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1 <tool id="chewBBACA" name="chewBBACA" version="2.0">
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2 <description>BSR-Based Allele Calling Algorithm
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="3.6">Python</requirement>
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6 <requirement type="package" version="1.15.3">numpy</requirement>
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7 <requirement type="package" version="0.19.1">scipy</requirement>
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8 <requirement type="package" version="5.22.2.1">perl</requirement>
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9 <requirement type="package" version="1.72">biopython</requirement>
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10 <requirement type="package" version="3.8.1">plotly</requirement>
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11 <requirement type="package" version="1.8.2">SPARQLWrapper</requirement>
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12 <requirement type="package" version="0.23.4">pandas</requirement>
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13 <requirement type="package" version="2.5.0">blast</requirement>
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14 <requirement type="package" version="2.6.3">prodigal</requirement>
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15 <requirement type="package" version="2.1">clustalw</requirement>
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16 <requirement type="package" version="7.313">mafft</requirement>
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17 <requirement type="package" version="2.0.16">chewbbaca</requirement>
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18 </requirements>
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19 <!-- basic error handling -->
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20 <stdio>
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21 <!-- Assume anything other than zero is an error -->
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22 <exit_code range="1:" level="fatal" description="Tool exception" />
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23 <exit_code range=":-1" level="fatal" description="Tool exception" />
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24 </stdio>
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25 <command>
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26 perl
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27 $__tool_directory__/chewBBACA.pl $selectFunction.myFunctions
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28 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
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29 '${",".join(map(str, $selectFunction.input1))}'
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30 #elif str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes')
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31 $selectFunction.input1
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32 #else
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33 'NULL'
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34 #end if
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35 #if str( $selectFunction.myFunctions ) == 'AlleleCall'
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36 #set $input_names = []
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37 #for $input in $selectFunction.input1
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38 $input_names.append($input.element_identifier)
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39 #end for
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40 #set $input_name = ",".join(map(str, $input_names))
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41 '$input_name'
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42 #else
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43 'NULL'
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44 #end if
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45 #if str( $selectFunction.myFunctions ) == 'CreateSchema'
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46 '$schema'
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47 #elif str( $selectFunction.myFunctions ) == 'AlleleCall'
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48 '$statistics,$contigsinfo,$alleles,$logginginfo,$repeatedloci'
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49 #elif str( $selectFunction.myFunctions ) == 'SchemaEvaluator'
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50 '$schemaplot'
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51 #elif str( $selectFunction.myFunctions ) == 'TestGenomeQuality'
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52 '$thresholdplot,$removedgenomes'
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53 #elif str( $selectFunction.myFunctions ) == 'RemoveGenes'
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54 '$removedgenes'
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55 #else
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56 'NULL'
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57 #end if
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58
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59 "chewBBACA.py $selectFunction.myFunctions
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60 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall', 'TestGenomeQuality', 'ExtractCgMLST')
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61 -o output_dir
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62 #end if
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63 #if str( $selectFunction.myFunctions ) == 'RemoveGenes'
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64 -o output_removegenes
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65 #end if
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66 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
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67 -i input_dir
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68 --cpu \${GALAXY_SLOTS:-4}
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69 #end if
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70 #if str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes')
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71 -i $selectFunction.input1
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72 #end if
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73 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
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74 #if $selectFunction.bsr
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75 --bsr $selectFunction.bsr
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76 #end if
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77
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78 #if $selectFunction.ptfmode.ptf_select=="system"
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79 --ptf ${ filter( lambda x: str( x[0] ) == str( $selectFunction.ptfmode.ptf_system ), $__app__.tool_data_tables[ 'chewbbaca_ptfs' ].get_fields() )[0][-1] }
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80 #elif $selectFunction.ptfmode.ptf_select=="user"
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81 --ptf $selectFunction.ptfmode.ptf_user
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82 #end if
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83 #end if
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84 #if str( $selectFunction.myFunctions ) == 'CreateSchema'
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85 #if $selectFunction.minBpLocus
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86 -l $selectFunction.minBpLocus
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87 #end if
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88 #end if
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89 #if str( $selectFunction.myFunctions ) == 'AlleleCall'
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90 #if $selectFunction.mode.schema_select=="system"
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91 -g ${ filter( lambda x: str( x[0] ) == str( $selectFunction.mode.reference ), $__app__.tool_data_tables[ 'chewbbaca_schemas' ].get_fields() )[0][-1] }
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92 #else
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93 -g $selectFunction.mode.genes
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94 #end if
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95 #end if
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96 #if str( $selectFunction.myFunctions ) == 'SchemaEvaluator'
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97 --cpu \${GALAXY_SLOTS:-4}
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98 #if $selectFunction.conserved
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99 -p
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100 #end if
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101 -l output_rms/SchemaEvaluator.html
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102 -ta $selectFunction.ncbiTA
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103 -t $selectFunction.threshold
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104 #if $selectFunction.title
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105 --title '$selectFunction.title'
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106 #end if
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107 -s $selectFunction.numBoxplots
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108 #if $selectFunction.light
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109 --light
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110 #end if
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111 #end if
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112 #if str( $selectFunction.myFunctions ) == 'TestGenomeQuality'
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113 -n $selectFunction.maxNumIterations
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114 -t $selectFunction.maxThreshold
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115 -s $selectFunction.stepThreshold
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116 #end if
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117 #if str( $selectFunction.myFunctions ) == 'ExtractCgMLST'
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118 #if $selectFunction.genes
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119 -r $selectFunction.genes
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120 #end if
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121 #if $selectFunction.genomes
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122 -g $selectFunction.genomes
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123 #end if
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124 #if $selectFunction.maxPresence
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125 -p $selectFunction.maxPresence
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126 #end if
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127 #end if
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128 #if str( $selectFunction.myFunctions ) == 'RemoveGenes'
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129 -g $selectFunction.genes
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130 #end if
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131 "
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132 </command>
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133
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134 <inputs>
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135 <conditional name="selectFunction">
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136 <param name="myFunctions" type="select" label="Select function">
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137 <option value="CreateSchema">CreateSchema: Create a gene by gene schema based on genomes</option>
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138 <option value="AlleleCall" selected="true">AlleleCall: Perform allele call for target genomes</option>
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139 <option value="SchemaEvaluator">SchemaEvaluator: Tool that builds an html output to better navigate/visualize your schema</option>
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140 <option value="TestGenomeQuality">TestGenomeQuality: Analyze your allele call output to refine schemas</option>
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141 <option value="ExtractCgMLST">ExtractCgMLST: Select a subset of loci without missing data (to be used as PHYLOViZ input)</option>
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142 <option value="RemoveGenes">RemoveGenes: Remove a provided list of loci from your allele call output</option>
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143 </param>
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144 <when value="CreateSchema">
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145 <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" />
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146 <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" />
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147 <conditional name="ptfmode">
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148 <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?">
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149 <option value="system" selected="True">System training file</option>
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150 <option value="user">Own training file</option>
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151 </param>
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152 <when value="system">
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153 <param name="ptf_system" type="select" label="Choose Prodigal training file">
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154 <options from_data_table="chewbbaca_ptfs" />
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155 </param>
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156 </when>
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157 <when value="user">
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158 <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" />
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159 </when>
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160 </conditional>
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161 <param name="minBpLocus" type="integer" value="200" optional="true" label="minimum bp locus lenght" help="Integer" />
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162 </when>
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163 <when value="AlleleCall">
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164 <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" />
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165 <conditional name="mode">
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166 <param name="schema_select" type="select" display="radio" label="Which schema would you like to use as a reference?">
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167 <option value="system" selected="True">System reference</option>
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168 <option value="user">Own reference</option>
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169 </param>
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170 <when value="system">
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171 <param name="reference" type="select" label="Choose reference">
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172 <options from_data_table="chewbbaca_schemas" />
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173 </param>
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174 </when>
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175 <when value="user">
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176 <param name="genes" format="txt" type="data" label="File with list of genes (fasta)" />
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177 </when>
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178 </conditional>
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179 <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" />
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180 <conditional name="ptfmode">
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181 <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?">
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182 <option value="system">System training file</option>
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183 <option value="user">Own training file</option>
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184 <option value="noptf" selected="True">No training file</option>
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185 </param>
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186 <when value="system">
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187 <param name="ptf_system" type="select" label="Choose Prodigal training file">
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188 <options from_data_table="chewbbaca_ptfs" />
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189 </param>
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190 </when>
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191 <when value="user">
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192 <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" />
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193 </when>
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194 <when value="noptf" />
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195 </conditional>
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196 <!--<param name="forceContinue" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force continue" />-->
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197 <!--<param name="forceReset" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force reset" />-->
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198 <!--<param name="jsonFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="report in json file" />-->
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199 </when>
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200 <when value="SchemaEvaluator">
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201 <param name="input1" format="txt" type="data" label="File with list of genes (fasta)" />
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202 <param name="conserved" type="boolean" truevalue="true" falsevalue="false" checked="False" label="One bad allele still makes gene conserved" />
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203 <param name="ncbiTA" type="integer" value="11" optional="true" label="ncbi translation table" help="Integer" />
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204 <param name="threshold" type="float" value="0.05" optional="true" label="Threshold" />
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205 <param name="title" type="text" value="My Analyzed wg/cg MLST Schema - Rate My Schema" optional="true" label="title on the html plot" />
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206 <param name="numBoxplots" type="integer" value="500" optional="true" label="number of boxplots per page (more than 500 can make the page very slow)" help="Integer" />
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207 <param name="light" type="boolean" truevalue="true" falsevalue="false" checked="False" label="skip clustal and mafft run" />
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208 </when>
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209 <when value="TestGenomeQuality">
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210 <param name="input1" format="tsv" type="data" label="raw allele call matrix file" />
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211 <param name="maxNumIterations" type="integer" value="12" label="maximum number of iterations" help="Each iteration removes a set of genomes over the defined threshold (-t) and recalculates all loci presence percentages" />
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212 <param name="maxThreshold" type="integer" value="200" label="maximum threshold of bad calls above 95 percent" help="This threshold represents the maximum number of missing loci allowed, for each genome independently, before removing it (genome)" />
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213 <param name="stepThreshold" type="integer" value="5" label="step between each threshold analysis (suggested 5)" help="Integer" />
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214 </when>
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215 <when value="ExtractCgMLST">
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216 <param name="input1" format="tsv" type="data" label="input file to clean" />
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217 <param name="genes" format="txt" type="data" optional="true" label="list of genes to remove, one per line" help="e.g. the list of gene detected by ParalogPrunning.py" />
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218 <param name="genomes" format="txt" type="data" optional="true" label="list of genomes to remove, one per line" help="e.g. list of genomes to be removed selected based on testGenomeQuality results" />
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219 <param name="maxPresence" type="float" value="1.0" optional="true" label="maximum presence (e.g 0.95)" >
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220 <validator type="in_range" min="0" max="1" />
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221 </param>
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222 </when>
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223 <when value="RemoveGenes">
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224 <param name="input1" format="tsv" type="data" label="main matrix file from which to remove" />
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225 <param name="genes" format="txt" type="data" label="list of genes to remove" />
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226 </when>
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227 </conditional>
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228 </inputs>
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229
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230 <!-- define outputs -->
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231 <outputs>
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232 <data format="txt" name="schema" label="${tool.name}:CreateSchema on ${on_string}" >
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233 <filter>selectFunction['myFunctions'] == "CreateSchema"</filter>
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234 </data>
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235 <data format="tsv" name="statistics" label="${tool.name}:AlleleCall on ${on_string}: Statistics" >
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236 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
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237 </data>
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238 <data format="tsv" name="contigsinfo" label="${tool.name}:AlleleCall on ${on_string}: Contigs Info" >
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239 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
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240 </data>
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241 <data format="tsv" name="alleles" label="${tool.name}:AlleleCall on ${on_string}: Alleles" >
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242 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
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243 </data>
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244 <data format="txt" name="logginginfo" label="${tool.name}:AlleleCall on ${on_string}: Logging info" >
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245 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
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246 </data>
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247 <data format="txt" name="repeatedloci" label="${tool.name}:AlleleCall on ${on_string}: Repeated Loci" >
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248 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
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249 </data>
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250 <data format="tar" name="schemaplot" label="${tool.name}:SchemaEvaluator on ${on_string}" >
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251 <filter>selectFunction['myFunctions'] == "SchemaEvaluator"</filter>
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252 </data>
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253 <data format="html" name="thresholdplot" from_work_dir="output_dir/GenomeQualityPlot.html" label="${tool.name}:TestGenomeQuality on ${on_string}: Plot" >
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254 <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter>
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255 </data>
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256 <data format="tsv" name="removedgenomes" from_work_dir="output_dir/removedGenomes.txt" label="${tool.name}:TestGenomeQuality on ${on_string}: Removed genomes" >
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257 <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter>
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258 </data>
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259 <data format="tsv" name="cgmlst" from_work_dir="output_dir/cgMLST.tsv" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLST" >
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260 <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter>
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261 </data>
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262 <data format="txt" name="cgmlstschema" from_work_dir="output_dir/cgMLSTschema.txt" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLSTschema" >
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263 <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter>
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264 </data>
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265 <data format="tsv" name="removedgenes" from_work_dir="output_removegenes.tsv" label="${tool.name}:RemoveGenes on ${on_string}" >
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266 <filter>selectFunction['myFunctions'] == "RemoveGenes"</filter>
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267 </data>
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268 </outputs>
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269 <tests>
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270 <test>
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271 <param name="selectFunction['myFunctions']" value="AlleleCall" />
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272 <param name="input1" value="a_contigs.fasta" ftype="fasta" />
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273 <param name="selectFunction.mode['schema_select']" value="system" />
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274 <param name="selectFunction.mode['reference']" value="schema_pubMLST" />
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275 <param name="selectFunction.mode['ptf_select']" value="noptf" />
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276 <output name="statistics" >
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277 <assert_contents>
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278 <has_text text="a_contigs.fasta" />
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279 </assert_contents>
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280 </output>
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281 </test>
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282 </tests>
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283 <help>
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284 **chewBBACA** stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow"
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285 but at this point still it needs a bit of work to make that claim so we just add "chew" to add extra coolness to the software name.
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286
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287 The development of the tools have been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2
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288 ("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento”
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289 from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014)
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290 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
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291 </help>
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292 <citations>
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293 <citation type="bibtex">@ARTICLE{andrews_s,
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294 author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN and Machado, MP and Oleastro, M and Borges, V and Isidro, J and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK and Halkilahti,
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295 J and Jaakkonen, A and Palma, F and Culebro, A and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M and Garaizer, J and Bikandi, J and Hilbert,
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296 F and Taboada, EN and Carriço, JA},
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297 keywords = {bioinformatics, ngs, mlst},
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298 title = {{INNUENDO whole and core genome MLST databases and schemas for foodborne pathogens}},
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299 url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}
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300 }</citation>
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301 <citation type="doi">10.1099/mgen.0.000166</citation>
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302 <citation type="doi">10.1371/journal.pgen.1007261</citation>
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303 </citations>
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304 </tool>
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