 -r 72b8ce355fae varscan_somatic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_somatic.xml	Tue Jul 10 13:35:40 2018 -0400
@@ -0,0 +1,101 @@
+<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0">
+    <description>Call germline/somatic variants from tumor-normal pileups</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+        varscan somatic
+            '${normal_pileup}'
+            '${tumor_pileup}'
+            galaxy_out
+            --min-coverage ${min_coverage}
+            --min-reads2 ${min_reads2}
+            --min-avg-qual ${min_avg_qual}
+            --min-var-freq ${min_var_freq}
+            --min-freq-for-hom ${min_freq_for_hom}
+            --normal-purity ${normal_purity}
+            --tumor-purity ${tumor_purity}
+            --tumor-purity ${tumor_purity}
+            --min-coverage-normal ${min_coverage_normal}
+            --somatic-p-value ${somatic_p_value}
+            --p-value ${p_value}
+            #if str($strand_filter) == 'yes':
+              --strand-filter 1
+            #end if
+
+            --output-vcf 1
+    ]]></command>
+
+    <inputs>
+        <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+        <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+
+        <expand macro="min_coverage" />
+        <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
+            label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" />
+        <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200"
+            label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" />
+        <expand macro="min_reads2" />
+        <expand macro="min_avg_qual" />
+        <expand macro="min_var_freq" value="0.10" />
+        <expand macro="min_freq_for_hom" />
+        <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00"
+            label="Estimated purity (non-tumor content) of normal sample"/>
+        <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00"
+            label="Estimated purity (tumor content) of tumor sample"/>
+        <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/>
+        <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
+            label="p-value threshold for calling somatic sites"/>
+        <expand macro="strand_filter" />
+    </inputs>
+    <outputs>
+        <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/>
+        <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
+            <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
+            <param name="min_coverage" value="2" />
+            <param name="min_coverage_normal" value="2" />
+            <param name="min_coverage_tumor" value="2" />
+            <param name="min_reads2" value="1" />
+            <param name="min_avg_qual" value="5" />
+            <param name="min_var_freq" value="0.01" />
+            <param name="min_freq_for_hom" value="0.75" />
+            <param name="normal_purity" value="0.6" />
+            <param name="tumor_purity" value="0.6" />
+            <param name="p_value" value="0.99" />
+            <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
+            <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" />
+        </test>
+    </tests>
+
+    <help>
+**VarScan Overview**
+
+VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
+It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
+
+This tool calls germline/somatic variants from tumor-normal pileups.
+
+.. _VarScan: http://dkoboldt.github.io/varscan/
+.. _online: http://dkoboldt.github.io/varscan/using-varscan.html
+
+**Input**
+
+::
+
+  mpileup file - The SAMtools mpileup files for the normal and tumor tissue
+ 
+
+**Output**
+
+VarScan produces a VCF 4.1 dataset as output.
+
+
+    </help>
+    <expand macro="citations" />
+</tool>