# HG changeset patch
# User devteam
# Date 1384645536 18000
# Node ID 306a1fcf3369f126f279b1b3e5dfff2d444d9f73
# Parent  1cf258cb4fd7819f2692a2cbb708426e2910401d
Deleted selected files

diff -r 1cf258cb4fd7 -r 306a1fcf3369 varscan/test-data/test_in1.pileup
--- a/varscan/test-data/test_in1.pileup	Sat Nov 16 18:45:02 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-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 1cf258cb4fd7 -r 306a1fcf3369 varscan/test-data/test_out1.vcf
--- a/varscan/test-data/test_out1.vcf	Sat Nov 16 18:45:02 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-##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 1cf258cb4fd7 -r 306a1fcf3369 varscan/tool-dependencies.xml
--- a/varscan/tool-dependencies.xml	Sat Nov 16 18:45:02 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="varscan" version="2.3.6">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
-                <action type="move_file">
-                    <source>VarScan.v2.3.6.jar</source>
-                    <destination>$INSTALL_DIR/jars</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>
diff -r 1cf258cb4fd7 -r 306a1fcf3369 varscan/varscan.xml
--- a/varscan/varscan.xml	Sat Nov 16 18:45:02 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-<tool id="varscan" name="Varscan" version="0.1">
-    <description>for variant detection</description>
-
-    <requirements>
-        <requirement type="package" version="2.3.6">varscan</requirement>
-    </requirements>
-
-    <!-- 
-    The version command string is not yet a template that can be filled in, so version command is not yet possible.
-    <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&amp;1 | head -n 1</version_command>
-    -->
-
-    <command>
-        ## Set up samples list file.
-        #if $sample_names.strip() != '':
-	       echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
-        #end if
-
-        ## Set up command + input.
-        java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
-        --min-coverage ${min_coverage} 
-        --min-reads2 ${min_supporting_reads} 
-        --min-avg-qual ${min_avg_qual}
-        --min-var-freq ${min_var_freq}
-        --min-freq-for-hom ${min_freq_for_hom}
-        --p-value ${p_value}
-        #if str($strand_filter) == 'yes':
-          --strand-filter 1
-        #end if
-
-        ## Report only variants in consensus.
-        #if str($cmd) == 'mpileup2cns':
-          --variants
-        #end if
-        
-        ## Set up outputs.
-        --output-vcf 1 > $output
-
-        #if $sample_names.strip() != '':
-            --vcf-sample-list samples_list.txt
-        #end if
-    </command>
-
-    <inputs>
-        <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
-
-        <param name="cmd" type="select" label="Analysis type">
-          <option value="mpileup2snp" selected="True">single nucleotide variation</option>
-          <option value="mpileup2indel">insertions and deletions</option>
-          <option value="mpileup2cns">consensus genotype</option>
-        </param>
-
-        <param 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"/>
-        <param name="min_supporting_reads" type="integer" value="2" min="1" max="200" label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
-        <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/>
-        <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/>
-        <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/>
-        <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/>
-        <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>
-        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
-    </inputs>
-
-    <stdio>
-        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
-        <regex match=".*" source="both" level="log" description="tool progress"/>
-    </stdio>
-
-    <outputs>
-        <data name="output" format="vcf"/>
-    </outputs>
-
-    <trackster_conf>
-    </trackster_conf>
-
-    <tests>
-        <test>
-            <param name="input" value="test_in1.pileup" />
-            <param name="cmd" value="mpileup2cns" />
-            <param name="min_coverage" value="8" />
-            <param name="min_supporting_reads" value="2" />
-            <param name="min_avg_qual" value="15" />
-            <param name="min_var_freq" value="0.01" />
-            <param name="min_freq_for_hom" value="0.75" />
-            <param name="p_value" value="0.99" />
-            <param name="strand_filter" value="no" />
-            <param name="sample_names" value="" />
-            <output name="output" file="test_out1.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_.
-
-Please cite: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., and Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111 
-
-.. _VarScan: http://varscan.sourceforge.net/
-.. _online: http://varscan.sourceforge.net/using-varscan.html
-
-**Input**
-
-::
-
-  mpileup file - The SAMtools mpileup file
- 
-
-**Output**
-
-VarScan produces a VCF 4.1 dataset as output.
-
-**Parameters**
-
-::
-
-  analysis type
-    single nucleotide detection     Identify SNPs from an mpileup file
-    insertions and deletion       Identify indels an mpileup file
-    consensus genotype     Call consensus and variants from an mpileup file
-
-  min-coverage  
-    Minimum read depth at a position to make a call [8]
-
-  min-reads2    
-    Minimum supporting reads at a position to call variants [2]
-
-  min-avg-qual  
-    Minimum base quality at a position to count a read [15]
-
-  min-var-freq  
-        Minimum variant allele frequency threshold [0.01]
-
-  min-freq-for-hom
-    Minimum frequency to call homozygote [0.75]
-  
-  p-value
-    Default p-value threshold for calling variants [99e-02]
-  
-  strand-filter
-    Ignore variants with >90% support on one strand [1]
-  
-  output-vcf
-    If set to 1, outputs in VCF format
-  
-  vcf-sample-list
-    For VCF output, a list of sample names in order, one per line
-  
-  variants
-    Report only variant (SNP/indel) positions [0]
-
-    </help>
-</tool>
diff -r 1cf258cb4fd7 -r 306a1fcf3369 varscan/varscan_mpileup.xml
--- a/varscan/varscan_mpileup.xml	Sat Nov 16 18:45:02 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,155 +0,0 @@
-<tool id="varscan" name="Varscan" version="0.1">
-    <description>for variant detection</description>
-
-    <requirements>
-        <requirement type="package" version="2.3.6">varscan</requirement>
-    </requirements>
-
-    <!-- 
-    The version command string is not yet a template that can be filled in, so version command is not yet possible.
-    <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&amp;1 | head -n 1</version_command>
-    -->
-
-    <command>
-        ## Set up samples list file.
-        #if $sample_names.strip() != '':
-	       echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
-        #end if
-
-        ## Set up command + input.
-        java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
-        --min-coverage ${min_coverage} 
-        --min-reads2 ${min_supporting_reads} 
-        --min-avg-qual ${min_avg_qual}
-        --min-var-freq ${min_var_freq}
-        --min-freq-for-hom ${min_freq_for_hom}
-        --p-value ${p_value}
-        #if str($strand_filter) == 'yes':
-          --strand-filter 1
-        #end if
-
-        ## Report only variants in consensus.
-        #if str($cmd) == 'mpileup2cns':
-          --variants
-        #end if
-        
-        ## Set up outputs.
-        --output-vcf 1 > $output
-
-        #if $sample_names.strip() != '':
-            --vcf-sample-list samples_list.txt
-        #end if
-    </command>
-
-    <inputs>
-        <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
-
-        <param name="cmd" type="select" label="Analysis type">
-          <option value="mpileup2snp" selected="True">single nucleotide variation</option>
-          <option value="mpileup2indel">insertions and deletions</option>
-          <option value="mpileup2cns">consensus genotype</option>
-        </param>
-
-        <param 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"/>
-        <param name="min_supporting_reads" type="integer" value="2" min="1" max="200" label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
-        <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/>
-        <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/>
-        <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/>
-        <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/>
-        <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>
-        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
-    </inputs>
-
-    <stdio>
-        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
-        <regex match=".*" source="both" level="log" description="tool progress"/>
-    </stdio>
-
-    <outputs>
-        <data name="output" format="vcf"/>
-    </outputs>
-
-    <trackster_conf>
-    </trackster_conf>
-
-    <tests>
-        <test>
-            <param name="input" value="test_in1.pileup" />
-            <param name="cmd" value="mpileup2cns" />
-            <param name="min_coverage" value="8" />
-            <param name="min_supporting_reads" value="2" />
-            <param name="min_avg_qual" value="15" />
-            <param name="min_var_freq" value="0.01" />
-            <param name="min_freq_for_hom" value="0.75" />
-            <param name="p_value" value="0.99" />
-            <param name="strand_filter" value="no" />
-            <param name="sample_names" value="" />
-            <output name="output" file="test_out1.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_.
-
-Please cite: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., and Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111 
-
-.. _VarScan: http://varscan.sourceforge.net/
-.. _online: http://varscan.sourceforge.net/using-varscan.html
-
-**Input**
-
-::
-
-  mpileup file - The SAMtools mpileup file
- 
-
-**Output**
-
-VarScan produces a VCF 4.1 dataset as output.
-
-**Parameters**
-
-::
-
-  commands
-    mpileup2snp     Identify SNPs from an mpileup file
-    mpileup2indel       Identify indels an mpileup file
-    mpileup2cns     Call consensus and variants from an mpileup file
-
-  min-coverage  
-    Minimum read depth at a position to make a call [8]
-
-  min-reads2    
-    Minimum supporting reads at a position to call variants [2]
-
-  min-avg-qual  
-    Minimum base quality at a position to count a read [15]
-
-  min-var-freq  
-        Minimum variant allele frequency threshold [0.01]
-
-  min-freq-for-hom
-    Minimum frequency to call homozygote [0.75]
-  
-  p-value
-    Default p-value threshold for calling variants [99e-02]
-  
-  strand-filter
-    Ignore variants with >90% support on one strand [1]
-  
-  output-vcf
-    If set to 1, outputs in VCF format
-  
-  vcf-sample-list
-    For VCF output, a list of sample names in order, one per line
-  
-  variants
-    Report only variant (SNP/indel) positions [0]
-
-    </help>
-</tool>