Mercurial > repos > nml > sistr_cmd

annotate sistr_cmd.xml @ 0:ebee10be4297 draft

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planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
author nml
date Wed, 01 Mar 2017 12:35:39 -0500
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children 9d7e381dfa5a
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0
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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
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17 #if $output_format == "tab"
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18 -o sistr-report.tab
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19 #elif $output_format == "csv"
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20 -o sistr-report.csv
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21 #elif $output_format == "json"
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22 -o sistr-report.json
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23 #end if
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24 -p $cgmlst_profiles
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25 -n $novel_alleles
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26 -a $alleles_output
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27 $use_full_cgmlst_db
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28 $no_cgmlst
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29 $run_mash
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30 $qc
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31 --threads "\${GALAXY_SLOTS:-1}"
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32 -T "\${TMPDIR:-/tmp}"
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33 $keep_tmp
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34 $verbosity
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35 ]]></command>
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36 <inputs>
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37 <param
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38 name="input_fastas"
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39 type="data"
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40 label="Input Genome(s)"
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41 optional="false"
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42 multiple="true"
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43 format="fasta"
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44 />
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45 <param
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46 name="output_format"
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47 type="select"
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48 label="Results output format"
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49 multiple="false">
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50 <option value="tab" selected="true">
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51 Tabular (tab-delimited values)
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52 </option>
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53 <option value="csv">
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54 CSV (Comma Separated Values)
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55 </option>
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56 <option value="json">
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57 JSON (JavaScript Object Notation)
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58 </option>
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59 </param>
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60 <param
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61 name="use_full_cgmlst_db"
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62 type="boolean"
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63 checked="false"
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64 truevalue="--use-full-cgmlst-db"
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65 falsevalue=""
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66 label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database."
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67 />
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68 <param
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69 name="run_mash"
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70 type="boolean"
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71 checked="true"
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72 truevalue="--run-mash"
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73 falsevalue=""
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74 label="Run Mash MinHash-based serovar prediction"
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75 />
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76 <param
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77 name="no_cgmlst"
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78 type="boolean"
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79 checked="false"
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80 truevalue="--no-cgmlst"
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81 falsevalue=""
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82 label="Skip running cgMLST-based serovar prediction"
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83 />
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84 <param
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85 name="qc"
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86 type="boolean"
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87 checked="true"
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88 truevalue="--qc"
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89 falsevalue=""
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90 label="Basic QC of results"
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91 />
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92 <param
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93 name="keep_tmp"
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94 type="boolean"
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95 checked="false"
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96 falsevalue=""
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97 truevalue="--keep-tmp"
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98 label="Keep temporary analysis directory"
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99 />
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100 <param
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101 name="verbosity"
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102 type="select"
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103 label="Logging verbosity">
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104 <option value="">
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105 Error messages only
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106 </option>
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107 <option value="-v">
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108 Show warning messages
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109 </option>
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110 <option value="-vv" selected="true">
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111 Show info messages
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112 </option>
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113 <option value="-vvv">
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114 Show debug messages
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115 </option>
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116 </param>
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117 </inputs>
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118 <outputs>
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119 <data
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120 name="output_prediction_csv"
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121 format="csv"
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122 label="SISTR Results"
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123 from_work_dir="sistr-report.csv">
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124 <filter>output_format == "csv"</filter>
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125 </data>
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126 <data
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127 name="output_prediction_json"
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128 format="json"
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129 label="SISTR Results"
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130 from_work_dir="sistr-report.json">
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131 <filter>output_format == "json"</filter>
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132 </data>
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133 <data
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134 name="output_prediction_tab"
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135 format="tabular"
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136 label="SISTR Results"
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137 from_work_dir="sistr-report.tab">
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138 <filter>output_format == "tab"</filter>
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139 </data>
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140 <data
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141 name="cgmlst_profiles"
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142 format="csv"
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143 label="cgMLST results" />
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144 <data
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145 name="novel_alleles"
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146 format="fasta"
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147 label="Novel cgMLST alleles" />
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148 <data
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149 name="alleles_output"
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150 format="json"
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151 label="cgMLST allele match results" />
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="input_fastas" value="AE014613-699860.fasta"/>
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156 <param name="output_format" value="tab"/>
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157 <output
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158 name="novel_alleles"
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159 value="novel-alleles.fasta"
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160 ftype="fasta"
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161 compare="sim_size"/>
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162 <output
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163 name="cgmlst_profiles"
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164 value="cgmlst-profiles.csv"
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165 ftype="csv"
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166 lines_diff="2">
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167 <assert_contents>
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168 <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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169 </assert_contents>
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170 </output>
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171 <output
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172 name="output_prediction_tab"
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173 value="sistr-results.tab"
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174 ftype="tabular"
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175 lines_diff="2">
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176 <assert_contents>
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177 <has_text text="AE014613-699860" />
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178 <has_text text="Typhi" />
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179 <has_text text="enterica" />
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180 <has_text text="-:-:-" />
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181 <has_n_columns n="19" />
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182 </assert_contents>
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183 </output>
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184 <output
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185 name="alleles_output"
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186 value="alleles-output.json"
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187 ftype="json"
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188 compare="sim_size"/>
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189 </test>
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190 <test>
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191 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
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192 <param name="output_format" value="tab"/>
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193 <output
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194 name="novel_alleles"
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195 value="novel-alleles-13-1101.fasta"
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196 ftype="fasta"
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197 compare="sim_size"/>
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198 <output
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199 name="cgmlst_profiles"
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200 value="cgmlst-profiles-13-1101.csv"
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201 ftype="csv"
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202 lines_diff="2">
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203 </output>
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204 <output
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205 name="output_prediction_tab"
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206 value="sistr-results-13-1101.tab"
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207 ftype="tabular"
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208 lines_diff="2">
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209 <assert_contents>
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210 <has_text text="13-1101-Paratyphi_B" />
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211 <has_text text="Paratyphi B var. Java" />
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212 <has_text text="enterica" />
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213 <has_text text="1,4,[5],12" />
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214 <has_text text="PASS" />
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215 <has_text text="2375035975"/>
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216 <has_n_columns n="21" />
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217 </assert_contents>
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218 </output>
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219 <output
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220 name="alleles_output"
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221 value="alleles-output-13-1101.json"
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222 ftype="json"
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223 compare="sim_size"/>
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224 </test>
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225 <test>
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226 <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/>
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227 <param name="output_format" value="tab"/>
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228 <output
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229 name="novel_alleles"
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230 value="novel-alleles-13-1101.fasta"
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231 ftype="fasta"
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232 compare="sim_size"/>
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233 <output
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234 name="cgmlst_profiles"
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235 value="cgmlst-profiles-13-1101.csv"
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236 ftype="csv"
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237 lines_diff="2">
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238 </output>
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239 <output
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240 name="output_prediction_tab"
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241 value="sistr-results-13-1101.tab"
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242 ftype="tabular"
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243 lines_diff="2">
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244 <assert_contents>
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245 <has_text text="13-1101 Paratyphi_B" />
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246 <has_text text="Paratyphi B var. Java" />
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247 <has_text text="enterica" />
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248 <has_text text="1,4,[5],12" />
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249 <has_text text="PASS" />
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250 <has_text text="2375035975"/>
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251 <has_n_columns n="21" />
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252 </assert_contents>
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253 </output>
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254 <output
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255 name="alleles_output"
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256 value="alleles-output-13-1101.json"
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257 ftype="json"
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258 compare="sim_size"/>
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259 </test>
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260 </tests>
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261 <help>
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262 <![CDATA[
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263
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264 Usage::
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265
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266 usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
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267 [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES]
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268 [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
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269 [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
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270 [-v] [-V]
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271 [F [F ...]]
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272
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273 SISTR (Salmonella In Silico Typing Resource) Command-line Tool
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274 ==============================================================
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275 Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
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276
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277 Note about using the "--use-full-cgmlst-db" flag:
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278 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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279
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280 If you find this program useful in your research, please cite as:
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281
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282 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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283 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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284 PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
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285
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286 positional arguments:
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287 F Input genome FASTA file
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288
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289 optional arguments:
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290 -h, --help show this help message and exit
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291 -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
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292 fasta file path to genome name pair
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293 -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
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294 Output format (json, csv, pickle)
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295 -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
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296 SISTR serovar prediction output path
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297 -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
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298 Output CSV file destination for cgMLST allelic
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299 profiles
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300 -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
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301 Output FASTA file destination of novel cgMLST alleles
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302 from input genomes
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303 -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
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304 Output path of allele sequences and info to JSON
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305 -T TMP_DIR, --tmp-dir TMP_DIR
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306 Base temporary working directory for intermediate
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307 analysis files.
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308 -K, --keep-tmp Keep temporary analysis files.
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309 --use-full-cgmlst-db Use the full set of cgMLST alleles which can include
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310 highly similar alleles. By default the smaller
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311 "centroid" alleles or representative alleles are used
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312 for each marker.
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313 --no-cgmlst Do not run cgMLST serovar prediction
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314 -m, --run-mash Determine Mash MinHash genomic distances to Salmonella
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315 genomes with trusted serovar designations. Mash binary
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316 must be in accessible via $PATH (e.g. /usr/bin).
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317 --qc Perform basic QC to provide level of confidence in
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318 serovar prediction results.
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319 -t THREADS, --threads THREADS
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320 Number of parallel threads to run sistr_cmd analysis.
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321 -v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
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322 show debug info)
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323 -V, --version show program's version number and exit
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324 ]]>
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325
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326 </help>
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327 <citations>
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328 <!-- Citation for SISTR PLOS ONE paper -->
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329 <citation type="doi">10.1371/journal.pone.0147101</citation>
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330 </citations>
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331 </tool>