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annotate seqsero2.xml @ 11:e8ce538c84a3 draft

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author cstrittmatter
date Fri, 01 May 2020 13:58:10 -0400
parents 43f6b7f6ebb3
children 08832c0d3cbd
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1 <tool id="seqsero2v110" name="SeqSero2 v1.1.0" version="5">
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2 <description>Salmonella serotype prediction</description>
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3 <requirements>
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4 <requirement type="package" version="3.6">python</requirement>
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5 <requirement type="package" version="1.74">biopython</requirement>
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6 <requirement type="package" version="2.7.1">blast</requirement>
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7 <requirement type="package" version="1.9">samtools</requirement>
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8 <requirement type="package" version="2.9.1">sra-tools</requirement>
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9 <requirement type="package" version="0.7.17">bwa</requirement>
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10 <requirement type="package" version="3.13.1">spades</requirement>
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11 <requirement type="package" version="2.27.1">bedtools</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 echo "SeqSero2 v1.1.0" ;
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15 mkdir ./output;
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16
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17 #if $reads.reads_select == 'history'
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18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
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19 #set $forward = $reads.forward
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20 #set $reverse = $reads.reverse
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21 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
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22 #set $tval = 2
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23 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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24 gunzip -c $reverse > reverse.fastq;
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25 #set $reverse = './reverse.fastq'
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26 gunzip -c $forward > forward.fastq;
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27 #set $forward = './forward.fastq'
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28 #end if
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29 ln -s $forward ${name}_1.fastq;
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30 ln -s $reverse ${name}_2.fastq;
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31 #else if $reads.reads_select == 'collection'
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32 #set $name = $reads.coll.name.replace(' ', '_')
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33 #set $forward = $reads.coll.forward
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34 #set $reverse = $reads.coll.reverse
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35 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
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36 #set $tval = 2
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37 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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38 gunzip -c $reverse > reverse.fastq;
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39 #set $reverse = './reverse.fastq'
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40 gunzip -c $forward > forward.fastq;
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41 #set $forward = './forward.fastq'
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42 #end if
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43 ln -s $forward ${name}_1.fastq;
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44 ln -s $reverse ${name}_2.fastq;
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45 #else
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46 #set $name = $reads.assembly.name.replace(' ', '_')
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47 #set $ga = $reads.assembly
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48 #set $infile = $name + ".fasta"
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49 ln -s $ga ${name}.fasta;
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50 #set $tval = 4
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51 #set $mode='k'
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52 #end if
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53 echo $name ;
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54 echo "-=-=-=-=-" ;
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55 touch output/SeqSero_log.txt ;
1
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56 python $__tool_directory__/bin/SeqSero2_package.py
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57 -p \${GALAXY_SLOTS:-4}
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58 -t $tval
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59 -m $mode
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60 -d ./output
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61 #if $mode == 'a':
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62 -b $maptype
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63 #end if
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64 -i $infile &&
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65 echo "-=-=-=-=-" &&
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66 cat output/SeqSero_log.txt &&
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67 echo "-=-=-=-=-" &&
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68 ls -lah ./output
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69 ]]></command>
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70 <inputs>
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71
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72 <conditional name="reads">
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73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
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74 <option value="collection">Paired collection from your history</option>
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75 <option value="history">Two FASTQ datasets from your history</option>
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76 <option value="genome">Genome Assembly</option>
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77 </param>
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78 <when value="collection">
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79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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80 </when>
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81 <when value="history">
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82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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84 </when>
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85 <when value="genome">
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86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
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87 </when>
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88 </conditional>
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89
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90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
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91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
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92 <!-- <param name="numofthr" type="select" label="Number of threads">
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93 <option value="1">1</option>
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94 <option value="2">2</option>
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95 <option value="3">3</option>
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96 <option value="4">4</option> -->
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97 <!-- </param> -->
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98
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99 <param label="Analysis mode" type="select" name="mode">
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100 <option value="a">allele mode</option>
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101 <option value="k">k-mer mode</option>
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102 </param>
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103
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104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
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105 <option value="mem">mem</option>
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106 <option value="sam">sam</option>
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107 </param>
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108
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109
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110
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111 </inputs>
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112 <outputs>
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113 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
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114 </outputs>
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115 <tests>
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116 <!-- <test>
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117 <param name="reads_select" value="history" />
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118 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
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119 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
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120 <output name="results" file="Seqsero_result.tsv" />
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121 </test>
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122 <test>
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123 <param name="reads_select" value="collection" />
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124 <param name="coll">
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125 <collection type="paired">
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126 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
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127 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
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128 </collection>
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129 </param>
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130 <output name="results" file="Seqsero_result.tsv" />
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131 </test> -->
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132 <test>
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133 <param name="mode" value="k" />
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134 <param name="reads_select" value="history" />
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135 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
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136 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
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137 <output name="results" file="Seqsero_result_25k.tsv" />
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138 </test>
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139 <test>
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140 <param name="mode" value="k" />
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141 <param name="reads_select" value="collection" />
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142 <param name="coll">
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143 <collection type="paired">
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144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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146 </collection>
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147 </param>
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148 <output name="results" file="Seqsero_result_25k_coll.tsv" />
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149 </test>
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150 <test>
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151 <param name="mode" value="a" />
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152 <param name="reads_select" value="history" />
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153 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
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154 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
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155 <assert_stdout>
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156 <has_text text="predicted antigenic profile does not exist" />
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157 </assert_stdout>
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158 </test>
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159 <!-- <test>
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160 <param name="mode" value="a" />
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161 <param name="reads_select" value="collection" />
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162 <param name="coll">
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163 <collection type="paired">
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164 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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165 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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166 </collection>
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167 </param>
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168 <output name="results" file="Seqsero_result_allele.tsv" />
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169 </test> -->
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170 </tests>
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171 <help><![CDATA[
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172
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173 **Usage: SeqSero2.py**
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174
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175 **Algorithms for BWA mapping**
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176
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177 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
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178
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179 ]]></help>
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180 <citations>
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181 <citation type="bibtex">
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182 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
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183 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
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184 journal={J Clin Microbiol}, publisher={ASM},
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185 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
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186 year={2015}, month={Max},
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187 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
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188 }</citation>
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189 <citation type="bibtex">
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190 @misc{cfsan_biostatistics_group_2017,
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191 title={CFSAN Biostatistics Group fork of SeqSero2},
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192 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
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193 </citation>
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194 </citations>
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195
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196 </tool>