Mercurial > repos > nml > sistr_cmd

annotate sistr_cmd.xml @ 1:9d7e381dfa5a draft

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author nml
date Fri, 03 Mar 2017 14:31:21 -0500
parents ebee10be4297
children 13632190a0ff
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1 <tool id="sistr_cmd" name="sistr_cmd" version="0.3.4">
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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="0.3.4">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 $output_format
1
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17 -o sistr-report.$output_format
0
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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 $verbosity
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29 ]]></command>
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30 <inputs>
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31 <param
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32 name="input_fastas"
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33 type="data"
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34 label="Input Genome(s)"
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35 optional="false"
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36 multiple="true"
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37 format="fasta"
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38 />
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39 <param
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40 name="output_format"
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41 type="select"
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42 label="Results output format"
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43 multiple="false">
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44 <option value="tab" selected="true">
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45 Tabular (tab-delimited values)
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46 </option>
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47 <option value="csv">
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48 CSV (Comma Separated Values)
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49 </option>
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50 <option value="json">
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51 JSON (JavaScript Object Notation)
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52 </option>
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53 </param>
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54 <param
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55 name="use_full_cgmlst_db"
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56 type="boolean"
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57 checked="false"
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58 truevalue="--use-full-cgmlst-db"
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59 falsevalue=""
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60 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database."
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61 />
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62 <param
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63 name="run_mash"
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64 type="boolean"
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65 checked="true"
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66 truevalue="--run-mash"
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67 falsevalue=""
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68 label="Run Mash MinHash-based serovar prediction"
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69 />
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70 <param
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71 name="no_cgmlst"
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72 type="boolean"
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73 checked="false"
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74 truevalue="--no-cgmlst"
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75 falsevalue=""
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76 label="Skip running cgMLST-based serovar prediction"
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77 />
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78 <param
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79 name="qc"
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80 type="boolean"
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81 checked="true"
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82 truevalue="--qc"
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83 falsevalue=""
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84 label="Basic QC of results"
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85 />
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86 <param
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87 name="keep_tmp"
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88 type="boolean"
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89 checked="false"
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90 falsevalue=""
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91 truevalue="--keep-tmp"
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92 label="Keep temporary analysis directory"
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93 />
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94 <param
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95 name="verbosity"
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96 type="select"
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97 label="Logging verbosity">
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98 <option value="">
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99 Error messages only
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100 </option>
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101 <option value="-v">
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102 Show warning messages
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103 </option>
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104 <option value="-vv" selected="true">
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105 Show info messages
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106 </option>
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107 <option value="-vvv">
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108 Show debug messages
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109 </option>
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110 </param>
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111 </inputs>
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112 <outputs>
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113 <data
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114 name="output_prediction_csv"
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115 format="csv"
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116 label="SISTR Results"
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117 from_work_dir="sistr-report.csv">
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118 <filter>output_format == "csv"</filter>
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119 </data>
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120 <data
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121 name="output_prediction_json"
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122 format="json"
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123 label="SISTR Results"
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124 from_work_dir="sistr-report.json">
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125 <filter>output_format == "json"</filter>
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126 </data>
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127 <data
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128 name="output_prediction_tab"
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129 format="tabular"
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130 label="SISTR Results"
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131 from_work_dir="sistr-report.tab">
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132 <filter>output_format == "tab"</filter>
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133 </data>
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134 <data
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135 name="cgmlst_profiles"
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136 format="csv"
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137 label="cgMLST results" />
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138 <data
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139 name="novel_alleles"
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140 format="fasta"
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141 label="Novel cgMLST alleles" />
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142 <data
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143 name="alleles_output"
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144 format="json"
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145 label="cgMLST allele match results" />
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146 </outputs>
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147 <tests>
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148 <test>
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149 <param name="input_fastas" value="AE014613-699860.fasta"/>
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150 <param name="output_format" value="tab"/>
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151 <output
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152 name="novel_alleles"
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153 value="novel-alleles.fasta"
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154 ftype="fasta"
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155 compare="sim_size"/>
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156 <output
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157 name="cgmlst_profiles"
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158 value="cgmlst-profiles.csv"
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159 ftype="csv"
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160 lines_diff="2">
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161 <assert_contents>
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162 <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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163 </assert_contents>
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164 </output>
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165 <output
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166 name="output_prediction_tab"
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167 value="sistr-results.tab"
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168 ftype="tabular"
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169 lines_diff="2">
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170 <assert_contents>
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171 <has_text text="AE014613-699860" />
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172 <has_text text="Typhi" />
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173 <has_text text="enterica" />
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174 <has_text text="-:-:-" />
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175 <has_n_columns n="19" />
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176 </assert_contents>
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177 </output>
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178 <output
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179 name="alleles_output"
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180 value="alleles-output.json"
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181 ftype="json"
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182 compare="sim_size"/>
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183 </test>
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184 <test>
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185 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
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186 <param name="output_format" value="tab"/>
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187 <output
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188 name="novel_alleles"
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189 value="novel-alleles-13-1101.fasta"
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190 ftype="fasta"
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191 compare="sim_size"/>
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192 <output
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193 name="cgmlst_profiles"
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194 value="cgmlst-profiles-13-1101.csv"
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195 ftype="csv"
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196 lines_diff="2">
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197 </output>
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198 <output
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199 name="output_prediction_tab"
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200 value="sistr-results-13-1101.tab"
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201 ftype="tabular"
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202 lines_diff="2">
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203 <assert_contents>
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204 <has_text text="13-1101-Paratyphi_B" />
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205 <has_text text="Paratyphi B var. Java" />
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206 <has_text text="enterica" />
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207 <has_text text="1,4,[5],12" />
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208 <has_text text="PASS" />
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209 <has_text text="2375035975"/>
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210 <has_n_columns n="21" />
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211 </assert_contents>
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212 </output>
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213 <output
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214 name="alleles_output"
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215 value="alleles-output-13-1101.json"
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216 ftype="json"
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217 compare="sim_size"/>
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218 </test>
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219 <test>
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220 <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/>
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221 <param name="output_format" value="tab"/>
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222 <output
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223 name="novel_alleles"
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224 value="novel-alleles-13-1101.fasta"
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225 ftype="fasta"
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226 compare="sim_size"/>
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227 <output
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228 name="cgmlst_profiles"
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229 value="cgmlst-profiles-13-1101.csv"
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230 ftype="csv"
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231 lines_diff="2">
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232 </output>
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233 <output
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234 name="output_prediction_tab"
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235 value="sistr-results-13-1101.tab"
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236 ftype="tabular"
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237 lines_diff="2">
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238 <assert_contents>
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239 <has_text text="13-1101 Paratyphi_B" />
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240 <has_text text="Paratyphi B var. Java" />
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241 <has_text text="enterica" />
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242 <has_text text="1,4,[5],12" />
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243 <has_text text="PASS" />
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244 <has_text text="2375035975"/>
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245 <has_n_columns n="21" />
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246 </assert_contents>
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247 </output>
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248 <output
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249 name="alleles_output"
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250 value="alleles-output-13-1101.json"
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251 ftype="json"
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252 compare="sim_size"/>
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253 </test>
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254 </tests>
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255 <help>
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256 <![CDATA[
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257
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258 Usage::
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259
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260 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
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261 [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES]
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262 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
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263 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
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264 [-v] [-V]
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265 [F [F ...]]
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266
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267 SISTR (Salmonella In Silico Typing Resource) Command-line Tool
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268 ==============================================================
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269 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
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270
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271 Note about using the "--use-full-cgmlst-db" flag:
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272 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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273
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274 If you find this program useful in your research, please cite as:
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275
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276 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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277 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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278 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
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279
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280 positional arguments:
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281 F Input genome FASTA file
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282
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283 optional arguments:
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284 -h, --help show this help message and exit
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285 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
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286 fasta file path to genome name pair
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287 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
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288 Output format (json, csv, pickle)
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289 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
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290 SISTR serovar prediction output path
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291 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
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292 Output CSV file destination for cgMLST allelic
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293 profiles
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294 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
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295 Output FASTA file destination of novel cgMLST alleles
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296 from input genomes
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297 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
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298 Output path of allele sequences and info to JSON
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299 -T TMP_DIR, --tmp-dir TMP_DIR
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300 Base temporary working directory for intermediate
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301 analysis files.
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302 -K, --keep-tmp Keep temporary analysis files.
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303 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include
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304 highly similar alleles. By default the smaller
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305 "centroid" alleles or representative alleles are used
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306 for each marker.
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307 --no-cgmlst Do not run cgMLST serovar prediction
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308 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella
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309 genomes with trusted serovar designations. Mash binary
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310 must be in accessible via $PATH (e.g. /usr/bin).
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311 --qc Perform basic QC to provide level of confidence in
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312 serovar prediction results.
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313 -t THREADS, --threads THREADS
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314 Number of parallel threads to run sistr_cmd analysis.
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315 -v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
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316 show debug info)
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317 -V, --version show program's version number and exit
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318 ]]>
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319
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320 </help>
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321 <citations>
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322 <!-- Citation for SISTR PLOS ONE paper -->
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323 <citation type="doi">10.1371/journal.pone.0147101</citation>
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324 </citations>
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325 </tool>