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annotate hydra.xml @ 4:8cdffc02d2e2 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
author nml
date Wed, 25 Apr 2018 10:38:00 -0400
parents a7093d5933a8
children b69e898b8109
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1 <tool id="hydra" name="Hydra pipeline" version="0.2.0">
0
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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="0.3.1">quasitools</requirement>
0
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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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1
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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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0
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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 $min_qual:
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52 -mq '$min_qual'
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53 #end if
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55 #if $min_depth:
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56 -md '$min_depth'
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57 #end if
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59 #if $min_ac:
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60 -ma '$min_ac'
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61 #end if
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63 #if $min_freq:
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64 -mf '$min_freq'
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65 #end if
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66
4
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67 #if $consensus.consensus_bool == "true_consensus":
0
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68 --generate_consensus
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69
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70 #if $consensus.fasta_id.type == "default":
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71 --id
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72 #if $data_type.type == "paired":
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73 '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}'
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74 #elif $data_type.type == "single":
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75 '${fastq_input1.element_identifier}'
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76 #end if
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77 #elif $consensus.fasta_id.type == "custom":
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78 --id '$consensus.fasta_id.custom_id'
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79 #end if
0
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80 #end if
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81
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82 #if $filter_ns:
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83 --ns
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84 #end if
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85
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86 -o output
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87
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88 ]]></command>
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89 <inputs>
1
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90 <conditional name="data_type">
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91 <param name="type" type="select" label="Specify the read type.">
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92 <option value="single">Single-end Data</option>
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93 <option value="paired">Paired-end Data</option>
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94 <option value="collection">Collection Paired-end Data</option>
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95 </param>
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96 <when value="single">
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97 <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
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98 </when>
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99 <when value="paired">
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100 <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
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101 <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
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102 </when>
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103 <when value="collection">
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104 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
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105 </when>
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106 </conditional>
0
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107 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />
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108 <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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109 <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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110 <param name="length_cutoff" type="integer" optional="true" min="0" 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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111 <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." />
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112 <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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113 <param name="min_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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114 <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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115 <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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116 <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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117 <conditional name="consensus">
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118 <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio">
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119 <option value="true_consensus">True</option>
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120 <option selected="true" value="false_consensus">False</option>
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121 </param>
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122 <when value="true_consensus">
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123 <conditional name="fasta_id">
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124 <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">
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125 <option value="default" >Use fasta dataset name</option>
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126 <option value="custom">Use custom name</option>
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127 </param>
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128 <when value="default">
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129 </when>
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130 <when value="custom">
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131 <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>
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132 </when>
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133 </conditional>
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134 </when>
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135 <when value="false_consensus">
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136 </when>
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137 </conditional>
0
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138 <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" />
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139 </inputs>
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140 <outputs>
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141 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
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142 <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" />
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143 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" />
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144 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
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145 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
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146 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
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147 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
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148 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
4
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149 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
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150 <filter>consensus['consensus_bool'] == "true_consensus"</filter>
2
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151 </data>
0
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152 </outputs>
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153 <tests>
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154 <test>
1
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155 <param name="type" value="single"/>
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156 <param name="fastq_input1" value="forward.fastq" />
0
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157 <output name="output_coverage">
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158 <assert_contents>
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159 <has_text text="frame: 0" />
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160 <has_text text="1,0" />
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161 <has_text text="948,0" />
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162 </assert_contents>
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163 </output>
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164 <output name="output_dr">
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165 <assert_contents>
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166 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" />
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167 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" />
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168 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" />
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169 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" />
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170 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" />
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171 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" />
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172 <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" />
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173 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" />
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174 <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" />
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175 </assert_contents>
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176 </output>
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177 <output name="output_hydra">
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178 <assert_contents>
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179 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/>
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180 <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" />
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181 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" />
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182 </assert_contents>
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183 </output>
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184 <output name="output_aa_mt">
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185 <assert_contents>
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186 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
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187 <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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188 <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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189 </assert_contents>
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190 </output>
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191 <output name="output_stats">
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192 <assert_contents>
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193 <has_text text="Input Size: 25000"/>
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194 <has_text text="Number of reads filtered due to length: 15074"/>
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195 <has_text text="Number of reads filtered due to average quality score: 501"/>
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196 <has_text text="Number of reads filtered due to presence of Ns: 0"/>
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197 <has_text text="Number of reads filtered due to excess coverage: 0"/>
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198 <has_text text="Number of reads filtered due to poor mapping: 12"/>
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199 <has_text text="Percentage of reads filtered: 62.35"/>
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200 </assert_contents>
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201 </output>
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202 </test>
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203 </tests>
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204 <help><![CDATA[
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205
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206 HyDRA - HIV Drug Resistance Analyzer
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207 ====================================
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208
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209 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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210
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211 Authors
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212 -------
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213
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214 The HyDRA pipeline was developed by Eric Enns and David Peddle.
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215
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216 Stages
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217 ------
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218
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219 The HyDRA pipleine proceeds through the following stages:
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220
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221 1. Quality Control/Filtering
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222 2. Reference mapping using bowtie2.
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223 3. Variant Calling and filtering using a Poisson distribution.
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224 4. AA Mutation Calling and filtering.
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225 5. Drug Resistance report generation.
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226
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227 Details
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228 -------
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229
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230 The following is an example for running the pipeline, using our included test dataset:
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231 * Output directory name: "/tmp/hydra_out"
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232 * Forward reads: "reads_w_K103N.fastq"
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233
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234 ### Output ###
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235
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236 The detailed output directory tree looks as follows:
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237
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238 /tmp/hydra_out/
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239 * align.bam
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240 * align.bam.bai
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241 * coverage_file.csv
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242 * dr_report.csv
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243 * filtered.fastq
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244 * hydra.vcf
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245 * mutation_report.hmcf
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246 * stats.txt
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247
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248 The description of each of these directories/files are as follows:
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249
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250 * __run.conf__: The configuration used when this output was produced.
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251 * __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq
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252 * __align.bam__: The alignment file in bam format.
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253 * __align.bam.bai__: The index to the alignment file.
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254 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.
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255 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
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256 * __filtered.fastq__: The reads remaining after the filtering stage.
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257 * __hydra.vcf__: The variants found by the pipeline.
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258 * __mutation_report.hmcf__: The AA mutations found by the pipeline.
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259 * __stats.txt__: A log file detailing size after filtering and major stages.
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260
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261 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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262
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263 Example: __dr_report.csv__
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264
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265 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
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266 RT,NNRTI,Yes,K,103,N,9.03,155
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267
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268 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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269
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270 Example: __mutation_report.hmcf__
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271
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272 ##fileformat=HMCFv1
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273 ##fileDate=20150008
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274 ##source=HyDRA
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275 ##reference=/home/ericenns/hydra/var/hxb2_pol.fas
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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276 ##INFO=<ID=MC,Number=.,Description="String">
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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277 ##INFO=<ID=MCF,Number=.,Description="String">
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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278 ##INFO=<ID=WC,Number=.,Description="String">
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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279 ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01">
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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280 #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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281 RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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282
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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283 ]]></help>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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284 <citations>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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285 </citations>
71976cfc9022 planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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286 </tool>