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annotate hydra.xml @ 6:9fb9fed71486 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
author nml
date Fri, 12 Oct 2018 09:16:03 -0400
parents b69e898b8109
children dcd43b402eb3
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1 <tool id="hydra" name="Hydra pipeline" version="0.4.2">
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2 <description>Identifies drug resistance within an NGS dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.4.2">quasitools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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8 quasitools hydra
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10 ## Preparing file input.
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11 #if $data_type.type == "paired":
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13 '$data_type.fastq_input1'
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14 '$data_type.fastq_input2'
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16 #elif $data_type.type == "collection":
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18 '$data_type.fastq_input1.forward'
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19 '$data_type.fastq_input1.reverse'
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21 #elif $data_type.type == "single":
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23 '$data_type.fastq_input1'
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25 #end if
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27 #if $mutation_db:
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28 -m '$mutation_db'
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29 #end if
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31 #if $reporting_threshold:
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32 -rt '$reporting_threshold'
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33 #end if
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35 #if $consensus_pct:
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36 -cp '$consensus_pct'
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37 #end if
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39 #if $length_cutoff:
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40 -lc '$length_cutoff'
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41 #end if
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43 #if $score_cutoff:
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44 -sc '$score_cutoff'
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45 #end if
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47 #if $error_rate:
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48 -e '$error_rate'
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49 #end if
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51 #if $min_read_qual:
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52 -rq '$min_read_qual'
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53 #end if
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55 #if $min_variant_qual:
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56 -vq '$min_variant_qual'
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57 #end if
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59 #if $min_depth:
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60 -md '$min_depth'
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61 #end if
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63 #if $min_ac:
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64 -ma '$min_ac'
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65 #end if
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67 #if $min_freq:
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68 -mf '$min_freq'
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69 #end if
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70
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71 #if $consensus.consensus_bool == "true_consensus":
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72 --generate_consensus
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74 #if $consensus.fasta_id.type == "default":
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75 --id
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76 #if $data_type.type == "paired":
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77 '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}'
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78 #elif $data_type.type == "single":
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79 '${fastq_input1.element_identifier}'
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80 #end if
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81 #elif $consensus.fasta_id.type == "custom":
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82 --id '$consensus.fasta_id.custom_id'
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83 #end if
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84 #end if
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85
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86 #if $low_quality.qual_selector == "filter_ns":
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87 --ns
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88 #elif $low_quality.qual_selector == "mask_reads":
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89 --mask_reads
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90 #end if
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91
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92 #if $score_type.score_selector == "median":
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93 --median
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94 #elif $score_type.score_selector == "mean":
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95 --mean
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96 #end if
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97
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98 $trim_reads
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99
0
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100 -o output
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101
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102 ]]></command>
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103 <inputs>
1
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104 <conditional name="data_type">
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105 <param name="type" type="select" label="Specify the read type.">
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106 <option value="single">Single-end Data</option>
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107 <option value="paired">Paired-end Data</option>
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108 <option value="collection">Collection Paired-end Data</option>
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109 </param>
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110 <when value="single">
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111 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
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112 </when>
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113 <when value="paired">
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114 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
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115 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
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116 </when>
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117 <when value="collection">
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118 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
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119 </when>
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120 </conditional>
0
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121 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />
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122 <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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123 <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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124 <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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125 <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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126 <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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127 <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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128 <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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129 <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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130 <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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131 <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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132 <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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133 <conditional name="consensus">
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134 <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio">
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135 <option value="true_consensus">True</option>
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136 <option selected="true" value="false_consensus">False</option>
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137 </param>
5
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138 <when value="true_consensus">
4
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139 <conditional name="fasta_id">
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140 <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">
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141 <option value="default" >Use fasta dataset name</option>
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142 <option value="custom">Use custom name</option>
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143 </param>
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144 <when value="default">
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145 </when>
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146 <when value="custom">
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147 <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>
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148 </when>
5
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149 </conditional>
4
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150 </when>
5
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151 <when value="false_consensus">
4
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152 </when>
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153 </conditional>
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154 <conditional name="low_quality">
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155 <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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156 <option value="filter_ns">Filter out regions with n's</option>
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157 <option value="mask_reads">Mask low coverage regions with n's</option>
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158 <option value="neither" selected="true">Do not filter or mask low coverage regions.</option>
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159 </param>
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160 <when value="filter_ns">
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161 </when>
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162 <when value="mask_reads">
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163 </when>
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164 <when value="neither">
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165 </when>
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166 </conditional>
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167 <conditional name="score_type">
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168 <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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169 <option value="median" selected="true">Use median score</option>
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170 <option value="mean">Use mean score</option>
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171 </param>
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172 <when value="median">
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173 </when>
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174 <when value="mean">
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175 </when>
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176 </conditional>
0
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177 </inputs>
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178 <outputs>
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179 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
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180 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" />
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181 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
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182 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
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183 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
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184 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
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185 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
4
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186 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
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187 <filter>consensus['consensus_bool'] == "true_consensus"</filter>
2
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188 </data>
0
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189 </outputs>
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190 <tests>
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191 <test>
1
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192 <param name="type" value="single"/>
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193 <param name="fastq_input1" value="forward.fastq" />
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194 <param name="score_selector" value="mean" />
0
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195 <output name="output_coverage">
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196 <assert_contents>
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197 <has_text text="frame: 0" />
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198 <has_text text="1,0" />
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199 <has_text text="948,0" />
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200 </assert_contents>
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201 </output>
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202 <output name="output_dr">
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203 <assert_contents>
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204 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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205 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" />
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206 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" />
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207 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" />
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208 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" />
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209 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" />
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210 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" />
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211 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" />
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212 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" />
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213 </assert_contents>
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214 </output>
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215 <output name="output_hydra">
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216 <assert_contents>
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217 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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218 <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" />
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219 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" />
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220 </assert_contents>
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221 </output>
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222 <output name="output_aa_mt">
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223 <assert_contents>
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224 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
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225 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s101\sP\sPASS\s0.1423\s1574\sWC=aaa;MC=CCa;MCF=0.1423;CAT=NNRTI;SRVL=Yes" />
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226 <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." />
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227 </assert_contents>
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228 </output>
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229 <output name="output_stats">
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230 <assert_contents>
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231 <has_text text="Input Size: 25000"/>
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232 <has_text text="Number of reads filtered due to length: 15074"/>
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233 <has_text text="Number of reads filtered due to average quality score: 501"/>
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234 <has_text text="Number of reads filtered due to presence of Ns: 0"/>
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235 <has_text text="Number of reads filtered due to excess coverage: 0"/>
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236 <has_text text="Number of reads filtered due to poor mapping: 12"/>
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237 <has_text text="Percentage of reads filtered: 62.35"/>
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238 </assert_contents>
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239 </output>
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240 </test>
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241 </tests>
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242 <help><![CDATA[
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243
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244 HyDRA - HIV Drug Resistance Analyzer
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245 ====================================
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246
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247 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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248
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249 Authors
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250 -------
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251
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252 The HyDRA pipeline was developed by Eric Enns and David Peddle.
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253
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254 Stages
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255 ------
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256
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257 The HyDRA pipleine proceeds through the following stages:
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258
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259 1. Quality Control/Filtering
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260 2. Reference mapping using bowtie2.
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261 3. Variant Calling and filtering using a Poisson distribution.
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262 4. AA Mutation Calling and filtering.
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263 5. Drug Resistance report generation.
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264
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265 Details
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266 -------
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267
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268 The following is an example for running the pipeline, using our included test dataset:
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269 * Output directory name: "/tmp/hydra_out"
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270 * Forward reads: "reads_w_K103N.fastq"
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271
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272 ### Output ###
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273
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274 The detailed output directory tree looks as follows:
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275
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276 /tmp/hydra_out/
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277 * align.bam
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278 * coverage_file.csv
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279 * dr_report.csv
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280 * filtered.fastq
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281 * hydra.vcf
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282 * mutation_report.hmcf
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283 * stats.txt
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284
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285 The description of each of these directories/files are as follows:
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286
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287 * __run.conf__: The configuration used when this output was produced.
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288 * __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq
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289 * __align.bam__: The alignment file in bam format.
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290 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.
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291 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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292 * __filtered.fastq__: The reads remaining after the filtering stage.
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293 * __hydra.vcf__: The variants found by the pipeline.
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294 * __mutation_report.hmcf__: The AA mutations found by the pipeline.
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295 * __stats.txt__: A log file detailing size after filtering and major stages.
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296
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297 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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298
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299 Example: __dr_report.csv__
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300
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301 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
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302 RT,NNRTI,Yes,K,103,N,9.03,155
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303
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304 The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below.
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305
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306 Example: __mutation_report.hmcf__
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307
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308 ##fileformat=HMCFv1
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309 ##fileDate=20150008
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310 ##source=HyDRA
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311 ##reference=/home/ericenns/hydra/var/hxb2_pol.fas
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312 ##INFO=<ID=MC,Number=.,Description="String">
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313 ##INFO=<ID=MCF,Number=.,Description="String">
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314 ##INFO=<ID=WC,Number=.,Description="String">
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315 ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01">
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316 #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO
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317 RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903
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318
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319 ]]></help>
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320 <citations>
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321 </citations>
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322 </tool>