Mercurial > repos > nml > sistr_cmd

annotate sistr_cmd.xml @ 4:17fcac7ddf54 draft

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"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
author nml
date Thu, 06 Aug 2020 11:48:49 -0400
parents 5c8ff92e38a9
children 24a7a95867b0
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1 <tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@">
0
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2 <description>
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3 Salmonella In Silico Typing Resource commandline tool for serovar prediction
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4 </description>
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5 <macros>
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6 <token name="@VERSION@">1.1.1</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@VERSION@">sistr_cmd</requirement>
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 <command><![CDATA[
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15 sistr
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16 #for $fasta in $input_fastas
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17 -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}'
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18 #end for
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19 -f $output_format
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20 -o sistr-report.$output_format
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21 -p $cgmlst_profiles
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22 -n $novel_alleles
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23 -a $alleles_output
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24 $use_full_cgmlst_db
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25 $no_cgmlst
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26 $run_mash
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27 $qc
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28 --threads "\${GALAXY_SLOTS:-1}"
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29 -T "\${TMPDIR:-/tmp}"
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30 $keep_tmp
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31 $more_output
0
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32 $verbosity
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33 ]]></command>
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34 <inputs>
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35 <param
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36 name="input_fastas"
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37 type="data"
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38 label="Input Genome(s)"
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39 optional="false"
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40 multiple="true"
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41 format="fasta"
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42 />
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43 <param
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44 name="output_format"
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45 type="select"
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46 label="Results output format"
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47 multiple="false">
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48 <option value="tab" selected="true">
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49 Tabular (tab-delimited values)
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50 </option>
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51 <option value="csv">
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52 CSV (Comma Separated Values)
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53 </option>
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54 <option value="json">
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55 JSON (JavaScript Object Notation)
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56 </option>
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57 </param>
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58 <param
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59 name="use_full_cgmlst_db"
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60 type="boolean"
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61 checked="false"
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62 truevalue="--use-full-cgmlst-db"
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63 falsevalue=""
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64 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database."
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65 />
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66 <param
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67 name="run_mash"
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68 type="boolean"
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69 checked="true"
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70 truevalue="--run-mash"
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71 falsevalue=""
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72 label="Run Mash MinHash-based serovar prediction"
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73 />
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74 <param
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75 name="no_cgmlst"
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76 type="boolean"
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77 checked="false"
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78 truevalue="--no-cgmlst"
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79 falsevalue=""
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80 label="Skip running cgMLST-based serovar prediction"
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81 />
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82 <param
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83 name="qc"
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84 type="boolean"
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85 checked="true"
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86 truevalue="--qc"
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87 falsevalue=""
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88 label="Basic QC of results"
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89 />
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90 <param
3
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91 name="more_output"
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92 type="select"
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93 label="Results verbosity">
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94 <option value="" selected="true">
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95 Basic results only
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96 </option>
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97 <option value="-M">
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98 Report top antigen BLAST results
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99 </option>
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100 <option value="-MM" >
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101 Report all antigen BLAST results
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102 </option>
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103 </param>
2
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104 <param
0
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105 name="keep_tmp"
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106 type="boolean"
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107 checked="false"
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108 falsevalue=""
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109 truevalue="--keep-tmp"
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110 label="Keep temporary analysis directory"
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111 />
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112 <param
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113 name="verbosity"
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114 type="select"
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115 label="Logging verbosity">
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116 <option value="">
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117 Error messages only
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118 </option>
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119 <option value="-v">
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120 Show warning messages
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121 </option>
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122 <option value="-vv" selected="true">
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123 Show info messages
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124 </option>
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125 <option value="-vvv">
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126 Show debug messages
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127 </option>
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128 </param>
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129 </inputs>
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130 <outputs>
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131 <data
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132 name="output_prediction_csv"
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133 format="csv"
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134 label="SISTR Results"
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135 from_work_dir="sistr-report.csv">
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136 <filter>output_format == "csv"</filter>
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137 </data>
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138 <data
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139 name="output_prediction_json"
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140 format="json"
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141 label="SISTR Results"
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142 from_work_dir="sistr-report.json">
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143 <filter>output_format == "json"</filter>
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144 </data>
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145 <data
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146 name="output_prediction_tab"
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147 format="tabular"
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148 label="SISTR Results"
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149 from_work_dir="sistr-report.tab">
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150 <filter>output_format == "tab"</filter>
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151 </data>
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152 <data
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153 name="cgmlst_profiles"
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154 format="csv"
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155 label="cgMLST results" />
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156 <data
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157 name="novel_alleles"
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158 format="fasta"
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159 label="Novel cgMLST alleles" />
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160 <data
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161 name="alleles_output"
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162 format="json"
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163 label="cgMLST allele match results" />
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164 </outputs>
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165 <tests>
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166 <test>
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167 <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/>
0
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168 <param name="output_format" value="tab"/>
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169 <output
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170 name="cgmlst_profiles"
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171 value="cgmlst-profiles.csv"
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172 ftype="csv"
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173 compare="diff">
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174 </output>
4
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175 <output name="output_prediction_tab"
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176 ftype="tabular"
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177 value="sistr-results.tabular"
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178 compare="sim_size">
0
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179 <assert_contents>
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180 <has_text text="AE014613-699860" />
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181 <has_text text="Typhi" />
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182 <has_text text="enterica" />
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183 <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/>
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184 <has_text text="2014-LET-0419"/>
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185 <has_n_columns n="22" />
0
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186 </assert_contents>
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187 </output>
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188 <output
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189 name="alleles_output"
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190 value="alleles-output.json"
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191 ftype="json"
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192 compare="sim_size">
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193 <assert_contents>
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194 <has_text text="NZ_AOXE01000059.1"/>
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195 <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/>
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196 <has_text text="NZ_AOXE01000033.1"/>
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197 <has_text text="NZ_AOXE01000052.1"/>
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198 </assert_contents>
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199 </output>
0
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200 </test>
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201 <test>
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202 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta" ftype="fasta"/>
0
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203 <param name="output_format" value="tab"/>
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204 <output
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205 name="novel_alleles"
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206 value="novel-alleles-13-1101.fasta"
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207 ftype="fasta"
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208 compare="sim_size"/>
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209 <output
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210 name="cgmlst_profiles"
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211 value="cgmlst-profiles-13-1101.csv"
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212 ftype="csv"
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213 compare="diff">
0
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214 </output>
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215 <output
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216 name="output_prediction_tab"
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217 value="sistr-results-13-1101.tabular"
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218 ftype="tabular"
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219 compare="sim_size">
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220 <assert_contents>
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221 <has_text text="13-1101-Paratyphi_B"/>
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222 <has_text text="Paratyphi B var. Java"/>
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223 <has_text text="enterica"/>
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224 <has_text text="1,4,[5],12"/>
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225 <has_text text="PASS"/>
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226 <has_n_columns n="22"/>
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227 </assert_contents>
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228 </output>
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229 <output
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230 name="alleles_output"
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231 value="alleles-output-13-1101.json"
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232 ftype="json"
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233 compare="sim_size">
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234 <assert_contents>
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235 <has_text text="13-1101-Paratyphi_B"/>
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236 <has_text text="NZ_AOXE01000059.1"/>
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237 </assert_contents>
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238 </output>
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239 </test>
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240 </tests>
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241 <help>
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242 <![CDATA[
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243
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244 Usage::
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245
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246 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
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247 [-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES]
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248 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
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249 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
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250 [-v] [-V]
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251 [F [F ...]]
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252
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253 SISTR (Salmonella In Silico Typing Resource) Command-line Tool
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254 ==============================================================
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255 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
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256
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257 Note about using the "--use-full-cgmlst-db" flag:
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258 The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
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259
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260 If you find this program useful in your research, please cite as:
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261
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262 The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
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263 Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
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264 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
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265
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266 positional arguments:
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267 F Input genome FASTA file
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268
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269 optional arguments:
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270 -h, --help show this help message and exit
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271 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
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272 fasta file path to genome name pair
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273 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
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274 Output format (json, csv, pickle)
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275 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
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276 SISTR serovar prediction output path
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277 -M, --more-results Output more detailed results (-M) and all antigen
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278 search blastn results (-MM)
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279 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
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280 Output CSV file destination for cgMLST allelic
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281 profiles
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282 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
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283 Output FASTA file destination of novel cgMLST alleles
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284 from input genomes
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285 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
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286 Output path of allele sequences and info to JSON
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287 -T TMP_DIR, --tmp-dir TMP_DIR
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288 Base temporary working directory for intermediate
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289 analysis files.
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290 -K, --keep-tmp Keep temporary analysis files.
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291 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include
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292 highly similar alleles. By default the smaller
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293 "centroid" alleles or representative alleles are used
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294 for each marker.
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295 --no-cgmlst Do not run cgMLST serovar prediction
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296 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella
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297 genomes with trusted serovar designations. Mash binary
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298 must be in accessible via $PATH (e.g. /usr/bin).
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299 --qc Perform basic QC to provide level of confidence in
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300 serovar prediction results.
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301 -t THREADS, --threads THREADS
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302 Number of parallel threads to run sistr_cmd analysis.
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303 -v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
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304 show debug info)
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305 -V, --version show program's version number and exit
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306 ]]>
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307
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308 </help>
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309 <citations>
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310 <!-- Citation for SISTR PLOS ONE paper -->
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311 <citation type="doi">10.1371/journal.pone.0147101</citation>
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312 </citations>
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313 </tool>