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1 <tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="1.0.0">
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2 <description>from input data</description>
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3 <requirements>
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4 <requirement type="package" version="1.76">biopython</requirement>
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5 <requirement type="package" version="5.3">pyyaml</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import os
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9 #import re
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10 #set gzipped = 'false'
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11 #set input_type = $input_type_cond.input_type
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12 #set input_reads_dir = 'input_reads'
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13 #set output_dbkey_dir = 'output_dbkey'
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14 #set output_metrics_dir = 'output_metrics'
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15 mkdir -p $input_reads_dir &&
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16 mkdir -p $output_dbkey_dir &&
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17 mkdir -p $output_metrics_dir &&
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18 #if str($input_type) == "single":
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19 #set read_type_cond = $input_type_cond.read_type_cond
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20 #set read1 = $read_type_cond.read1
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21 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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22 #if str($read_type_cond.read_type) == "single":
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23 ln -s '${read1}' '${read1_identifier}' &&
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24 #if $read1.is_of_type('fastqsanger.gz'):
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25 #set gzipped = 'true'
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26 #end if
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27 #else:
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28 #set read2 = $read_type_cond.read2
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29 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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30 ln -s '${read1}' '${read1_identifier}' &&
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31 ln -s '${read2}' '${read2_identifier}' &&
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32 #if $read1.is_of_type('fastqsanger.gz') and $read2.is_of_type('fastqsanger.gz'):
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33 #set gzipped = 'true'
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34 #end if
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35 #end if
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36 #else:
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3
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37 #set collection_type = $input_type_cond.collection_type_cond.collection_type
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1
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38 #for $i in $input_type_cond.collection_type_cond.reads_collection:
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0
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39 #if $i.is_of_type('fastqsanger.gz'):
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40 #set gzipped = 'true'
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41 #end if
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42 #set filename = $i.file_name
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3
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43 #if str($collection_type) == 'single_reads':
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44 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
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45 #else:
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46 ## Galaxy builds lists of pairs as nested lists with elements
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47 ## named forward and reverse. When flattened, these lists
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48 ## will work as inputs to the Parse parameter value expression
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49 ## tool in workflows. However, the output list created by the
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50 ## expression tool will not function correctly with the bwa_mem
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51 ## mapper. Naming the identifier as follows is a solution.
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52 #set identifier = re.sub('[^\s\w\-]', '_', str($i.name))
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53 #end if
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1
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54 ln -s '$filename' '$input_reads_dir/$identifier' &&
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0
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55 #end for
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56 #end if
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57 python '$__tool_directory__/vsnp_determine_ref_from_data.py'
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58 #if str($input_type) == "single":
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59 #if str($read_type_cond.read_type) == "single":
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60 --read1 '${read1_identifier}'
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61 #else:
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62 --read1 '${read1_identifier}'
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63 --read2 '${read2_identifier}'
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64 #end if
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65 --output_dbkey '$output_dbkey'
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66 --output_metrics '$output_metrics'
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67 #end if
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68 --gzipped $gzipped
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69 --processes $processes
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1
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70 #if str($in_test_mode) == "false":
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71 #set $dnaprint_fields = $__app__.tool_data_tables['vsnp_dnaprints'].get_fields()
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72 #for $i in $dnaprint_fields:
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73 --dnaprint_fields '${i[0]}' '${i[2]}'
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74 #end for
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75 #else:
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76 --in_test_mode '$in_test_mode'
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77 #end if
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0
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78 ]]></command>
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79 <inputs>
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80 <conditional name="input_type_cond">
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81 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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82 <option value="single" selected="true">Single files</option>
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83 <option value="collection">Collection of files</option>
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84 </param>
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85 <when value="single">
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86 <conditional name="read_type_cond">
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87 <param name="read_type" type="select" label="Choose the read type">
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88 <option value="paired" selected="true">Paired</option>
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89 <option value="single">Single</option>
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90 </param>
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91 <when value="paired">
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92 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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93 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
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94 </when>
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95 <when value="single">
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96 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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97 </when>
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98 </conditional>
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99 </when>
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100 <when value="collection">
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1
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101 <conditional name="collection_type_cond">
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102 <param name="collection_type" type="select" label="Collection of single reads or paired reads?">
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103 <option value="single_reads" selected="true">Single reads</option>
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104 <option value="paired_reads">Paired reads</option>
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105 </param>
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106 <when value="single_reads">
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107 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/>
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108 </when>
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109 <when value="paired_reads">
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110 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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111 </when>
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112 </conditional>
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0
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113 </when>
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114 </conditional>
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115 <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
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1
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116 <!-- Functional testing -->
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117 <param name="in_test_mode" type="hidden" value="false"/>
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0
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118 </inputs>
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119 <outputs>
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120 <data name="output_dbkey" format="txt" label="${tool.name} (dbkey) on ${on_string}">
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121 <filter>input_type_cond['input_type'] == 'single'</filter>
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122 </data>
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123 <data name="output_metrics" format="txt" label="${tool.name} (metrics) on ${on_string}">
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124 <filter>input_type_cond['input_type'] == 'single'</filter>
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125 </data>
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126 <collection name="output_dbkey_collection" type="list" label="${tool.name} (dbkey) on ${on_string}">
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1
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127 <discover_datasets pattern="__name__" directory="output_dbkey" format="txt"/>
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128 <filter>input_type_cond['input_type'] == 'collection'</filter>
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129 </collection>
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2
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130 <collection name="output_metrics_collection" type="list" label="${tool.name} (metrics) on ${on_string}">
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1
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131 <discover_datasets pattern="__name__" directory="output_metrics" format="txt"/>
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0
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132 <filter>input_type_cond['input_type'] == 'collection'</filter>
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133 </collection>
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134 </outputs>
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135 <tests>
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136 <test>
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1
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137 <param name="in_test_mode" value="true"/>
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138 <param name="read_type" value="single"/>
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139 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz"/>
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0
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140 <output name="output_dbkey" file="output_dbkey.txt" ftype="txt"/>
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141 <output name="output_metrics" file="output_metrics.txt" ftype="txt"/>
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142 </test>
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1
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143 <test>
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144 <param name="in_test_mode" value="true"/>
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145 <param name="input_type" value="collection"/>
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146 <param name="collection_type" value="paired_reads"/>
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147 <param name="reads_collection">
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148 <collection type="paired">
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149 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz"/>
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150 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz"/>
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151 </collection>
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152 </param>
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153 <output_collection name="output_dbkey_collection" type="list">
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154 <element name="forward.txt" file="forward_dbkey.txt" ftype="txt"/>
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155 <element name="reverse.txt" file="reverse_dbkey.txt" ftype="txt"/>
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156 </output_collection>
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157 <output_collection name="output_metrics_collection" type="list">
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158 <element name="forward.txt" file="forward_metrics.txt" ftype="txt"/>
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159 <element name="reverse.txt" file="reverse_metrics.txt" ftype="txt"/>
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160 </output_collection>
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161 </test>
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162 </tests>
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163 <help>
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164 **What it does**
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165
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166 Accepts a single fastqsanger read, a set of paired reads, or a collection of reads and inspects the data to discover the
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167 best reference genome for aligning the reads. This tool is, in essence, a DNA sniffer, and is the first Galaxy tool to
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168 perform this task. While inspecting the data, a string of 0's and 1's is compiled based on the data contents, and we call
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169 the complete string a "DNA print". All of the "DNA prints" files installed by the complementary **vSNP DNAprints data
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170 manager** tool are then inspected to find a match for the compiled "DNA print" string. These files are each associated
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171 with a Galaxy "dbkey" (i.e., genome build), so when a metach is found, the associated "dbkey" is passed to a mapper (e.g.,
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172 **Map with BWA-MEM**) to align the reads to the associated reference.
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173
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174 The tool produces 2 text files, a "dbkey" file that contains the dbkey string and a "metrics" file that provides information
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175 used to compile the "DNA print" string.
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176
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177 This tool is important for samples containing bacterial species because many of the samples have a "mixed bag" of species,
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178 and discovering the primary species is critical. DNA print matchig is currently supported for the following genomes.
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179
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180 * Mycobacterium bovis AF2122/97
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181 * Brucella abortus bv. 1 str. 9-941
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182 * Brucella abortus strain BER
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183 * Brucella canis ATCC 23365
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184 * Brucella ceti TE10759-12
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185 * Brucella melitensis bv. 1 str. 16M
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186 * Brucella melitensis bv. 3 str. Ether
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187 * Brucella melitensis BwIM_SOM_36b
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188 * Brucella melitensis ATCC 23457
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189 * Brucella ovis ATCC 25840
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190 * Brucella suis 1330
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191 * Mycobacterium tuberculosis H37Rv
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192 * Mycobacterium avium subsp. paratuberculosis strain Telford
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193 * Mycobacterium avium subsp. paratuberculosis K-10
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194 * Brucella suis ATCC 23445
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195 * Brucella suis bv. 3 str. 686
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196
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197 **Required Options**
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198
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199 * **Choose the category of the files to be analyzed** - select "Single files" or "Collection of files", then select the appropriate history items (single or paired fastqsanger reads or a collection of fastqsanger reads) based on the selected option.
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200 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
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201 </help>
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202 <citations>
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203 <citation type="bibtex">
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204 @misc{None,
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205 journal = {None},
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206 author = {1. Stuber T},
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207 title = {Manuscript in preparation},
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208 year = {None},
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209 url = {https://github.com/USDA-VS/vSNP},}
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210 </citation>
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211 </citations>
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212 </tool>
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213
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