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annotate vardict.xml @ 0:2975b29bcaa1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
author iuc
date Tue, 25 Aug 2020 05:41:19 -0400
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2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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1 <tool id="vardict_java" name="VarDict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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2 <description>calls SNVs and indels for tumor-normal pairs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
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8 <requirement type="package" version="5.0.1">gawk</requirement>
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9 <requirement type="package" version="1.10">samtools</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #if $select_mode.mode == "paired"
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13 ln -s '$select_mode.normal' ./normal.bam &&
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14 ln -s '$select_mode.normal.metadata.bam_index' ./normal.bam.bai &&
2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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15 #end if
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16 ln -s '$select_mode.tumor' ./tumor.bam &&
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17 ln -s '$select_mode.tumor.metadata.bam_index' ./tumor.bam.bai &&
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18
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19 ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
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20 #if $reference_source.reference_source_selector == "history":
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21 ln -s '$reference_source.ref_file' ./ref.fa &&
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22 samtools faidx ./ref.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for vardict' >&2 &&
2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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23 #else if $reference_source.reference_source_selector == "cached"
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24 ln -s '$reference_source.ref_file.fields.path' ./ref.fa &&
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25 ln -s '${reference_source.ref_file.fields.path}.fai' ./ref.fa.fai &&
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26 #end if
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27
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28 ## build BED file from chromosome list
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29 #if $interval_file:
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30 grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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31 #else
2975b29bcaa1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"
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32 ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
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33 #end if
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34 awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed &&
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35
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36 vardict-java
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37 #if $select_mode.mode == "paired"
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38 -b "./tumor.bam|./normal.bam"
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39 -N 'Tumor'
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40 #else
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41 -b "./tumor.bam"
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42 -N 'Sample'
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43 #end if
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44 -G ./ref.fa
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45 -z
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46 -th \${GALAXY_SLOTS:-1}
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47
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48 -f '$advancedsettings.f'
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49 -k '$advancedsettings.k'
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50 -r '$advancedsettings.r'
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51 -B '$advancedsettings.B'
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52 -Q '$advancedsettings.Q'
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53 -q '$advancedsettings.q'
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54 -m '$advancedsettings.m'
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55 -T '$advancedsettings.T'
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56 -X '$advancedsettings.X'
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57 -P '$advancedsettings.P'
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58 -o '$advancedsettings.o'
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59 -O '$advancedsettings.O'
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60 -V '$advancedsettings.V'
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61
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62 ## construct VFC table
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63 -c 1 -S 2 -E 3 -g 4
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64 ./regions.bed
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65
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66 ## postprocessing
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67 #if $select_mode.mode == "paired"
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68 | testsomatic.R
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69 | var2vcf_paired.pl
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70 -N 'Tumor|Normal'
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71 #else
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72 | teststrandbias.R
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73 | var2vcf_valid.pl
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74 -N 'Sample'
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75 -E
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76 #end if
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77 -f '$advancedsettings.f'
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78
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79 > '$all_variants' &&
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80
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81 ## Filter for PASS variants
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82 awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' '$all_variants' > '$passed_variants'
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83 ]]></command>
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84 <inputs>
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85 <conditional name="select_mode">
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86 <param name="mode" type="select" label="Choose run mode">
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87 <option value="single">Single sample mode</option>
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88 <option value="paired" selected="True">Paired variant calling</option>
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89 </param>
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90 <when value="single">
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91 <expand macro="input_default" />
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92 </when>
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93 <when value="paired">
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94 <param name="normal" type="data" format="bam" label="Normal file" />
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95 <expand macro="input_default" />
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96 </when>
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97 </conditional>
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98 <section name="advancedsettings" title="Advanced Settings" expanded="False">
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99 <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" />
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100 <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" />
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101 <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" />
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102 <param argument="-B" type="integer" min="0" value="2" label="Minimum number of reads for determining strand bias" />
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103 <param argument="-Q" type="integer" min="0" value="1" label="Minimum mapping quality for reads to be considered" />
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104 <param argument="-m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" />
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105 <param argument="-T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" />
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106 <param argument="-X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />
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107 <param argument="-P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />
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108 <param argument="-q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />
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109 <param argument="-o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />
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110 <param argument="-O" type="float" min="0" value="0" label="Minimum average mapping quality" />
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111 <param argument="-V" type="float" min="0.0" max="1.0" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />
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112 </section>
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113 <expand macro="ref_select" />
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114 </inputs>
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115 <outputs>
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116 <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />
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117 <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />
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118 </outputs>
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119 <tests>
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120 <test expect_num_outputs="2">
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121 <conditional name="select_mode">
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122 <param name="mode" value="paired" />
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123 <param name="normal" ftype="bam" value="normal.bam" />
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124 <param name="tumor" ftype="bam" value="tumor.bam" />
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125 </conditional>
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126 <conditional name="reference_source">
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127 <param name="reference_source_selector" value="history"/>
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128 <param name="ref_file" ftype="fasta" value="genome.fasta" />
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129 </conditional>
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130 <output name="all_variants" file="all_variants_paired.vcf" />
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131 <output name="passed_variants" file="passed_variants_paired.vcf" />
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132 </test>
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133 <test expect_num_outputs="2">
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134 <conditional name="select_mode">
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135 <param name="mode" value="paired" />
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136 <param name="normal" ftype="bam" value="normal.bam" />
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137 <param name="tumor" ftype="bam" value="tumor.bam" />
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138 </conditional>
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139 <conditional name="reference_source">
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140 <param name="reference_source_selector" value="cached"/>
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141 <param name="ref_file" value="test_buildid"/>
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142 </conditional>
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143 <output name="all_variants" file="all_variants_paired.vcf" />
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144 <output name="passed_variants" file="passed_variants_paired.vcf" />
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145 </test>
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146 <test expect_num_outputs="2">
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147 <conditional name="select_mode">
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148 <param name="mode" value="single" />
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149 <param name="tumor" ftype="bam" value="tumor.bam" />
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150 </conditional>
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151 <conditional name="reference_source">
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152 <param name="reference_source_selector" value="cached"/>
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153 <param name="ref_file" value="test_buildid"/>
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154 </conditional>
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155 <output name="all_variants" file="all_variants_single.vcf" />
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156 <output name="passed_variants" file="passed_variants_single.vcf" />
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157 </test>
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158 </tests>
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159 <help>
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160 <![CDATA[
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161 VarDict
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162 =======
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163
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164 VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files.
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165 VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments,
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166 rescue of long indels by realigning bwa soft clipped reads and better scalability than many other Java based variant callers.
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167
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168 For more information see the VarDict documentation_.
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169
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170 .. _documentation: https://github.com/AstraZeneca-NGS/VarDictJava
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171 ]]>
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172 </help>
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173 <citations>
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174 <citation type="doi">10.1093/nar/gkw227</citation>
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175 </citations>
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176 </tool>