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1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
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0
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2 <requirements>
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2
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3 <requirement type="package" version="0.2.0">srst2</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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3
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6
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0
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7 #if $paired_conditional.sPaired == "paired"
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3
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8 #if $paired_conditional.fastq1.is_of_type("fastq.gz")
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9 zcat $paired_conditional.fastq1 > sample_1.fastq;
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10 zcat $paired_conditional.fastq2 > sample_2.fastq;
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11 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
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12 zcat $paired_conditional.fastq1 > sample_1.fastq;
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13 zcat $paired_conditional.fastq2 > sample_2.fastq;
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14 #else
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15 ln -s $paired_conditional.fastq1 sample_1.fastq;
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16 ln -s $paired_conditional.fastq2 sample_2.fastq;
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17 #end if
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5
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18 #else if $paired_conditional.sPaired == "paired_coll"
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3
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19 #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
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20 zcat $paired_conditional.coll.forward > sample_1.fastq;
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21 zcat $paired_conditional.coll.reverse > sample_2.fastq;
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22 #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz")
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23 zcat $paired_conditional.coll.forward > sample_1.fastq;
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24 zcat $paired_conditional.coll.reverse > sample_2.fastq;
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25 #else
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26 ln -s $paired_conditional.coll.forward sample_1.fastq;
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27 ln -s $paired_conditional.coll.reverse sample_2.fastq;
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28 #end if
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5
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29 #else if $paired_conditional.sPaired == "single"
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3
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30 #if $paired_conditional.fastq1.is_of_type("fastq.gz")
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31 zcat $paired_conditional.fastq1 > sample_1.fastq;
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32 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
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33 zcat $paired_conditional.fastq1 > sample_1.fastq;
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34 #else
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35 ln -s $paired_conditional.fastq1 sample_1.fastq;
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36 #end if
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0
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37 #end if
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38
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39 srst2
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40
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41 #if $paired_conditional.sPaired == "single"
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5
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42 --input_se sample_1.fastq
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3
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43 #else
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2
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44 --input_pe sample_1.fastq sample_2.fastq
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0
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45 #end if
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46
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47 --output srst2out
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48 --save_scores
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49
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50 #if $job_type.job == "mlst"
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51 --mlst_definitions $job_type.mlst_definitions
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52 --mlst_db $job_type.mlst_db
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53 --mlst_delimiter $job_type.mlstdelim
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54 --mlst_max_mismatch $job_type.mlst_max_mismatch
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55 #else if $job_type.job == "gene"
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56 --gene_db $job_type.genedb
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57 --gene_max_mismatch $job_type.gene_max_mismatch
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2
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58 #else if $job_type.job == "nost"
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59 --mlst_db $job_type.mlst_db
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60 --mlst_delimiter $job_type.mlstdelim
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61 --mlst_max_mismatch $job_type.mlst_max_mismatch
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0
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62 #end if
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63
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64 #if $options.select == "advanced"
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65 #if $options.min_coverage
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66 --min_coverage $options.min_coverage
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67 #end if
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68 #if $options.max_divergence
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69 --max_divergence $options.max_divergence
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70 #end if
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71 #if $options.min_depth
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72 --min_depth $options.min_depth
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73 #end if
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74 #if $options.min_edge_depth
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75 --min_edge_depth $options.min_edge_depth
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76 #end if
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77 #if $options.prob_err
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78 --prob_err $options.prob_err
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79 #end if
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80 #if $options.stop_after
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81 --stop_after $options.stop_after
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82 #end if
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83 --other "'-p \${GALAXY_SLOTS:-1}
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84 #if $options.maxins
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85 --maxins $options.maxins
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86 --minins $options.minins
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87 #end if
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88 '"
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89 #if $options.mapq
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90 --mapq $options.mapq
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91 #end if
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92 #if $options.baseq
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93 --baseq $options.baseq
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94 #end if
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95 #else
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96 --other "'-p \${GALAXY_SLOTS:-1}'"
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97 #end if
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98
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99 #if $job_type.job == "mlst"
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100 ; python $__tool_directory__/scoreProfiles.py --mlst_definitions $job_type.mlst_definitions --profile_cov $job_type.profile_cov --profile_max_mismatch $job_type.profile_max_mismatch --output srst2.pscores
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101 #end if
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102
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103 ]]></command>
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104 <inputs>
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105 <conditional name="paired_conditional">
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106 <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?">
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2
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107 <option value="single">Single FASTQ</option>
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108 <option value="paired">Forward and Reverse FASTQ</option>
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109 <option value="paired_coll">Paired FASTQ Collection</option>
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0
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110 </param>
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111 <when value="single">
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4
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112 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="FASTQ" />
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0
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113 </when>
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114 <when value="paired">
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4
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115 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Forward FASTQ file" help="FASTQ" />
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116 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Reverse FASTQ file" help="FASTQ" />
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0
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117 </when>
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2
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118 <when value="paired_coll">
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4
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119 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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2
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120 </when>
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0
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121 </conditional>
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122
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123 <conditional name="job_type">
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124 <param name="job" type="select" label="MLST, MLST with ST, or Gene Presence/Absence?">
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125 <option value="nost">MLST</option>
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126 <option value="mlst">MLST with ST Definitions</option>
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127 <option value="gene">Gene</option>
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128 </param>
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2
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129 <when value="nost">
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130 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
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131 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default '_')" />
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132 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
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133 </when>
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0
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134 <when value="mlst">
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135 <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" />
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136 <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" />
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137 <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default '_')" />
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138 <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read" />
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139 <param type="float" name="profile_max_mismatch" value="1" format="txt" label="Maximum number of mismatches for reporting ST profile" />
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140 <param type="float" name="profile_cov" value="98" format="txt" label="Minimum mean % coverage for reporting ST profile" />
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141
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142 </when>
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143 <when value="gene">
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144 <param name="genedb" type="data" format="fasta" label="Fasta file for gene database" />
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145 <param name="gene_max_mismatch" type="integer" value="10" format="txt" label="Maximum number of mistaches per read (default 10)" />
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146 </when>
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147 </conditional>
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148
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149 <conditional name="options">
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150 <param name="select" type="select" label="Options Type">
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151 <option value="basic">Basic</option>
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152 <option value="advanced">Advanced</option>
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153 </param>
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154 <when value="advanced">
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155 <param name="min_coverage" type="integer" label="Minimum %coverage cutoff for gene reporting" value="90"/>
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156 <param name="max_divergence" type="integer" label="Maximum %divergence cutoff for gene reporting" value="10"/>
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157 <param name="min_depth" type="integer" label="Minimum mean depth to flag as dubious allele call" value="5"/>
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158 <param name="min_edge_depth" type="integer" label="Minimum edge depth to flag as dubious allele call" value="2"/>
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159 <param name="prob_err" type="float" label="Probability of sequencing error" value="0.01"/>
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160 <param name="stop_after" type="integer" label="Stop mapping after this number of reads have been mapped (otherwise map all)" optional="true"/>
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161 <param name="mapq" type="integer" label="Samtools -q parameter" value="1"/>
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162 <param name="baseq" type="integer" label="Samtools -Q parameter" value="20"/>
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163 <param name="minins" type="integer" label="Bowtie 2 -I parameter. The minimum fragment length for valid paired-end alignments." value="0" >
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164 <validator type="in_range" message="Must be less than -X parameter." min="0"/>
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165 </param>
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166 <param name="maxins" type="integer" label="Bowtie 2 -X parameter. The maximum fragment length for valid paired-end alignments." value="1000" >
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167 <validator type="in_range" message="Must be greater than -I parameter." min="0"/>
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168 </param>
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169 </when>
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170 <when value="basic"/>
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171 </conditional>
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172
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173 </inputs>
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174
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175 <outputs>
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176 <data format="tabular" label="SRST2 Results" name="results" from_work_dir="*.txt"/>
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177 <data format="tabular" label="SRST2 Allele Scores" name="scores" from_work_dir="*.scores">
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178 <filter>job_type['job'] == "mlst"</filter>
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179 </data>
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180 <data format="tabular" label="SRST2 Profile Scores" name="pscores" from_work_dir="*.pscores">
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181 <filter> job_type['job'] == "mlst"</filter>
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182 </data>
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183 <data format="tabular" label="SRST2 Predicted Alleles" name="alleles" from_work_dir="*results.txt">
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184 <filter> job_type['job'] == "mlst"</filter>
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185 </data>
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186 <data format="tabular" label="SRST2 Gene Scores" name="gscores" from_work_dir="*.scores">
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187 <filter>job_type['job'] == "gene"</filter>
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188 </data>
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189 </outputs>
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190
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191 <help><![CDATA[
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192
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193 SRST2 - Short Read Sequence Typer (v2)
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194
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195 This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
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196
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197 ]]></help>
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198
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199
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200 <citations>
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201 <citation type="bibtex">
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202 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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203 title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs},
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204 url={https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6},
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205 journal={Genome Medicine}, publisher={BioMed Central},
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206 author={Pope, Bernard J and Dashnow, Harriet and Zobel, Justin and Holt, Kathryn E and Raven, Lesley-Ann and Schultz, Mark B and Inouye, Michael and Tomita, Takehiro},
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207 year={2014}, month={Nov}} ,
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208 }</citation>
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209 </citations>
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210 </tool>
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