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1 <tool id="varscan" name="Varscan" version="0.1">
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2 <description>for variant detection</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.3.6">varscan</requirement>
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6 </requirements>
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7
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8 <!--
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9 The version command string is not yet a template that can be filled in, so version command is not yet possible.
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10 <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&1 | head -n 1</version_command>
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11 -->
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12
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13 <command>
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14 ## Set up samples list file.
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15 #if $sample_names.strip() != '':
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16 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt;
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17 #end if
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18
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19 ## Set up command + input.
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20 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
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21 --min-coverage ${min_coverage}
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22 --min-reads2 ${min_supporting_reads}
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23 --min-avg-qual ${min_avg_qual}
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24 --min-var-freq ${min_var_freq}
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25 --min-freq-for-hom ${min_freq_for_hom}
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26 --p-value ${p_value}
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27 #if str($strand_filter) == 'yes':
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28 --strand-filter 1
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29 #end if
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30
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31 ## Report only variants in consensus.
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32 #if str($cmd) == 'mpileup2cns':
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33 --variants
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34 #end if
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35
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36 ## Set up outputs.
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37 --output-vcf 1 > $output
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38
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39 #if $sample_names.strip() != '':
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40 --vcf-sample-list samples_list.txt
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41 #end if
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42 </command>
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43
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44 <inputs>
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45 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
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46
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47 <param name="cmd" type="select" label="Analysis type">
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48 <option value="mpileup2snp" selected="True">single nucleotide variation</option>
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49 <option value="mpileup2indel">insertions and deletions</option>
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50 <option value="mpileup2cns">consensus genotype</option>
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51 </param>
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52
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53 <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"/>
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54 <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"/>
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55 <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/>
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56 <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/>
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57 <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/>
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58 <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/>
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59 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
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60 <option value="no" selected="True">no</option>
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61 <option value="yes">yes</option>
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62 </param>
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63 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
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64 </inputs>
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65
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66 <stdio>
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67 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
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68 <regex match=".*" source="both" level="log" description="tool progress"/>
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69 </stdio>
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70
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71 <outputs>
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72 <data name="output" format="vcf"/>
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73 </outputs>
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74
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75 <trackster_conf>
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76 </trackster_conf>
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77
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78 <tests>
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79 <test>
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80 <param name="input" value="test_in1.pileup" />
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81 <param name="cmd" value="mpileup2cns" />
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82 <param name="min_coverage" value="8" />
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83 <param name="min_supporting_reads" value="2" />
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84 <param name="min_avg_qual" value="15" />
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85 <param name="min_var_freq" value="0.01" />
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86 <param name="min_freq_for_hom" value="0.75" />
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87 <param name="p_value" value="0.99" />
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88 <param name="strand_filter" value="no" />
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89 <param name="sample_names" value="" />
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90 <output name="output" file="test_out1.vcf" lines_diff="0" />
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91 </test>
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92 </tests>
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93
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94 <help>
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95 **VarScan Overview**
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96
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97 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_.
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98
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99 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
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100
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101 .. _VarScan: http://varscan.sourceforge.net/
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102 .. _online: http://varscan.sourceforge.net/using-varscan.html
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103
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104 **Input**
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105
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106 ::
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107
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108 mpileup file - The SAMtools mpileup file
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109
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110
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111 **Output**
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112
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113 VarScan produces a VCF 4.1 dataset as output.
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114
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115 **Parameters**
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116
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117 ::
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118
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119 commands
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120 mpileup2snp Identify SNPs from an mpileup file
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121 mpileup2indel Identify indels an mpileup file
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122 mpileup2cns Call consensus and variants from an mpileup file
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123
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124 min-coverage
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125 Minimum read depth at a position to make a call [8]
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126
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127 min-reads2
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128 Minimum supporting reads at a position to call variants [2]
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129
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130 min-avg-qual
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131 Minimum base quality at a position to count a read [15]
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132
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133 min-var-freq
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134 Minimum variant allele frequency threshold [0.01]
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135
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136 min-freq-for-hom
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137 Minimum frequency to call homozygote [0.75]
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138
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139 p-value
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140 Default p-value threshold for calling variants [99e-02]
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141
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142 strand-filter
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143 Ignore variants with >90% support on one strand [1]
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144
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145 output-vcf
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146 If set to 1, outputs in VCF format
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147
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148 vcf-sample-list
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149 For VCF output, a list of sample names in order, one per line
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150
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151 variants
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152 Report only variant (SNP/indel) positions [0]
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153
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154 </help>
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155 </tool>
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