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annotate biohansel.xml @ 8:4fa9d5e748d4 draft

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planemo upload for repository https://github.com/phac-nml/biohansel commit 759c65786566b73806fccaed05802fe01ec4226a
author nml
date Tue, 21 May 2019 15:05:40 -0400
parents 3360158bb0c5
children e305df0b1af7
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1 <tool id="biohansel" name="biohansel" version="2.2.0">
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2 <description>SNP subtyping of genome sequence reads or assemblies</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.0">bio_hansel</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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9 #import re
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11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
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12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
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13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)')
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15 #def is_gzipped_fastq($data_input)
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16 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
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17 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
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18 #end def
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20 #def get_fastq_ext($data_input)
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21 ## Get file extension for FASTQ data param
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22 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq'
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23 #end def
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25 #def base_sample_name($name)
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26 ## Get the base sample name and append 1/2 depending on if forward/reverse read
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27 #set $illumina_match = $ILLUMINA_REGEX.match($name)
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28 #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name)
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29
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30 #if $illumina_match
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31 #return $illumina_match.group(1)
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32 #elif $fastq_dump_match
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33 #return $fastq_dump_match.group(1)
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34 #elif $re.search(r'_R(1|2)', $name):
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35 #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name)
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36 #elif $re.match(r'.+_\d\.', $name):
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37 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
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38 #else
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39 #return $name
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40 #end if
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41 #end def
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43 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)
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44 ## Get paired FASTQ filename for a data param with appropriate file extension
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45 ## with '_1' or '_2' appended if forward or reverse reads, respectively.
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46 #set $name = $name if $name is not None else $data_input.name
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47 #set $name = $base_sample_name($name)
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48 #set $postfix = '1' if $is_forward else '2'
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49 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input))
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50 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
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51 #end def
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53 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)
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54 #if $input.type == 'fasta'
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55 #set $input_files = '"{}"'.format($input.fasta.name)
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56 ln -s "$input.fasta" $input_files &&
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57 #elif $input.type == 'paired'
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58 #set $forward_filename = $get_paired_fastq_filename($input.forward)
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59 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
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60 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
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61 ln -s "$input.forward" $forward_filename &&
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62 ln -s "$input.reverse" $reverse_filename &&
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63 #elif $input.type == 'single'
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64 #set $input_files = '"{}"'.format($input.single.name)
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65 ln -s "$input.single" $input_files &&
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66 #elif $input.type == 'paired_collection'
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67 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward)
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68 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False)
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69 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
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70 ln -s "$input.paired_collection.forward" $forward_filename &&
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71 ln -s "$input.paired_collection.reverse" $reverse_filename &&
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72 #end if
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74 ## Checking for custom scheme.
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75 #if $type_of_scheme.scheme_check == "custom":
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76 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
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77 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
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78 #end if
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79 #end if
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81 #def get_subtype_metadata_filename($data_input)
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82 ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv
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83 #set $filename = $data_input.name
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84 #if $data_input.is_of_type('tabular')
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85 #return '{}.tab'.format($filename)
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86 #elif $data_input.is_of_type('csv')
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87 #return '{}.csv'.format($filename)
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88 #else
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89 #return None
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90 #end if
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91 #end def
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92
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93 ## Symlink to subtype metadata table if it is specified
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94 #if $subtype_metadata
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95 #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata)
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96 #if $subtype_metadata_filename
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97 ln -s '$subtype_metadata' '$subtype_metadata_filename' &&
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98 #end if
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99 #else
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100 #set global $subtype_metadata_filename = None
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101 #end if
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102
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103 #################################
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104 ## biohansel command starts here:
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105 #################################
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106 hansel
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107 -vvv
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108 -t "\${GALAXY_SLOTS:-1}"
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109 -o results.tab
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110 -O match_results.tab
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111 -S tech_results.tab
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112 $dev_args.use_json
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113 $input_files
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114 --scheme
7
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115 #if $type_of_scheme.scheme_check == "custom":
0
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116 '$type_of_scheme.scheme_input.name'
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117 #else:
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118 $type_of_scheme.scheme_type
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119 #end if
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120 #if $subtype_metadata_filename
4
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121 --scheme-metadata '$subtype_metadata_filename'
0
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122 #end if
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123 #if $kmer_vals.kmer_min
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124 --min-kmer-freq $kmer_vals.kmer_min
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125 #end if
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126 #if $kmer_vals.kmer_max
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127 --max-kmer-freq $kmer_vals.kmer_max
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128 #end if
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129 #if $qc_vals.low_cov_depth_freq
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130 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
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131 #end if
8
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132 #if $qc_vals.max_missing_kmers
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133 --max-missing-kmers $qc_vals.max_missing_kmers
0
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134 #end if
8
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135 #if $qc_vals.min_ambiguous_kmers
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136 --min-ambiguous-kmers $qc_vals.min_ambiguous_kmers
0
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137 #end if
8
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138 #if $qc_vals.max_intermediate_kmers
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139 --max-intermediate-kmers $qc_vals.max_intermediate_kmers
0
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140 #end if
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141 #if $qc_vals.low_coverage_warning
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142 --low-cov-warning $qc_vals.low_coverage_warning
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143 #end if
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144 ]]>
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145 </command>
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146 <inputs>
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147 <conditional name="input">
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148 <param name="type" type="select" label="Sequence Data Type">
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149 <option value="fasta">Contigs (FASTA)</option>
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150 <option value="paired">Paired-end reads (FASTQ)</option>
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151 <option value="single">Single-end reads (FASTQ)</option>
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152 <option value="paired_collection">Paired-end reads collection (FASTQ)</option>
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153 </param>
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154 <when value="fasta">
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155 <param name="fasta"
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156 type="data" format="fasta"
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157 optional="false"
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158 label="Contigs (FASTA)"
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159 />
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160 </when>
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161 <when value="paired">
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162 <param name="forward"
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163 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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164 optional="false"
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165 label="Forward reads (FASTQ)"
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166 help="Must have ASCII encoded quality scores"
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167 />
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168 <param name="reverse"
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169 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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170 optional="false"
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171 label="Reverse reads (FASTQ)"
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172 help="File format must match the Forward FASTQ file"
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173 />
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174 </when>
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175 <when value="single">
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176 <param name="single"
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177 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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178 optional="false"
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179 label="Single-end reads (FASTQ)"
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180 />
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181 </when>
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182 <when value="paired_collection">
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183 <param name="paired_collection"
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184 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt"
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185 collection_type="paired"
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186 optional="false"
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187 label="Paired-end reads collection (FASTQ)"
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188 />
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189 </when>
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190 </conditional>
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191 <conditional name="type_of_scheme">
7
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192 <param name="scheme_check" type="select"
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193 label="Subtyping Schemes"
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194 help="Use included scheme or custom">
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195 <option value="standard">Included Biohansel Schemes</option>
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196 <option value="custom">Select User Custom Scheme</option>
0
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197 </param>
7
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198 <when value="standard">
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199 <param name="scheme_type" type="select"
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200 label="Included SNP Subtyping Scheme">
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201 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
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202 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
8
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203 <option value="typhi">Salmonella Typhi subtyping scheme</option>
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204 <option value="typhimurium">Salmonella Typhimurium subtyping scheme</option>
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205 <option value="tb_speciation">Mycobacterium Tuberculosis subtyping scheme</option>
7
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206 </param>
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207 </when>
0
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208 <when value="custom">
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209 <param name="scheme_input"
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210 type="data" format="fasta"
7
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211 label="Your Custom Biohansel SNP Subtyping Scheme"/>
0
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212 </when>
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213 </conditional>
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214 <param name="subtype_metadata"
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215 type="data" format="tabular,csv"
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216 optional="true"
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217 label="Scheme Subtype Metadata Table [Optional]"
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218 help="CSV or tab-delimited format only. Must contain a 'subtype' column."
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219 />
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220 <!-- K-mer frequencies. -->
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221 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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222 <param name="kmer_min" type="integer"
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223 argument="--min-kmer-freq"
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224 optional="true"
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225 min="0" value="8"
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226 label="Min k-mer frequency/coverage"
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227 help="default = 8"/>
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228 <param name="kmer_max" type="integer"
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229 argument="--max-kmer-freq"
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230 optional="true"
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231 min="1" value="1000"
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232 label="Max k-mer frequency/coverage"
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233 help="default = 1000"/>
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234 </section>
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235 <!-- Quality Checking Parameters -->
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236 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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237 <param name="low_cov_depth_freq" type="integer"
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238 argument="--low-cov-depth-freq"
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239 value="20" min="0"
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240 optional="true"
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241 label="QC: Frequency below this coverage are considered low coverage"
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242 help="default = 20"/>
8
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243 <param name="min_ambiguous_kmers" type="integer"
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244 argument="--min-ambiguous-kmers"
0
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245 optional="true"
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246 value="3" min="0"
8
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247 label="QC: Min number of kmers missing for Ambiguous Result"
0
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248 help="default = 3"/>
8
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249 <param name="max_missing_kmers" type="float"
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250 argument="--max-missing-kmers"
0
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251 optional="true"
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252 value="0.05" min="0" max="1"
8
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253 label="QC: Decimal Proportion of max allowed missing kmers" help="default = 0.05, valid values {0.0 - 1.0}"/>
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254 <param name="max_intermediate_kmers" type="float"
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255 argument="--max-intermediate-kmers"
0
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256 optional="true"
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257 value="0.05" min="0" max="1"
8
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258 label="QC: Decimal Proportion of max allowed missing kmers for an intermediate subtype"
0
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259 help="default = 0.05, valid values {0.0 - 1.0}"/>
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260 <param name="low_coverage_warning" type="integer"
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261 argument="--low-cov-warning"
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262 optional="true"
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263 value="20"
8
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264 label="QC: Overall kmer coverage below this value will trigger a low coverage warning"
0
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265 help="default = 20"/>
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266 </section>
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267 <section name="dev_args" title="Developer Options" expanded="False">
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268 <param name="use_json"
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269 type="boolean"
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270 checked="false"
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271 truevalue="--json"
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272 falsevalue=""
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273 label="Output JSON results"
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274 help="Use this option of you need json representations of analysis' details"/>
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275 </section>
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276 </inputs>
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277 <outputs>
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278 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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279 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
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280 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
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281 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
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282 <filter>dev_args['use_json']</filter>
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283 </data>
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284 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
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285 <filter>dev_args['use_json']</filter>
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286 </data>
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287 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
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288 <filter>dev_args['use_json']</filter>
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289 </data>
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290 </outputs>
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291 <tests>
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292 <test>
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293 <conditional name="input">
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294 <param name="type" value="fasta"/>
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295 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
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296 </conditional>
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297 <param name="type_of_scheme" value="heidelberg"/>
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298 <output name="results.tab"
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299 value="SRR1002850_SMALL.fasta-results.tab"
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300 ftype="tabular"
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301 compare="sim_size"
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302 delta="1000">
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303 </output>
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304 <output name="match_results.tab"
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305 value="SRR1002850_SMALL.fasta-match_results.tab"
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306 ftype="tabular"
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307 compare="sim_size"
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308 delta="16000">
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309 </output>
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310 <output name="tech_results.tab"
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311 value="SRR1002850_SMALL.fasta-tech_results.tab"
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312 ftype="tabular"
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313 lines_diff="0">
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314 </output>
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315 </test>
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316 <test>
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317 <conditional name="input">
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318 <param name="type" value="paired"/>
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319 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
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320 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
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321 </conditional>
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322 <param name="type_of_scheme" value="heidelberg"/>
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323 <output name="tech_results.tab"
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324 value="SRR5646583_SMALL-tech_results.tab"
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325 ftype="tabular"
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326 lines_diff="0">
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327 </output>
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328 <output name="results.tab"
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329 value="SRR5646583_SMALL-results.tab"
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330 ftype="tabular"
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331 compare="sim_size"
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332 delta="1000">
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333 </output>
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334 <output name="match_results.tab"
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335 value="SRR5646583_SMALL-match_results.tab"
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336 ftype="tabular"
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337 compare="sim_size"
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338 delta="16000">
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339 </output>
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340 </test>
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341 </tests>
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342 <help><![CDATA[
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343 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
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344
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345 **Usage**
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346
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347 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
8
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348 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg, Enteritidis, Typhimurium, or Typhi subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
0
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349 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
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350 4) Click ``Execute``
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351
8
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352 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_ or the `biohansel read the docs page <https://bio-hansel.readthedocs.io/en/readthedocs/>`_.
0
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353
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354
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355 **Example analysis results of a single FASTA file**
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356
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357 Contents of ``results.tab``:
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358
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359 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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360 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | qc_status | qc_message |
0
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361 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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362 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | |
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363 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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364
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365
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366 Contents of ``match_results.tab``:
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367
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368 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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369 | kmername | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_kmer | sample | file_path | scheme | scheme_version | qc_status | qc_message |
0
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370 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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371 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
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372 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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373 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
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374 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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375
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376 *Next 201 lines omitted.*
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377
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378
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379
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380 **Example analysis results of a single FASTQ readset**
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381
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382
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383 Contents of ``results.tab``:
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384
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385 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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386 | sample | scheme | scheme_version | subtype | all_subtypes | kmers_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_kmers_matching_all | n_kmers_matching_all_expected | n_kmers_matching_positive | n_kmers_matching_positive_expected | n_kmers_matching_subtype | n_kmers_matching_subtype_expected | file_path | avg_kmer_coverage | qc_status | qc_message |
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387 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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388 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | |
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389 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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390
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391 Contents of ``match_results.tab``:
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392
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393 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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394 | kmername | seq | freq | refposition | subtype | is_pos_kmer | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
0
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395 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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396 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
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397 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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398 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
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399 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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400
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401 *Next 202 lines omitted.*
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402
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403
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404 **Example Subtype Metadata**
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405
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406 A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want.
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407
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408
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409 +-------------+-------+--------+------------------+
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410 | subtype | clade | source | disease_symptoms |
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411 +-------------+-------+--------+------------------+
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412 | 1 | I | geese | death |
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413 +-------------+-------+--------+------------------+
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414 | 1.1 | I | moose | burns |
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415 +-------------+-------+--------+------------------+
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416 | 2.2.1.1.1 | II | mouse | boils |
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417 +-------------+-------+--------+------------------+
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418 | 2.2.2.2.1.4 | IIa | house | rash |
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419 +-------------+-------+--------+------------------+
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420
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421 The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively.
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422
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423
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424 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
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425
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426 ]]></help>
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427 <citations>
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428 <citation type="bibtex">@ARTICLE{a1,
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429 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
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430 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
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431 url = {https://github.com/phac-nml/biohansel}
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432 }
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433 }</citation>
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434 </citations>
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435 </tool>