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annotate biohansel.xml @ 6:ba6a0af656a6 draft

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planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
author nml
date Wed, 20 Mar 2019 13:44:02 -0400
parents c0b8de7aa02e
children 3360158bb0c5
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ba6a0af656a6 planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
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1 <tool id="biohansel" name="biohansel" version="2.1.5">
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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="2.1.1">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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73
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74 ## Checking for custom scheme.
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75 #if $type_of_scheme.scheme_type == "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' '$type_of_scheme.scheme_input.name' &&
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78 #end if
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79 #end if
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80
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81 #def get_subtype_metadata_filename($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
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115 #if $type_of_scheme.scheme_type == "custom":
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116 '$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
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132 #if $qc_vals.max_missing_tiles
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133 --max-missing-tiles $qc_vals.max_missing_tiles
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134 #end if
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135 #if $qc_vals.min_ambiguous_tiles
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136 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
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137 #end if
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138 #if $qc_vals.max_intermediate_tiles
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139 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
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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">
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192 <param name="scheme_type" type="select"
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193 label="SNP Subtyping Scheme"
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194 help="Select the SNP subtyping scheme you wish to subtype with">
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195 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
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196 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
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197 <option value="custom">Specify your own custom scheme</option>
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198 </param>
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199 <when value="heidelberg"/>
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200 <when value="enteritidis"/>
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201 <when value="custom">
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202 <param name="scheme_input"
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203 type="data" format="fasta"
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204 label="Your biohansel SNP Subtyping Scheme"/>
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205 </when>
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206 </conditional>
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207 <param name="subtype_metadata"
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208 type="data" format="tabular,csv"
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209 optional="true"
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210 label="Scheme Subtype Metadata Table [Optional]"
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211 help="CSV or tab-delimited format only. Must contain a 'subtype' column."
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212 />
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213 <!-- K-mer frequencies. -->
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214 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
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215 <param name="kmer_min" type="integer"
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216 argument="--min-kmer-freq"
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217 optional="true"
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218 min="0" value="8"
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219 label="Min k-mer frequency/coverage"
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220 help="default = 8"/>
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221 <param name="kmer_max" type="integer"
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222 argument="--max-kmer-freq"
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223 optional="true"
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224 min="1" value="1000"
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225 label="Max k-mer frequency/coverage"
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226 help="default = 1000"/>
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227 </section>
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228 <!-- Quality Checking Parameters -->
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229 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
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230 <param name="low_cov_depth_freq" type="integer"
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231 argument="--low-cov-depth-freq"
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232 value="20" min="0"
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233 optional="true"
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234 label="QC: Frequency below this coverage are considered low coverage"
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235 help="default = 20"/>
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236 <param name="min_ambiguous_tiles" type="integer"
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237 argument="--min-ambiguous-tiles"
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238 optional="true"
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239 value="3" min="0"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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240 label="QC: Min number of tiles missing for Ambiguous Result"
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241 help="default = 3"/>
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242 <param name="max_missing_tiles" type="float"
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243 argument="--max-missing-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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244 optional="true"
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245 value="0.05" min="0" max="1"
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246 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/>
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247 <param name="max_intermediate_tiles" type="float"
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248 argument="--max-intermediate-tiles"
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249 optional="true"
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250 value="0.05" min="0" max="1"
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251 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype"
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252 help="default = 0.05, valid values {0.0 - 1.0}"/>
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253 <param name="low_coverage_warning" type="integer"
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254 argument="--low-cov-warning"
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255 optional="true"
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256 value="20"
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257 label="QC: Overall tile coverage below this value will trigger a low coverage warning"
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258 help="default = 20"/>
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259 </section>
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260 <section name="dev_args" title="Developer Options" expanded="False">
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261 <param name="use_json"
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262 type="boolean"
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263 checked="false"
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264 truevalue="--json"
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265 falsevalue=""
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266 label="Output JSON results"
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267 help="Use this option of you need json representations of analysis' details"/>
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268 </section>
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269 </inputs>
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270 <outputs>
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271 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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272 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
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273 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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274 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
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275 <filter>dev_args['use_json']</filter>
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276 </data>
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277 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
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278 <filter>dev_args['use_json']</filter>
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279 </data>
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280 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
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281 <filter>dev_args['use_json']</filter>
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282 </data>
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283 </outputs>
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284 <tests>
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285 <test>
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286 <conditional name="input">
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287 <param name="type" value="fasta"/>
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288 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
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289 </conditional>
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290 <param name="type_of_scheme" value="heidelberg"/>
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291 <output name="results.tab"
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292 value="SRR1002850_SMALL.fasta-results.tab"
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293 ftype="tabular"
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294 compare="sim_size"
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295 delta="1000">
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296 </output>
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297 <output name="match_results.tab"
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298 value="SRR1002850_SMALL.fasta-match_results.tab"
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299 ftype="tabular"
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300 compare="sim_size"
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301 delta="16000">
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302 </output>
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303 <output name="tech_results.tab"
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304 value="SRR1002850_SMALL.fasta-tech_results.tab"
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305 ftype="tabular"
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306 lines_diff="0">
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307 </output>
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308 </test>
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309 <test>
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310 <conditional name="input">
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311 <param name="type" value="paired"/>
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312 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
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313 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
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314 </conditional>
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315 <param name="type_of_scheme" value="heidelberg"/>
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316 <output name="tech_results.tab"
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317 value="SRR5646583_SMALL-tech_results.tab"
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318 ftype="tabular"
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319 lines_diff="0">
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320 </output>
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321 <output name="results.tab"
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322 value="SRR5646583_SMALL-results.tab"
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323 ftype="tabular"
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324 compare="sim_size"
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325 delta="1000">
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326 </output>
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327 <output name="match_results.tab"
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328 value="SRR5646583_SMALL-match_results.tab"
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329 ftype="tabular"
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330 compare="sim_size"
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331 delta="16000">
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332 </output>
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333 </test>
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334 </tests>
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335 <help><![CDATA[
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336 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
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337
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338 **Usage**
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339
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340 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
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341 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping scheme, *Salmonella enterica* serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
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342 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
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343 4) Click ``Execute``
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344
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345 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_.
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346
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347
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348 **Example analysis results of a single FASTA file**
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349
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350 Contents of ``results.tab``:
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351
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352 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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353 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message |
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354 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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355 | 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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356 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
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357
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358
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359 Contents of ``match_results.tab``:
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360
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361 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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362 | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message |
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363 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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364 | 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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365 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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366 | 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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367 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
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368
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369 *Next 201 lines omitted.*
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370
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371
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372
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373 **Example analysis results of a single FASTQ readset**
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374
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375
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376 Contents of ``results.tab``:
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377
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378 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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379 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message |
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380 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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381 | 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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382 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
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383
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384 Contents of ``match_results.tab``:
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385
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386 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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387 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
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388 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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389 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
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390 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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391 | 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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392 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
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393
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394 *Next 202 lines omitted.*
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395
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396
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397 **Example Subtype Metadata**
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398
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399 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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400
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401
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402 +-------------+-------+--------+------------------+
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403 | subtype | clade | source | disease_symptoms |
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404 +-------------+-------+--------+------------------+
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405 | 1 | I | geese | death |
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406 +-------------+-------+--------+------------------+
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407 | 1.1 | I | moose | burns |
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408 +-------------+-------+--------+------------------+
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409 | 2.2.1.1.1 | II | mouse | boils |
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410 +-------------+-------+--------+------------------+
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411 | 2.2.2.2.1.4 | IIa | house | rash |
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412 +-------------+-------+--------+------------------+
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413
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414 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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415
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416
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417 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
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418
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419 ]]></help>
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420 <citations>
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421 <citation type="bibtex">@ARTICLE{a1,
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422 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
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423 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, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
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424 url = {https://github.com/phac-nml/bio_hansel}
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425 }
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426 }</citation>
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427 </citations>
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428 </tool>