Mercurial > repos > nml > sistr_cmd
annotate sistr_cmd.xml @ 2:13632190a0ff draft
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author | nml |
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date | Thu, 20 Apr 2017 14:33:38 -0400 |
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1 <tool id="sistr_cmd" name="sistr_cmd" version="0.3.6"> |
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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 <requirements> |
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6 <requirement type="package" version="0.3.6">sistr_cmd</requirement> |
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7 </requirements> |
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8 <stdio> |
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9 <exit_code range="1:" /> |
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10 </stdio> |
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11 <command><![CDATA[ |
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12 sistr |
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13 #for $fasta in $input_fastas |
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14 -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}' |
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15 #end for |
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16 -f $output_format |
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17 -o sistr-report.$output_format |
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18 -p $cgmlst_profiles |
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19 -n $novel_alleles |
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20 -a $alleles_output |
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21 $use_full_cgmlst_db |
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22 $no_cgmlst |
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23 $run_mash |
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24 $qc |
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25 --threads "\${GALAXY_SLOTS:-1}" |
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26 -T "\${TMPDIR:-/tmp}" |
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27 $keep_tmp |
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28 $full_output |
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29 $report_blast_results |
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30 $verbosity |
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31 ]]></command> |
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32 <inputs> |
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33 <param |
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34 name="input_fastas" |
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35 type="data" |
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36 label="Input Genome(s)" |
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37 optional="false" |
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38 multiple="true" |
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39 format="fasta" |
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40 /> |
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41 <param |
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42 name="output_format" |
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43 type="select" |
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44 label="Results output format" |
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45 multiple="false"> |
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46 <option value="tab" selected="true"> |
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47 Tabular (tab-delimited values) |
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48 </option> |
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49 <option value="csv"> |
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50 CSV (Comma Separated Values) |
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51 </option> |
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52 <option value="json"> |
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53 JSON (JavaScript Object Notation) |
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54 </option> |
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55 </param> |
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56 <param |
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57 name="use_full_cgmlst_db" |
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58 type="boolean" |
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59 checked="false" |
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60 truevalue="--use-full-cgmlst-db" |
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61 falsevalue="" |
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62 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database." |
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63 /> |
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64 <param |
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65 name="run_mash" |
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66 type="boolean" |
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67 checked="true" |
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68 truevalue="--run-mash" |
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69 falsevalue="" |
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70 label="Run Mash MinHash-based serovar prediction" |
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71 /> |
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72 <param |
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73 name="no_cgmlst" |
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74 type="boolean" |
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75 checked="false" |
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76 truevalue="--no-cgmlst" |
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77 falsevalue="" |
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78 label="Skip running cgMLST-based serovar prediction" |
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79 /> |
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80 <param |
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81 name="qc" |
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82 type="boolean" |
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83 checked="true" |
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84 truevalue="--qc" |
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85 falsevalue="" |
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86 label="Basic QC of results" |
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87 /> |
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88 <param |
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89 name="report_blast_results" |
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90 type="boolean" |
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91 checked="false" |
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92 truevalue="--report-blast-results" |
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93 falsevalue="" |
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94 label="Report all blastn results from antigen search" |
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95 /> |
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96 <param |
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97 name="full_output" |
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98 type="boolean" |
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99 checked="false" |
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100 truevalue="--full-output" |
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101 falsevalue="" |
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102 label="Report detailed results" |
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103 /> |
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104 <param |
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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"/> |
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168 <param name="output_format" value="tab"/> |
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169 <output |
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170 name="novel_alleles" |
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171 value="novel-alleles.fasta" |
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172 ftype="fasta" |
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173 compare="sim_size"/> |
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174 <output |
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175 name="cgmlst_profiles" |
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176 value="cgmlst-profiles.csv" |
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177 ftype="csv" |
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178 lines_diff="2"> |
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179 <assert_contents> |
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180 <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1123870984,278162969,490843778,3950769715,,,,,,4203409135,3569491948,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,2019769394,1109678443,,,,,,,,,"/> |
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181 </assert_contents> |
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182 </output> |
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183 <output |
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184 name="output_prediction_tab" |
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185 value="sistr-results.tab" |
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186 ftype="tabular" |
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187 lines_diff="2"> |
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188 <assert_contents> |
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189 <has_text text="AE014613-699860" /> |
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190 <has_text text="Typhi" /> |
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191 <has_text text="enterica" /> |
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192 <has_text text="-:-:-" /> |
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193 <has_n_columns n="21" /> |
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194 </assert_contents> |
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195 </output> |
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196 <output |
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197 name="alleles_output" |
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198 value="alleles-output.json" |
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199 ftype="json" |
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200 compare="sim_size"/> |
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201 </test> |
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202 <test> |
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203 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> |
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204 <param name="output_format" value="tab"/> |
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205 <output |
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206 name="novel_alleles" |
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207 value="novel-alleles-13-1101.fasta" |
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208 ftype="fasta" |
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209 compare="sim_size"/> |
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210 <output |
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211 name="cgmlst_profiles" |
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212 value="cgmlst-profiles-13-1101.csv" |
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213 ftype="csv" |
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214 lines_diff="2"> |
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215 </output> |
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216 <output |
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217 name="output_prediction_tab" |
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218 value="sistr-results-13-1101.tab" |
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219 ftype="tabular" |
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220 lines_diff="2"> |
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221 <assert_contents> |
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222 <has_text text="13-1101-Paratyphi_B" /> |
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223 <has_text text="Paratyphi B var. Java" /> |
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224 <has_text text="enterica" /> |
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225 <has_text text="1,4,[5],12" /> |
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226 <has_text text="PASS" /> |
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227 <has_n_columns n="21" /> |
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228 </assert_contents> |
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229 </output> |
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230 <output |
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231 name="alleles_output" |
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232 value="alleles-output-13-1101.json" |
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233 ftype="json" |
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234 compare="sim_size"/> |
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235 </test> |
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236 <test> |
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237 <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/> |
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238 <param name="output_format" value="tab"/> |
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239 <output |
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240 name="novel_alleles" |
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241 value="novel-alleles-13-1101.fasta" |
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242 ftype="fasta" |
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243 compare="sim_size"/> |
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244 <output |
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245 name="cgmlst_profiles" |
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246 value="cgmlst-profiles-13-1101.csv" |
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247 ftype="csv" |
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248 lines_diff="2"> |
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249 </output> |
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250 <output |
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251 name="output_prediction_tab" |
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252 value="sistr-results-13-1101.tab" |
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253 ftype="tabular" |
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254 lines_diff="2"> |
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255 <assert_contents> |
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256 <has_text text="13-1101 Paratyphi_B" /> |
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257 <has_text text="Paratyphi B var. Java" /> |
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258 <has_text text="enterica" /> |
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259 <has_text text="1,4,[5],12" /> |
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260 <has_text text="PASS" /> |
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261 <has_n_columns n="21" /> |
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262 </assert_contents> |
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263 </output> |
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264 <output |
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265 name="alleles_output" |
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266 value="alleles-output-13-1101.json" |
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267 ftype="json" |
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268 compare="sim_size"/> |
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269 </test> |
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270 </tests> |
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271 <help> |
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272 <![CDATA[ |
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273 |
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274 Usage:: |
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275 |
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276 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] |
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277 [-o OUTPUT_PREDICTION] [--full-output] |
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278 [--report-blast-results] [-p CGMLST_PROFILES] |
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279 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] |
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280 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] |
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281 [-v] [-V] |
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282 [F [F ...]] |
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283 |
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284 SISTR (Salmonella In Silico Typing Resource) Command-line Tool |
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285 ============================================================== |
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286 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. |
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287 |
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288 Note about using the "--use-full-cgmlst-db" flag: |
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289 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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290 |
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291 If you find this program useful in your research, please cite as: |
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292 |
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293 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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294 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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295 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 |
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296 |
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297 positional arguments: |
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298 F Input genome FASTA file |
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299 |
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300 optional arguments: |
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301 -h, --help show this help message and exit |
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302 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name |
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303 fasta file path to genome name pair |
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304 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT |
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305 Output format (json, csv, pickle) |
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306 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION |
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307 SISTR serovar prediction output path |
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308 --full-output Produce full detailed output |
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309 --report-blast-results |
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310 Report blastn results for each antigen gene |
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311 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES |
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312 Output CSV file destination for cgMLST allelic |
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313 profiles |
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314 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES |
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315 Output FASTA file destination of novel cgMLST alleles |
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316 from input genomes |
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317 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT |
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318 Output path of allele sequences and info to JSON |
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319 -T TMP_DIR, --tmp-dir TMP_DIR |
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320 Base temporary working directory for intermediate |
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321 analysis files. |
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322 -K, --keep-tmp Keep temporary analysis files. |
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323 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include |
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324 highly similar alleles. By default the smaller |
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325 "centroid" alleles or representative alleles are used |
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326 for each marker. |
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327 --no-cgmlst Do not run cgMLST serovar prediction |
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328 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella |
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329 genomes with trusted serovar designations. Mash binary |
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330 must be in accessible via $PATH (e.g. /usr/bin). |
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331 --qc Perform basic QC to provide level of confidence in |
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332 serovar prediction results. |
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333 -t THREADS, --threads THREADS |
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334 Number of parallel threads to run sistr_cmd analysis. |
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335 -v, --verbose Logging verbosity level (-v == show warnings; -vvv == |
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336 show debug info) |
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337 -V, --version show program's version number and exit |
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338 ]]> |
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339 |
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340 </help> |
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341 <citations> |
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342 <!-- Citation for SISTR PLOS ONE paper --> |
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343 <citation type="doi">10.1371/journal.pone.0147101</citation> |
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344 </citations> |
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345 </tool> |