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1 <tool id="microrunqc" name="microrunqc" version="1.0.2">
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2
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2
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3 <requirements>
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11
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4 <requirement type="package" version="2.4.0">skesa</requirement>
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5 <requirement type="package" version="2.23.0">mlst</requirement>
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6 <requirement type="package" version="0.7.17">bwa</requirement>
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7 <requirement type="package" version="1.0.1">fastq-scan</requirement>
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2
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8 </requirements>
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11
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12 skesa
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13
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14 #set fqscan = "text"
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15 #if $jobtype.select == "fastq_fr"
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16 #set outname = $jobtype.fastq1.name
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17 #set bwalist = str($jobtype.fastq1) + " " + str($jobtype.fastq2)
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18 --fastq $jobtype.fastq1,$jobtype.fastq2
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19 #if $jobtype.fastq1.is_of_type("fastq.gz")
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20 #set fqscan = "gz"
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21 #else if $jobtype.fastq1.is_of_type("fastqsanger.gz")
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22 #set fqscan = "gz"
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23 #end if
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24 #else if $jobtype.select == "fastq_pair"
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25 #set outname = $jobtype.coll.name
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26 #set bwalist = str($jobtype.coll.forward) + " " + str($jobtype.coll.reverse)
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27 --fastq $jobtype.coll.forward,$jobtype.coll.reverse
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28 #if $jobtype.coll.forward.is_of_type("fastq.gz")
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29 #set fqscan = "gz"
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30 #else if $jobtype.coll.forward.is_of_type("fastqsanger.gz")
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31 #set fqscan = "gz"
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32 #end if
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33 #end if
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34
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35 #set num_cores = 1
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36
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37 #if $options.select =="basic"
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38 --cores $num_cores
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39 --memory 8
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40 #else if $options.select=="advanced"
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41 #if $options.cores
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42 #set num_cores = $options.cores
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43 --cores $options.cores
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44 #end if
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45 #if $options.memory
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46 --memory $options.memory
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47 #end if
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48 #if $options.hash_count
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49 --hash_count
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50 #end if
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51 #if $options.estimated_kmers
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52 --estimated_kmers $options.estimated.kmers
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53 #end if
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54 #if $options.skip
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55 --skip_bloom_filter
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56 #end if
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57 #if $options.kmer
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58 --kmer $options.kmer
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59 #end if
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60 #if $options.min_count
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61 --min_count $options.min_count
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62 #end if
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63 #if $options.max_kmer_count
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64 --max_kmer_count $options.max_kmer_count
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65 #end if
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66 #if $options.vector_percent
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67 --vector_percent $options.vector_percent
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68 #end if
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69 #if $options.insert_size
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70 --insert_size $options.insert.size
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71 #end if
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72 #if $options.steps
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73 --steps $options.steps
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74 #end if
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75 #if $options.fraction
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76 --fraction $options.fraction
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77 #end if
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78 #if $options.max_snp_len
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79 --max_snp_len $options.max_snp_len
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80 #end if
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81 #if $options.min_contig
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82 --min_contig $options.min_contig
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83 #end if
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84 #if $options.allow_snps
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85 --allow_snps
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86 #end if
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87 #end if
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88
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89 > ${outname}.fasta;
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90
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91 bwa index ${outname}.fasta;
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92 bwa mem -t $num_cores ${outname}.fasta ${bwalist} | python $__tool_directory__/median_size.py > insert.median;
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93
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94 mlst --nopath --threads $num_cores --datadir $mlst_databases.fields.path/pubmlst --blastdb $mlst_databases.fields.path/blast/mlst.fa
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2
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95 #if $options.select=="advanced"
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96 #if $options.minid
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97 --minid $options.minid
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98 #end if
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99 #if $options.mincov
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100 --mincov $options.mincov
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101 #end if
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102 #if $options.minscore
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103 --minscore $options.minscore
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104 #end if
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105 #end if
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106 ${outname}.fasta > ${outname}.mlst_raw.tsv;
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107
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108 python $__tool_directory__/mlstAddFields.py ${outname}.mlst_raw.tsv $mlst_databases.fields.path/pubmlst > ${outname}.mlst.tsv;
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2
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109
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110 python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};
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111
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112 python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt
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113
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114 ]]></command>
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115 <inputs>
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116 <conditional name="jobtype">
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117 <param name="select" type="select" label="Select Input">
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118 <option value="fastq_fr">Forward and Reverse FASTQ</option>
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119 <option value="fastq_pair">Paired FASTQ Collection</option>
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120 </param>
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121 <when value="fastq_fr">
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122 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Forward FASTQ" />
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123 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Reverse FASTQ" />
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124 </when>
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125 <when value="fastq_pair">
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126 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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127 </when>
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128 </conditional>
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129
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130 <conditional name="options">
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131 <param name="select" type="select" label="Options Type">
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132 <option value="basic">Basic</option>
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133 <option value="advanced">Advanced</option>
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134 </param>
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135 <when value="advanced">
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136 <param name="cores" optional="true" type="integer" label="Number of cores to use (Default=16)" value=""/>
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137 <param name="memory" optional="true" type="integer" label="Memory available (Default=32GB)" value=""/>
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138 <param name="hash_count" optional="true" type="boolean" label="hash counter"/>
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139 <param name="estimated_kmers" optional="true" type="integer" label="Estimated number of unique kmers for bloom filter (Default=100)" value=""/>
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140 <param name="skip" optional="true" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/>
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141 <param name="kmer" optional="true" type="integer" label="Minimal kmer length for assembly (Default=21)" value=""/>
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142 <param name="min_count" optional="true" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/>
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143 <param name="max_kmer_count" optional="true" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/>
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144 <param name="vector_percent" optional="true" type="float" label="Count for vectors as a fraction of the read number (0-1,1=disabled)" value="">
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145 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
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146 </param>
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147 <param name="insert_size" optional="true" type="integer" label="Expected insert size for paired reads" value=""/>
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148 <param name="steps" optional="true" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads (Default=11)" value=""/>
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149 <param name="fraction" optional="true" type="float" label="Maximum noise to signal ratio acceptable for extension (Default=0.1)" value="">
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150 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/>
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151 </param>
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152 <param name="max_snp_len" optional="true" type="integer" label="Maximal snp length (Default=150)" value=""/>
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153 <param name="min_contig" optional="true" type="integer" label="Minimal contig length reported in output (Default=200)" value=""/>
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154 <param name="allow_snps" optional="true" type="boolean" label="Turn SNP discovery (Default=false)"/>
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155 <param name="mincov" type="integer" label="Minimum DNA %coverage" value="10" help="Minimum DNA %coverage to report partial allele at all (default 10, must be between 0-100)" optional="true" />
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156 <param name="minid" type="integer" label="Minimum DNA %identity" value="95" min="0" max="100" help="Minimum DNA %identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
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157 <param name="minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
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158 </when>
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159 <when value="basic"/>
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160 </conditional>
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161
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162 <param name="mlst_databases" label="Select a mlst database" type="select">
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163 <options from_data_table="mlst">
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164 <validator message="No database is available" type="no_options" />
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165 </options>
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166 </param>
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167
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168 </inputs>
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169 <outputs>
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170 <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/>
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171 <data format="tabular" name="results.mlst.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.mlst.tsv"/>
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172 <data format="tabular" name="qc_results.tsv" label="${tool.name} on ${on_string}: MLST" from_work_dir="*.txt"/>
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173 </outputs>
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174
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175 <help><![CDATA[
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176
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177 ]]></help>
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178 <citations>
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179 <citation type="bibtex">
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180 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
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181 title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes
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182 based on DeBruijn graphs. It uses conservative heuristics and is designed to
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183 create breaks at repeat regions in the genome. This leads to excellent sequence
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184 quality but not necessarily a large N50 statistic. It is a multi-threaded
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185 application that scales well with the number of processors. For different runs
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186 with the same inputs, including the order of reads, the order and orientation
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187 of contigs in the output is deterministic. },
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188 url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/},
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189 author={National Center for Biotechnology Information },
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190 }</citation>
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191
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192 <citation type="bibtex">
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193 @UNPUBLISHED{Seemann2016,
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194 author = "Seemann T",
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195 title = "MLST: Scan contig files against PubMLST typing schemes",
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196 year = "2016",
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197 url = {https://github.com/tseemann/mlst}
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198 }</citation>
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199 </citations>
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200 </tool>
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