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planemo upload commit 80c22275be05e29208e991019309dfffa9704f39
author nml
date Thu, 15 Feb 2018 12:08:11 -0500
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1 <tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.1">
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2 <description>
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3 Find closest matching NCBI RefSeq Genomes to your sequences
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.1.1">refseq_masher</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10
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11 #import re
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12
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13 #if $input.type == 'fasta'
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14 #set $input_files = '"{}"'.format($input.fasta.name)
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15 ln -s "$input.fasta" $input_files &&
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16 #elif $input.type == 'paired'
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17 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.forward.name) else '.fastq'
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18 #set $_forward = '"{}_1{}"'.format($re.sub(r'_[12]\..+$', '', $input.forward.name), $_forward_ext)
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19 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', $input.reverse.name) else '.fastq'
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20 #set $_reverse = '"{}_2{}"'.format($re.sub(r'_[12]\..+$', '', $input.reverse.name), $_reverse_ext)
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21 #set $input_files = '{} {}'.format($_forward, $_reverse)
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22 ln -s "$input.forward" $_forward &&
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23 ln -s "$input.reverse" $_reverse &&
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24 #elif $input.type == 'single'
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25 #set $input_files = '"{}"'.format($input.single.name)
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26 ln -s "$input.single" $input_files &&
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27 #elif $input.type == 'paired_collection'
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28 #set $_forward_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.forward)) else '.fastq'
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29 #set $_forward = '"{}_1{}"'.format($input.paired_collection.name, $_forward_ext)
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30 #set $_reverse_ext = '.fastq.gz' if $re.match(r'.*\.gz$', str($input.paired_collection.reverse)) else '.fastq'
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31 #set $_reverse = '"{}_2{}"'.format($input.paired_collection.name, $_reverse_ext)
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32 #set $input_files = '{} {}'.format($_forward, $_reverse)
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33 ln -s "$input.paired_collection.forward" $_forward &&
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34 ln -s "$input.paired_collection.reverse" $_reverse &&
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35 #end if
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36
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37 refseq_masher
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38 $adv.verbosity
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39 matches
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40 --output refseq_masher-matches.${adv.output_type}
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41 --output-type $adv.output_type
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42 --top-n-results $top_n_results
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43 #if $adv.min_kmer_threshold
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44 --min-kmer-threshold $adv.min_kmer_threshold
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45 #end if
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46 -T "\${TMPDIR:-/tmp}"
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47 $input_files
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48 ]]>
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49 </command>
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50 <inputs>
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51 <conditional name="input">
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52 <param name="type" type="select" label="Sequence input type">
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53 <option value="fasta">Genome FASTA</option>
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54 <option value="paired">Paired-end FASTQs</option>
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55 <option value="single">Single-end FASTQ</option>
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56 <option value="paired_collection">Paired-end FASTQ collection</option>
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57 </param>
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58 <when value="fasta">
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59 <param name="fasta"
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60 type="data" format="fasta"
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61 optional="false"
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62 label="Genome FASTA file"
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63 />
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64 </when>
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65 <when value="paired">
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66 <param name="forward"
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67 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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68 optional="false"
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69 label="Forward FASTQ file"
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70 />
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71 <param name="reverse"
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72 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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73 optional="false"
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74 label="Reverse FASTQ file"
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75 help="File format must match the Forward FASTQ file"
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76 />
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77 </when>
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78 <when value="single">
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79 <param name="single"
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80 type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"
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81 optional="false"
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82 label="Single-end FASTQ file"
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83 />
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84 </when>
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85 <when value="paired_collection">
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86 <param name="paired_collection"
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87 type="data_collection" format="fastq,fastqsanger,fastqillumina,fastqsolexa,fastq.gz,txt"
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88 collection_type="paired"
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89 optional="false"
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90 label="Paired-end FASTQ collection"
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91 />
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92 </when>
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93 </conditional>
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94 <param name="top_n_results"
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95 type="integer"
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96 min="0"
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97 value="20"
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98 optional="true"
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99 label="Top N matches to report (set to 0 to report all)"
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100 />
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101 <section name="adv" title="Advanced Options" expanded="false">
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102 <param name="min_kmer_threshold"
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103 type="integer"
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104 min="1"
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105 value="8"
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106 optional="true"
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107 label="Mash sketch of reads: Minimum copies of each k-mer required to pass noise filter for reads (default=8)"
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108 />
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109 <param name="output_type"
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110 type="select"
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111 label="Output type"
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112 multiple="false">
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113 <option value="tab" selected="true">
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114 Tabular (tab-delimited values)
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115 </option>
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116 <option value="csv">
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117 CSV (Comma Separated Values)
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118 </option>
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119 </param>
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120 <param name="verbosity"
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121 type="select"
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122 label="Logging verbosity">
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123 <option value="">Error messages only</option>
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124 <option value="-v">Show warning messages</option>
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125 <option value="-vv" selected="true">Show info messages</option>
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126 <option value="-vvv">Show debug messages</option>
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127 </param>
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128 </section>
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129 </inputs>
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130 <outputs>
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131 <data name="output_path_csv"
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132 format="csv"
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133 label="RefSeq Masher matches table"
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134 from_work_dir="refseq_masher-matches.csv">
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135 <filter>adv['output_type'] == 'csv'</filter>
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136 </data>
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137 <data name="output_path_tab"
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138 format="tabular"
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139 label="RefSeq Masher matches table"
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140 from_work_dir="refseq_masher-matches.tab">
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141 <filter>adv['output_type'] == 'tab'</filter>
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142 </data>
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143 </outputs>
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144 <tests>
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145 <test>
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146 <conditional name="input">
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147 <param name="type" value="fasta"/>
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148 <param name="fasta" value="Se-Enteritidis.fasta"/>
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149 </conditional>
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150 <param name="top_n_results" value="1"/>
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151 <section name="adv">
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152 <param name="output_type" value="tab"/>
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153 </section>
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154 <output name="output_path_tab"
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155 value="Se-Enteritidis-refseq_masher-matches.tab"
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156 ftype="tabular"
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157 lines_diff="0">
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158 </output>
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159 </test>
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160 <test>
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161 <conditional name="input">
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162 <param name="type" value="single"/>
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163 <param name="single" value="SRR1203042_1-head4000.fastq"/>
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164 </conditional>
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165 <param name="top_n_results" value="1"/>
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166 <section name="adv">
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167 <param name="output_type" value="tab"/>
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168 <param name="min_kmer_threshold" value="2"/>
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169 </section>
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170 <output name="output_path_tab"
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171 value="SRR1203042_1-head4000-refseq_masher-matches-m2.tab"
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172 ftype="tabular"
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173 lines_diff="0">
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174 </output>
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175 </test>
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176 </tests>
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177 <help>
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178 <![CDATA[
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179 RefSeq Masher - Genomic Distance
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180 ================================
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181
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182 Find what NCBI RefSeq genomes most closely match your sequence data using Mash_ with a Mash sketch database of 54,925 NCBI RefSeq Genomes.
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183
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184
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185 Source code available on Github at https://github.com/phac-nml/refseq_masher
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186
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187
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188 `matches` - find the closest matching NCBI RefSeq Genomes in your input sequences
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189 ---------------------------------------------------------------------------------
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190
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191 Command-line usage information::
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192
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193 Usage: refseq_masher matches [OPTIONS] INPUT...
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194
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195 Find NCBI RefSeq genome matches for an input genome fasta file
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196
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197 Input is expected to be one or more FASTA/FASTQ files or one or more
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198 directories containing FASTA/FASTQ files. Files can be Gzipped.
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199
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200 Options:
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201 --mash-bin TEXT Mash binary path (default="mash")
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202 -o, --output PATH Output file path (default="-"/stdout)
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203 --output-type [tab|csv] Output file type (tab|csv)
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204 -n, --top-n-results INTEGER Output top N results sorted by distance in
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205 ascending order (default=5)
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206 -m, --min-kmer-threshold INTEGER
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207 Mash sketch of reads: "Minimum copies of
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208 each k-mer required to pass noise filter for
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209 reads" (default=8)
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210 -h, --help Show this message and exit.
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211
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212
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213 Example
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214 ~~~~~~~
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215
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216 With the FNA.GZ_ file for *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_::
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217
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218
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219 # download sequence file
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220 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz
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221
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222 # find RefSeq matches
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223 refseq_masher -vv matches GCF_000329025.1_ASM32902v1_genomic.fna.gz
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224
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225
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226 **Log**::
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227
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228
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229 2018-01-29 11:02:13,786 INFO: Collected 1 FASTA inputs and 0 read sets [in ...refseq_masher/refseq_masher/utils.py:185]
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230 2018-01-29 11:02:13,786 INFO: Creating Mash sketch file for ...refseq_masher/GCF_000329025.1_ASM32902v1_genomic.fna.gz [in ...refseq_masher/refseq_masher/mash/sketch.py:24]
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231 2018-01-29 11:02:14,055 INFO: Created Mash sketch file at "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/sketch.py:40]
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232 2018-01-29 11:02:14,613 INFO: Ran Mash dist successfully (output length=11647035). Parsing Mash dist output [in ...refseq_masher/refseq_masher/mash/dist.py:64]
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233 2018-01-29 11:02:15,320 INFO: Parsed Mash dist output into Pandas DataFrame with 54924 rows [in ...refseq_masher/refseq_masher/mash/dist.py:67]
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234 2018-01-29 11:02:15,321 INFO: Deleting temporary sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" [in ...refseq_masher/refseq_masher/mash/dist.py:72]
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235 2018-01-29 11:02:15,321 INFO: Sketch file "/tmp/GCF_000329025.1_ASM32902v1_genomic.msh" deleted! [in ...refseq_masher/refseq_masher/mash/dist.py:74]
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236 2018-01-29 11:02:15,322 INFO: Ran Mash dist on all input. Merging NCBI taxonomic information into results output. [in ...refseq_masher/refseq_masher/cli.py:88]
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237 2018-01-29 11:02:15,323 INFO: Fetching all taxonomy info for 5 unique NCBI Taxonomy UIDs [in ...refseq_masher/refseq_masher/taxonomy.py:35]
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238 2018-01-29 11:02:15,325 INFO: Dropping columns with all NA values (ncol=32) [in ...refseq_masher/refseq_masher/taxonomy.py:38]
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239 2018-01-29 11:02:15,327 INFO: Columns with all NA values dropped (ncol=11) [in ...refseq_masher/refseq_masher/taxonomy.py:40]
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240 2018-01-29 11:02:15,327 INFO: Merging Mash results with relevant taxonomic information [in ...refseq_masher/refseq_masher/taxonomy.py:41]
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241 2018-01-29 11:02:15,329 INFO: Merged Mash results with taxonomy info [in ...refseq_masher/refseq_masher/taxonomy.py:43]
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242 2018-01-29 11:02:15,329 INFO: Merged taxonomic info into results output [in ...refseq_masher/refseq_masher/cli.py:90]
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243 2018-01-29 11:02:15,329 INFO: Reordering output columns [in ...refseq_masher/refseq_masher/cli.py:91]
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244 2018-01-29 11:02:15,331 INFO: Writing output to stdout [in ...refseq_masher/refseq_masher/writers.py:16]
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245
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246
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247 **Output**
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248
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249 +---------------------------------------+--------------------------------------------------------------------+----------+--------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------+---------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+-------------+---------+-------------+--------------+--------+---------------------+------------------------------------------------------------------------------------------------------------------------------------------+
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250 | sample | top_taxonomy_name | distance | pvalue | matching | full_taxonomy | taxonomic_subspecies | taxonomic_species | taxonomic_genus | taxonomic_family | taxonomic_order | taxonomic_class | taxonomic_phylum | taxonomic_superkingdom | subspecies | serovar | plasmid | bioproject | biosample | taxid | assembly_accession | match_id |
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251 +=======================================+====================================================================+==========+========+==========+=============================================================================================================================================================+=====================================+=====================+==================+====================+==================+=====================+===================+=========================+============+=============+=========+=============+==============+========+=====================+==========================================================================================================================================+
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252 | GCF_000329025.1_ASM32902v1_genomic | Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 | 0.0 | 0.0 | 400/400 | Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Enteritidis; str. CHS44 | Salmonella enterica subsp. enterica | Salmonella enterica | Salmonella | Enterobacteriaceae | Enterobacterales | Gammaproteobacteria | Proteobacteria | Bacteria | enterica | Enteritidis | | PRJNA185053 | SAMN01041154 | 702979 | NZ_ALFF | ./rcn/refseq-NZ-702979-PRJNA185053-SAMN01041154-NZ_ALFF-.-Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._CHS44.fna |
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253 +---------------------------------------+--------------------------------------------------------------------+----------+--------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------+---------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+-------------+---------+-------------+--------------+--------+---------------------+------------------------------------------------------------------------------------------------------------------------------------------+
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254
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255
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256 The top match is *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_ with a distance of 0.0 and 400/400 sketches matching, which is what we expected. There's other taxonomic information available in the results table that may be useful.
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257
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258
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259
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260 Legal
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261 -----
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262
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263 Copyright Government of Canada 2017
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264
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265 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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266
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267 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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268 this work except in compliance with the License. You may obtain a copy of the
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269 License at:
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270
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271 http://www.apache.org/licenses/LICENSE-2.0
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272
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273 Unless required by applicable law or agreed to in writing, software distributed
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274 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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275 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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276 specific language governing permissions and limitations under the License.
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277
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278 Contact
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279 -------
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280
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281 **Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca
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282
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283 .. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x
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284 .. _FNA.GZ: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz
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285 .. _CHS44: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/
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286
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287
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288 ]]>
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289 </help>
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290 <citations>
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291 <!-- Citation for Mash paper -->
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292 <citation type="doi">10.1186/s13059-016-0997-x</citation>
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293 </citations>
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294 </tool>