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annotate hydra.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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1 <tool id="hydra" name="Hydra pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Identifies drug resistance within an NGS dataset</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 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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9 quasitools hydra
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11 ## Preparing file input.
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12 #if $data_type.type == "paired":
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14 '$data_type.fastq_input1'
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15 '$data_type.fastq_input2'
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17 #elif $data_type.type == "collection":
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19 '$data_type.fastq_input1.forward'
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20 '$data_type.fastq_input1.reverse'
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22 #elif $data_type.type == "single":
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24 '$data_type.fastq_input1'
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26 #end if
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28 #if $mutation_db:
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29 -m '$mutation_db'
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30 #end if
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32 #if $reporting_threshold:
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33 -rt '$reporting_threshold'
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34 #end if
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36 #if $consensus_pct:
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37 -cp '$consensus_pct'
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38 #end if
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40 #if $length_cutoff:
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41 -lc '$length_cutoff'
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42 #end if
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44 #if $score_cutoff:
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45 -sc '$score_cutoff'
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46 #end if
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48 #if $error_rate:
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49 -e '$error_rate'
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50 #end if
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52 #if $min_read_qual:
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53 -rq '$min_read_qual'
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54 #end if
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56 #if $min_variant_qual:
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57 -vq '$min_variant_qual'
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58 #end if
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60 #if $min_depth:
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61 -md '$min_depth'
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62 #end if
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64 #if $min_ac:
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65 -ma '$min_ac'
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66 #end if
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68 #if $min_freq:
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69 -mf '$min_freq'
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70 #end if
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71
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72 #if $consensus.consensus_bool == "true_consensus":
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73 --generate_consensus
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75 #if $consensus.fasta_id.type == "default":
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76 --id
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77 #if $data_type.type == "paired":
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78 '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}'
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79 #elif $data_type.type == "single":
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80 '${fastq_input1.element_identifier}'
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81 #end if
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82 #elif $consensus.fasta_id.type == "custom":
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83 --id '$consensus.fasta_id.custom_id'
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84 #end if
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85 #end if
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86
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87 #if $low_quality.qual_selector == "filter_ns":
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88 --ns
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89 #elif $low_quality.qual_selector == "mask_reads":
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90 --mask_reads
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91 #end if
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92
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93 #if $score_type.score_selector == "median":
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94 --median
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95 #elif $score_type.score_selector == "mean":
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96 --mean
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97 #end if
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98
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99 $trim_reads
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100
0
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101 -o output
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102
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103 ]]></command>
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104 <inputs>
1
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105 <conditional name="data_type">
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106 <param name="type" type="select" label="Specify the read type.">
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107 <option value="single">Single-end Data</option>
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108 <option value="paired">Paired-end Data</option>
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109 <option value="collection">Collection Paired-end Data</option>
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110 </param>
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111 <when value="single">
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112 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
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113 </when>
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114 <when value="paired">
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115 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
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116 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
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117 </when>
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118 <when value="collection">
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119 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
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120 </when>
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121 </conditional>
0
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122 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />
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123 <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." />
2
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124 <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." />
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125 <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />
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126 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." />
0
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127 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/>
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128 <param name="min_variant_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." />
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129 <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." />
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130 <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." />
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131 <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." />
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132 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." />
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133 <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." />
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134 <conditional name="consensus">
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135 <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio">
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136 <option value="true_consensus">True</option>
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137 <option selected="true" value="false_consensus">False</option>
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138 </param>
5
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139 <when value="true_consensus">
4
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140 <conditional name="fasta_id">
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141 <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">
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142 <option value="default" >Use fasta dataset name</option>
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143 <option value="custom">Use custom name</option>
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144 </param>
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145 <when value="default">
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146 </when>
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147 <when value="custom">
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148 <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>
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149 </when>
5
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150 </conditional>
4
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151 </when>
5
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152 <when value="false_consensus">
4
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153 </when>
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154 </conditional>
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155 <conditional name="low_quality">
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156 <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio">
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157 <option value="filter_ns">Filter out regions with n's</option>
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158 <option value="mask_reads">Mask low coverage regions with n's</option>
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159 <option value="neither" selected="true">Do not filter or mask low coverage regions.</option>
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160 </param>
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161 <when value="filter_ns">
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162 </when>
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163 <when value="mask_reads">
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164 </when>
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165 <when value="neither">
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166 </when>
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167 </conditional>
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168 <conditional name="score_type">
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169 <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio">
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170 <option value="median" selected="true">Use median score</option>
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171 <option value="mean">Use mean score</option>
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172 </param>
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173 <when value="median">
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174 </when>
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175 <when value="mean">
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176 </when>
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177 </conditional>
0
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178 </inputs>
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179 <outputs>
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180 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
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181 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" />
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182 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
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183 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
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184 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
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185 <data format="txt" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.aavf" />
0
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186 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
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187 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
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188 <filter>consensus['consensus_bool'] == "true_consensus"</filter>
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189 </data>
0
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190 </outputs>
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191 <tests>
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192 <test>
1
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193 <param name="type" value="single"/>
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194 <param name="fastq_input1" value="forward.fastq" />
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195 <param name="score_selector" value="mean" />
0
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196 <output name="output_coverage">
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197 <assert_contents>
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198 <has_text text="frame: 0" />
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199 <has_text text="1,0" />
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200 <has_text text="948,0" />
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201 </assert_contents>
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202 </output>
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203 <output name="output_dr">
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204 <assert_contents>
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205 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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206 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" />
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207 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" />
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208 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" />
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209 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" />
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210 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" />
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211 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" />
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212 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" />
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213 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" />
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214 </assert_contents>
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215 </output>
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216 <output name="output_hydra">
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217 <assert_contents>
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218 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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219 <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" />
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220 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" />
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221 </assert_contents>
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222 </output>
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223 <output name="output_aa_mt">
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224 <assert_contents>
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225 <has_text_matching expression="#CHROM\tGENE\tPOS\tREF\tALT\tFILTER\tALT_FREQ\tCOVERAGE\tINFO"/>
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226 <has_text_matching expression="hxb2_pol\tRT\t101\tK\tP\tPASS\t0.1423\t1574\tRC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes" />
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227 <has_text_matching expression="hxb2_pol\tRT\t101\tK\tT\tmf0.01\t0.0013\t1574\tRC=aaa;AC=aCa;ACF=0.0013;CAT=.;SRVL=." />
0
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228 </assert_contents>
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229 </output>
8
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230
0
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231 <output name="output_stats">
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232 <assert_contents>
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233 <has_text text="Input Size: 25000"/>
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234 <has_text text="Number of reads filtered due to length: 15074"/>
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235 <has_text text="Number of reads filtered due to average quality score: 501"/>
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236 <has_text text="Number of reads filtered due to presence of Ns: 0"/>
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237 <has_text text="Number of reads filtered due to excess coverage: 0"/>
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238 <has_text text="Number of reads filtered due to poor mapping: 12"/>
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239 <has_text text="Percentage of reads filtered: 62.35"/>
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240 </assert_contents>
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241 </output>
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242 </test>
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243 </tests>
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244 <help><![CDATA[
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245
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246 HyDRA - HIV Drug Resistance Analyzer
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247 ====================================
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248
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249 The HyDRA pipeline provides a pipeline for identifying drug resistance within a Next Generation Sequencing dataset. The pipeline takes as input the raw reads produced by a Next Generation Sequencer and produces a report detailing found drug resistance per sample.
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250
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251 Authors
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252 -------
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253
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254 The HyDRA pipeline was developed by Eric Enns and David Peddle.
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255
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256 Stages
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257 ------
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258
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259 The HyDRA pipleine proceeds through the following stages:
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260
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261 1. Quality Control/Filtering
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262 2. Reference mapping using bowtie2.
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263 3. Variant Calling and filtering using a Poisson distribution.
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264 4. AA Mutation Calling and filtering.
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265 5. Drug Resistance report generation.
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266
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267 Details
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268 -------
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269
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270 The following is an example for running the pipeline, using our included test dataset:
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271 * Output directory name: "/tmp/hydra_out"
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272 * Forward reads: "reads_w_K103N.fastq"
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273
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274 ### Output ###
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275
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276 The detailed output directory tree looks as follows:
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277
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278 /tmp/hydra_out/
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279 * align.bam
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280 * coverage_file.csv
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281 * dr_report.csv
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282 * filtered.fastq
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283 * hydra.vcf
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284 * mutation_report.aavf
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285 * stats.txt
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286
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287 The description of each of these directories/files are as follows:
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288
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289 * __run.conf__: The configuration used when this output was produced.
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290 * __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq
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291 * __align.bam__: The alignment file in bam format.
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292 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.
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293 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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294 * __filtered.fastq__: The reads remaining after the filtering stage.
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295 * __hydra.vcf__: The variants found by the pipeline.
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296 * __mutation_report.aavf__: The AA mutations found by the pipeline.
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297 * __stats.txt__: A log file detailing size after filtering and major stages.
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298
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299 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below.
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300
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301 Example: __dr_report.csv__
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302
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303 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
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304 RT,NNRTI,Yes,K,103,N,9.03,155
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305
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306 The __mutation_report.aavf__ file is in AAVF format (https://github.com/winhiv/aavf-spec), an amino acid variant format inspired by the VCF format. The __mutation_report.aavf__ file details all of the AA mutations found by the pipeline. An example if this file is given below.
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307
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308 Example: __mutation_report.aavf__
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309
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310 ##fileformat=AAVFv1.0
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311 ##fileDate=20220615
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312 ##source=quasitools:hydra
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313 ##reference=hxb2_pol.fas
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314 ##INFO=<ID=RC,Number=1,Type=String,Description="Reference Codon">
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315 ##INFO=<ID=AC,Number=.,Type=String,Description="Alternate Codon">
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316 ##INFO=<ID=ACF,Number=.,Type=Float,Description="Alternate Codon Frequency,for each Alternate Codon,in the same order aslisted.">
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317 ##INFO=<ID=CAT,Number=.,Type=String,Description="Drug Resistance Category">
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318 ##INFO=<ID=SRVL,Number=.,Type=String,Description="Drug Resistance Surveillance">
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319 ##FILTER=<ID=af0.01,Description="Set if True; alt_freq<0.01">
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320 #CHROM GENE POS REF ALT FILTER ALT_FREQ COVERAGE INFO
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321 hxb2_pol RT 101 K P PASS 0.1423 1574 RC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes
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322
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323 ]]></help>
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324 <expand macro="citations" />
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325 </tool>