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1 <tool id="snippy" name="snippy" version="0.2.0">
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2 <requirements>
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3 <requirement type="package" version="3.0">snippy</requirement>
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4 <requirement type="package" version="1.2">samtools</requirement>
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1
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5 <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
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6 <requirement type="package" version="0.7.12">bwa</requirement>
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7 <requirement type="package" version="0.1.11">vcftools</requirement>
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8 <requirement type="package" version="4.0">snpeff</requirement>
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3
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9 <requirement type="package" version="8a5602bf07">vcflib</requirement>
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0
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14
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15 <command><![CDATA[
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16 cp $ref foo.fna &&
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17 snippy
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18 --outdir out
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19 --cpus "\${GALAXY_SLOTS:-1}"
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20 --ref foo.fna
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21 $cleanup
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22 #if str( $advanced.is_advanced ) == "advanced"
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23 --mapqual $advanced.mapqual
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24 --mincov $advanced.mincov
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25 --minfrac $advanced.minfrac
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26 #if $advanced.rgid
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27 --rgid $advanced.rgid
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28 #end if
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29 #if $advanced.bwaopt
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30 --bwaopt $advanced.bwaopt
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31 #end if
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32 #end if
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33 #if str( $fastq_input.fastq_input_selector ) == "paired"
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34 --pe1 $fastq_input.fastq_input1
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35 --pe2 $fastq_input.fastq_input2
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36 #end if
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37 #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
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38 --pe1 $fastq_input.fastq_input1.forward
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39 --pe2 $fastq_input.fastq_input1.reverse
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40 #end if
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41 #if str( $fastq_input.fastq_input_selector ) == "single"
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42 --se $fastq_input.fastq_input1
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43 #end if
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44 #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
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45 --peil $fastq_input.fastq_input1
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46 #end if
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47
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48 &&
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49
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50 gunzip out/snps.depth.gz
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51
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52
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53 ]]></command>
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54 <inputs>
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55 <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" />
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56 <conditional name="fastq_input">
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57 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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58 <option value="paired">Paired</option>
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59 <option value="single">Single</option>
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60 <option value="paired_collection">Paired Collection</option>
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61 <option value="paired_iv">Paired Interleaved</option>
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62 </param>
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63 <when value="paired">
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64 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
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65 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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66 </when>
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67 <when value="single">
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68 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
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69 </when>
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70 <when value="paired_collection">
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71 <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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72 </when>
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73 <when value="paired_iv">
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74 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
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75 </when>
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76 </conditional>
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77 <param name="cleanup" type="boolean" checked="true" truevalue="--cleanup" falsevalue="" label="Cleanup the non-snp output files" help="Remove all non-SNP files: BAMs, indices etc" />
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78 <conditional name="advanced">
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79 <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings">
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80 <option value="advanced">Show advanced settings</option>
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81 <option value="simple" selected="true">Hide advanced settings</option>
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82 </param>
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83 <when value="advanced">
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84 <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
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85 <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
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86 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
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87 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
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88 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
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89 </when>
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90 <when value="simple">
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91
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92 </when>
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93 </conditional>
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94 </inputs>
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95 <outputs>
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96 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>
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97 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
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98 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
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99 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
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100 <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
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101 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
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102 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
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103 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
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104 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
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105 <filter>cleanup is False</filter>
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106 </data>
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107 </outputs>
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108
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109 <tests>
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110 <test>
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111 <param name="ref" value="Ecoli.fna" ftype="fasta" />
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112 <param name="fastq_input_selector" value="paired" />
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113 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />
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114 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />
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115 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />
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116 </test>
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117 </tests>
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118
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119
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120 <help><![CDATA[
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121 This is a change to force a reinstall
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122 Synopsis:
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123 snippy 3.0 - fast bacterial variant calling from NGS reads
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124 Author:
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125 Torsten Seemann <torsten.seemann@gmail.com>
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126 Usage:
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127 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
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128 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
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129 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
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130 Options:
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131 --help This help
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132 --version Print version and exit
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133 --citation Print citation for referencing snippy
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134 --quiet No screen output (default OFF)
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135 --cpus [N] Maximum number of CPU cores to use (default '8')
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136 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
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137 --outdir [X] Output folder (default '')
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138 --prefix [X] Prefix for output files (default 'snps')
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139 --force Force overwrite of existing output folder (default OFF)
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140 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '')
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141 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '')
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142 --se|single [X] Single-end reads (default '')
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143 --peil [X] Reads, paired-end R1/R2 interleaved (default '')
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144 --mapqual [n.n] Minimum mapping quality to allow (default '60')
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145 --mincov [N] Minimum coverage of variant site (default '10')
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146 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9')
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147 --report Produce long report with visual alignment (slow) (default OFF)
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148 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)
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149 --rgid [X] Use this @RG ID: in the BAM header (default '')
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150 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
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151
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152 ]]></help>
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153
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154 <citations>
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155 <citation type="bibtex">@UNPUBLISHED{Seemann2013,
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156 author = "Seemann T",
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157 title = "snippy: fast bacterial variant calling from NGS reads",
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158 year = "2015",
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159 note = "https://github.com/tseemann/snippy"}
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160 </citation>
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161 </citations>
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162
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163 </tool>
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