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author jpayne
date Mon, 29 Sep 2025 20:04:28 +0000
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1 <tool id="seqsero2s" name="SeqSero2S" version="1">
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2 <description>Simplified Salmonella serotype prediction</description>
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3 <requirements>
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4 <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> -->
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5 <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir ./output;
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9
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10 #if $reads.reads_select == 'history'
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11 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
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12 #set $forward = $reads.forward
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13 #set $reverse = $reads.reverse
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14 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
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15 #set $tval = 2
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16 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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17 gunzip -c $reverse > reverse.fastq;
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18 #set $reverse = './reverse.fastq'
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19 gunzip -c $forward > forward.fastq;
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20 #set $forward = './forward.fastq'
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21 #end if
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22 ln -s $forward ${name}_1.fastq;
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23 ln -s $reverse ${name}_2.fastq;
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24 #else if $reads.reads_select == 'collection'
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25 #set $name = $reads.coll.name.replace(' ', '_')
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26 #set $forward = $reads.coll.forward
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27 #set $reverse = $reads.coll.reverse
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28 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
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29 #set $tval = 2
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30 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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31 gunzip -c $reverse > reverse.fastq;
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32 #set $reverse = './reverse.fastq'
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33 gunzip -c $forward > forward.fastq;
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34 #set $forward = './forward.fastq'
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35 #end if
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36 ln -s $forward ${name}_1.fastq;
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37 ln -s $reverse ${name}_2.fastq;
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38 #else
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39 #set $name = $reads.assembly.name.replace(' ', '_')
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40 #set $ga = $reads.assembly
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41 #set $infile = $name + ".fasta"
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42 ln -s $ga ${name}.fasta;
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43 #set $tval = 4
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44 #set $mode='k'
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45 #end if
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46 echo $name ;
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47 echo "-=-=-=-=-" ;
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48 touch output/SeqSero_log.txt ;
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49 /usr/local/bin/SeqSero2S.py --version ;
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50 echo "-=-=-=-=-" ;
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51 /usr/local/bin/SeqSero2S.py
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52 -p \${GALAXY_SLOTS:-1}
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53 -t $tval
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54 -m $mode
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55 -d ./output
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56 #if $mode == 'a':
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57 -b $maptype
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58 #end if
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59 -i $infile &&
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60 echo "-=-=-=-=-" &&
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61 cat output/SeqSero_log.txt &&
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62 echo "-=-=-=-=-" &&
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63 ls -lah ./output
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64 ]]></command>
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65 <inputs>
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66
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67 <conditional name="reads">
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68 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
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69 <option value="collection">Paired collection from your history</option>
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70 <option value="history">Two FASTQ datasets from your history</option>
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71 <option value="genome">Genome Assembly</option>
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72 </param>
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73 <when value="collection">
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74 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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75 </when>
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76 <when value="history">
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77 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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78 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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79 </when>
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80 <when value="genome">
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81 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
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82 </when>
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83 </conditional>
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84
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85 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
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86 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
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87 <!-- <param name="numofthr" type="select" label="Number of threads">
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88 <option value="1">1</option>
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89 <option value="2">2</option>
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90 <option value="3">3</option>
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91 <option value="4">4</option> -->
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92 <!-- </param> -->
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93
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94 <param label="Analysis mode" type="select" name="mode">
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95 <option value="a">allele mode</option>
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96 <option value="k">k-mer mode</option>
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97 </param>
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98
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99 <param name="maptype" type="select" label="Algorithms for BWA mapping">
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100 <option value="mem">mem</option>
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101 <option value="sam">sam</option>
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102 </param>
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103
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104
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105
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106 </inputs>
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107 <outputs>
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108 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
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109 </outputs>
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110 <tests>
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111 <!-- <test>
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112 <param name="reads_select" value="history" />
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113 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
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114 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
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115 <output name="results" file="Seqsero_result.tsv" />
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116 </test>
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117 <test>
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118 <param name="reads_select" value="collection" />
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119 <param name="coll">
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120 <collection type="paired">
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121 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
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122 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
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123 </collection>
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124 </param>
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125 <output name="results" file="Seqsero_result.tsv" />
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126 </test> -->
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127 <!-- <test>
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128 <param name="mode" value="k" />
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129 <param name="reads_select" value="history" />
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130 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
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131 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
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132 <output name="results" file="Seqsero_result_25k.tsv" />
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133 </test>
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134 <test>
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135 <param name="mode" value="k" />
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136 <param name="reads_select" value="collection" />
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137 <param name="coll">
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138 <collection type="paired">
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139 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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140 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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141 </collection>
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142 </param>
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143 <output name="results" file="Seqsero_result_25k_coll.tsv" />
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144 </test>
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145 <test>
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146 <param name="mode" value="a" />
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147 <param name="reads_select" value="history" />
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148 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
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149 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
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150 <assert_stdout>
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151 <has_text text="input genome cannot be identified as Salmonella" />
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152 </assert_stdout>
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153 </test> -->
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154 <!-- <test>
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155 <param name="mode" value="a" />
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156 <param name="reads_select" value="collection" />
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157 <param name="coll">
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158 <collection type="paired">
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159 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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160 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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161 </collection>
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162 </param>
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163 <output name="results" file="Seqsero_result_allele.tsv" />
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164 </test> -->
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165 <test>
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166 <param name="mode" value="k" />
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167 <param name="reads_select" value="genome" />
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168 <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" />
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169 <output name="results" file="test/taxonomy/salmonella/SeqSero_result/SeqSero_result.tsv" />
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170 </test>
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171 </tests>
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172 <help><![CDATA[
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173
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174 **Usage: SeqSero2.py**
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175
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176 **Algorithms for BWA mapping**
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177
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178 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
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179
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180 ]]></help>
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181 <citations>
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182 <citation type="bibtex">
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183 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
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184 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
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185 journal={J Clin Microbiol}, publisher={ASM},
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186 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
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187 year={2015}, month={Max},
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188 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
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189 }</citation>
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190 <citation type="bibtex">
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191 @misc{cfsan_biostatistics_group_2017,
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192 title={CFSAN Biostatistics Group fork of SeqSero2},
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193 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
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194 </citation>
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195 </citations>
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196
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197 </tool>