Mercurial > repos > nml > sistr_cmd
annotate sistr_cmd.xml @ 3:5c8ff92e38a9 draft
Update to 1.0.2
author | nml |
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date | Wed, 14 Jun 2017 14:36:59 -0400 |
parents | 13632190a0ff |
children | 17fcac7ddf54 |
rev | line source |
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3 | 1 <tool id="sistr_cmd" name="sistr_cmd" version="1.0.2"> |
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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> |
3 | 6 <requirement type="package" version="1.0.2">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 |
3 | 28 $more_output |
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29 $verbosity |
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30 ]]></command> |
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31 <inputs> |
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32 <param |
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33 name="input_fastas" |
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34 type="data" |
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35 label="Input Genome(s)" |
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36 optional="false" |
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37 multiple="true" |
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38 format="fasta" |
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39 /> |
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40 <param |
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41 name="output_format" |
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42 type="select" |
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43 label="Results output format" |
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44 multiple="false"> |
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45 <option value="tab" selected="true"> |
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46 Tabular (tab-delimited values) |
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47 </option> |
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48 <option value="csv"> |
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49 CSV (Comma Separated Values) |
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50 </option> |
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51 <option value="json"> |
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52 JSON (JavaScript Object Notation) |
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53 </option> |
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54 </param> |
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55 <param |
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56 name="use_full_cgmlst_db" |
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57 type="boolean" |
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58 checked="false" |
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59 truevalue="--use-full-cgmlst-db" |
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60 falsevalue="" |
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61 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database." |
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62 /> |
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63 <param |
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64 name="run_mash" |
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65 type="boolean" |
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66 checked="true" |
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67 truevalue="--run-mash" |
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68 falsevalue="" |
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69 label="Run Mash MinHash-based serovar prediction" |
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70 /> |
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71 <param |
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72 name="no_cgmlst" |
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73 type="boolean" |
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74 checked="false" |
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75 truevalue="--no-cgmlst" |
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76 falsevalue="" |
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77 label="Skip running cgMLST-based serovar prediction" |
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78 /> |
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79 <param |
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80 name="qc" |
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81 type="boolean" |
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82 checked="true" |
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83 truevalue="--qc" |
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84 falsevalue="" |
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85 label="Basic QC of results" |
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86 /> |
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87 <param |
3 | 88 name="more_output" |
89 type="select" | |
90 label="Results verbosity"> | |
91 <option value="" selected="true"> | |
92 Basic results only | |
93 </option> | |
94 <option value="-M"> | |
95 Report top antigen BLAST results | |
96 </option> | |
97 <option value="-MM" > | |
98 Report all antigen BLAST results | |
99 </option> | |
100 </param> | |
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101 <param |
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102 name="keep_tmp" |
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103 type="boolean" |
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104 checked="false" |
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105 falsevalue="" |
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106 truevalue="--keep-tmp" |
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107 label="Keep temporary analysis directory" |
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108 /> |
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109 <param |
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110 name="verbosity" |
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111 type="select" |
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112 label="Logging verbosity"> |
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113 <option value=""> |
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114 Error messages only |
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115 </option> |
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116 <option value="-v"> |
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117 Show warning messages |
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118 </option> |
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119 <option value="-vv" selected="true"> |
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120 Show info messages |
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121 </option> |
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122 <option value="-vvv"> |
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123 Show debug messages |
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124 </option> |
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125 </param> |
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126 </inputs> |
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127 <outputs> |
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128 <data |
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129 name="output_prediction_csv" |
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130 format="csv" |
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131 label="SISTR Results" |
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132 from_work_dir="sistr-report.csv"> |
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133 <filter>output_format == "csv"</filter> |
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134 </data> |
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135 <data |
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136 name="output_prediction_json" |
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137 format="json" |
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138 label="SISTR Results" |
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139 from_work_dir="sistr-report.json"> |
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140 <filter>output_format == "json"</filter> |
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141 </data> |
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142 <data |
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143 name="output_prediction_tab" |
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144 format="tabular" |
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145 label="SISTR Results" |
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146 from_work_dir="sistr-report.tab"> |
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147 <filter>output_format == "tab"</filter> |
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148 </data> |
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149 <data |
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150 name="cgmlst_profiles" |
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151 format="csv" |
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152 label="cgMLST results" /> |
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153 <data |
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154 name="novel_alleles" |
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155 format="fasta" |
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156 label="Novel cgMLST alleles" /> |
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157 <data |
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158 name="alleles_output" |
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159 format="json" |
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160 label="cgMLST allele match results" /> |
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161 </outputs> |
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162 <tests> |
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163 <test> |
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164 <param name="input_fastas" value="AE014613-699860.fasta"/> |
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165 <param name="output_format" value="tab"/> |
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166 <output |
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167 name="cgmlst_profiles" |
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168 value="cgmlst-profiles.csv" |
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169 ftype="csv" |
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170 lines_diff="2"> |
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171 <assert_contents> |
3 | 172 <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,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/> |
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173 </assert_contents> |
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174 </output> |
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175 <output |
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176 name="output_prediction_tab" |
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177 value="sistr-results.tab" |
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178 ftype="tabular" |
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179 lines_diff="2"> |
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180 <assert_contents> |
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181 <has_text text="AE014613-699860" /> |
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182 <has_text text="Typhi" /> |
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183 <has_text text="enterica" /> |
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184 <has_text text="-:-:-" /> |
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185 <has_n_columns n="21" /> |
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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 </test> |
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194 <test> |
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195 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> |
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196 <param name="output_format" value="tab"/> |
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197 <output |
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198 name="novel_alleles" |
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199 value="novel-alleles-13-1101.fasta" |
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200 ftype="fasta" |
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201 compare="sim_size"/> |
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202 <output |
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203 name="cgmlst_profiles" |
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204 value="cgmlst-profiles-13-1101.csv" |
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205 ftype="csv" |
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206 lines_diff="2"> |
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207 </output> |
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208 <output |
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209 name="output_prediction_tab" |
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210 value="sistr-results-13-1101.tab" |
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211 ftype="tabular" |
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212 lines_diff="2"> |
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213 <assert_contents> |
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214 <has_text text="13-1101-Paratyphi_B" /> |
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215 <has_text text="Paratyphi B var. Java" /> |
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216 <has_text text="enterica" /> |
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217 <has_text text="1,4,[5],12" /> |
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218 <has_text text="PASS" /> |
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219 <has_n_columns n="21" /> |
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220 </assert_contents> |
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221 </output> |
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222 <output |
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223 name="alleles_output" |
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224 value="alleles-output-13-1101.json" |
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225 ftype="json" |
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226 compare="sim_size"/> |
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227 </test> |
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228 <test> |
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229 <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/> |
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230 <param name="output_format" value="tab"/> |
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231 <output |
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232 name="novel_alleles" |
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233 value="novel-alleles-13-1101.fasta" |
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234 ftype="fasta" |
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235 compare="sim_size"/> |
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236 <output |
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237 name="cgmlst_profiles" |
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238 value="cgmlst-profiles-13-1101.csv" |
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239 ftype="csv" |
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240 lines_diff="2"> |
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241 </output> |
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242 <output |
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243 name="output_prediction_tab" |
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244 value="sistr-results-13-1101.tab" |
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245 ftype="tabular" |
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246 lines_diff="2"> |
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247 <assert_contents> |
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248 <has_text text="13-1101 Paratyphi_B" /> |
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249 <has_text text="Paratyphi B var. Java" /> |
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250 <has_text text="enterica" /> |
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251 <has_text text="1,4,[5],12" /> |
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252 <has_text text="PASS" /> |
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253 <has_n_columns n="21" /> |
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254 </assert_contents> |
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255 </output> |
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256 <output |
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257 name="alleles_output" |
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258 value="alleles-output-13-1101.json" |
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259 ftype="json" |
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260 compare="sim_size"/> |
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261 </test> |
3 | 262 <test> |
263 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> | |
264 <param name="output_format" value="json"/> | |
265 <param name="more_output" value="-MM"/> | |
266 <output | |
267 name="output_prediction_json" | |
268 value="sistr-results-13-1101.json" | |
269 ftype="json" | |
270 compare="sim_size"> | |
271 <assert_contents> | |
272 <has_text text="13-1101-Paratyphi_B" /> | |
273 <has_text text="Paratyphi B var. Java" /> | |
274 <has_text text="enterica" /> | |
275 <has_text text="1,4,[5],12" /> | |
276 <has_text text="PASS" /> | |
277 </assert_contents> | |
278 </output> | |
279 </test> | |
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280 </tests> |
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281 <help> |
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282 <![CDATA[ |
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283 |
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284 Usage:: |
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285 |
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286 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] |
3 | 287 [-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES] |
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288 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] |
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289 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] |
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290 [-v] [-V] |
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291 [F [F ...]] |
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292 |
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293 SISTR (Salmonella In Silico Typing Resource) Command-line Tool |
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294 ============================================================== |
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295 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. |
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296 |
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297 Note about using the "--use-full-cgmlst-db" flag: |
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298 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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299 |
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300 If you find this program useful in your research, please cite as: |
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301 |
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302 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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303 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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304 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 |
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305 |
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306 positional arguments: |
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307 F Input genome FASTA file |
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308 |
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309 optional arguments: |
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310 -h, --help show this help message and exit |
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311 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name |
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312 fasta file path to genome name pair |
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313 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT |
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314 Output format (json, csv, pickle) |
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315 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION |
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316 SISTR serovar prediction output path |
3 | 317 -M, --more-results Output more detailed results (-M) and all antigen |
318 search blastn results (-MM) | |
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319 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES |
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320 Output CSV file destination for cgMLST allelic |
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321 profiles |
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322 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES |
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323 Output FASTA file destination of novel cgMLST alleles |
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324 from input genomes |
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325 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT |
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326 Output path of allele sequences and info to JSON |
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327 -T TMP_DIR, --tmp-dir TMP_DIR |
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328 Base temporary working directory for intermediate |
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329 analysis files. |
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330 -K, --keep-tmp Keep temporary analysis files. |
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331 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include |
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332 highly similar alleles. By default the smaller |
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333 "centroid" alleles or representative alleles are used |
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334 for each marker. |
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335 --no-cgmlst Do not run cgMLST serovar prediction |
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336 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella |
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337 genomes with trusted serovar designations. Mash binary |
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338 must be in accessible via $PATH (e.g. /usr/bin). |
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339 --qc Perform basic QC to provide level of confidence in |
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340 serovar prediction results. |
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341 -t THREADS, --threads THREADS |
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342 Number of parallel threads to run sistr_cmd analysis. |
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343 -v, --verbose Logging verbosity level (-v == show warnings; -vvv == |
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344 show debug info) |
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345 -V, --version show program's version number and exit |
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346 ]]> |
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347 |
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348 </help> |
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349 <citations> |
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350 <!-- Citation for SISTR PLOS ONE paper --> |
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351 <citation type="doi">10.1371/journal.pone.0147101</citation> |
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352 </citations> |
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353 </tool> |