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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit bc5bbb26c53bf2455043cf4b8f552571e6f74530
author iuc
date Mon, 20 Jan 2025 10:10:04 +0000
parents fa016f1eea1a
children
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1 <tool id="snippy" name="snippy" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>
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3 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="exit_code"><![CDATA[
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12
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13 @REFERENCE_SOURCE_FILE@
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14
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15 #import re
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16 #if str( $fastq_input.fastq_input_selector ) == "paired"
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17 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
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18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
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19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
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20 #elif str( $fastq_input.fastq_input_selector ) == "single"
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21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
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22 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
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23 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
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24 #elif str( $fastq_input.fastq_input_selector ) == "contigs"
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25 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fasta_input.element_identifier)
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26 #end if
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27
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28 snippy
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29 --outdir '${dir_name}'
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30 --cpus \${GALAXY_SLOTS:-1}
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31 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
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32 @REFERENCE_COMMAND@
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33 --mapqual $adv.mapqual
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34 --mincov $adv.mincov
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35 --minfrac $adv.minfrac
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36 --minqual $adv.minqual
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37 #if $adv.rgid
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38 --rgid '$adv.rgid'
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39 #end if
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40 #if $adv.bwaopt
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41 --bwaopt '$adv.bwaopt'
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42 #end if
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43
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44 #if str( $fastq_input.fastq_input_selector ) == "paired"
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45 --R1 '$fastq_input.fastq_input1'
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46 --R2 '$fastq_input.fastq_input2'
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47 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
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48 --R1 '$fastq_input.fastq_input.forward'
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49 --R2 '$fastq_input.fastq_input.reverse'
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50 #elif str( $fastq_input.fastq_input_selector ) == "single"
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51 --se '$fastq_input.fastq_input_single'
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52 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
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53 --peil '$fastq_input.fastq_input_interleaved'
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54 #elif str( $fastq_input.fastq_input_selector ) == "contigs"
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55 --ctgs '$fastq_input.fasta_input'
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56 #end if
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57
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58 #if "outcon" in str($outputs) and $adv.rename_cons
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59 && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
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60 #end if
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61
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62 && cp -r '${dir_name}' out
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63 && tar -czf out.tgz '${dir_name}'
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64 ]]> </command>
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65
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66 <inputs>
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67 <expand macro="reference_selector" />
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68 <conditional name="fastq_input">
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69 <param name="fastq_input_selector" type="select" label="Input type" help="Select paired/single end raw read data or assembled contigs">
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70 <option value="paired">Paired end reads</option>
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71 <option value="single">Single end reads</option>
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72 <option value="paired_collection">Paired end reads in a collection</option>
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73 <option value="paired_iv">Interleaved paired end reads</option>
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74 <option value="contigs">Assembled Contigs</option>
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75 </param>
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76 <when value="paired">
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77 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
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78 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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79 </when>
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80 <when value="single">
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81 <param name="fastq_input_single" type="data" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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82 </when>
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83 <when value="paired_collection">
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84 <param name="fastq_input" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" 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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85 </when>
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86 <when value="paired_iv">
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87 <param name="fastq_input_interleaved" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
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88 </when>
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89 <when value="contigs">
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90 <param name="fasta_input" type="data" format="fasta" label="Select fasta dataset" help="Specify dataset with assembled contigs"/>
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91 </when>
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92
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93 </conditional>
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94
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95 <section name="adv" title="Advanced parameters" expanded="false">
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96 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
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97 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
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98 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
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99 <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
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100 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
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101 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
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102 <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
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103 </section>
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104
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105 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
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106 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
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107 <option value="outgff" selected="False">The variants in GFF3 format</option>
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108 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
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109 <option value="outsum" selected="False">A summary of the samples and mapping</option>
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110 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
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111 <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option>
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112 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
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113 <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option>
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114 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
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115 </param>
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116
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117 </inputs>
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118
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119 <outputs>
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120
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121 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf">
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122 <filter>outputs and 'outvcf' in outputs</filter>
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123 </data>
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124 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff">
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125 <filter>outputs and 'outgff' in outputs</filter>
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126 </data>
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127 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab">
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128 <filter>outputs and 'outtab' in outputs</filter>
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129 </data>
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130 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt">
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131 <filter>outputs and 'outsum' in outputs</filter>
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132 </data>
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133 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log">
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134 <filter>outputs and 'outlog' in outputs</filter>
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135 </data>
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136 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa">
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137 <filter>outputs and 'outaln' in outputs</filter>
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138 </data>
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139 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa">
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140 <filter>outputs and 'outcon' in outputs</filter>
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141 </data>
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142 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
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143 <filter>outputs and 'outbam' in outputs</filter>
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144 </data>
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145 <data format="zip" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
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146 <filter>outputs and 'outzip' in outputs</filter>
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147 </data>
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148
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149 </outputs>
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150
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151 <tests>
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152
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153 <test> <!-- test 0 - fasta ref no snps -->
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154 <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
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155 <conditional name="reference_source">
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156 <param name="reference_source_selector" value="history"/>
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157 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
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158 </conditional>
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159 <param name="fastq_input_selector" value="paired" />
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160 <param name="fastq_input1" ftype="fastqsanger.gz" value="a_1.fastq.gz" />
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161 <param name="fastq_input2" ftype="fastqsanger.gz" value="a_2.fastq.gz" />
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162 <param name="mincov" value="2" />
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163 <param name="minqual" value="60" />
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164 <param name="outputs" value="outgff,outsum" />
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165 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
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166 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
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167 </test>
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168
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169 <test> <!-- test 1 - fasta ref one snp -->
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170 <conditional name="reference_source">
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171 <param name="reference_source_selector" value="history"/>
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172 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
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173 </conditional>
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174 <param name="fastq_input_selector" value="paired" />
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175 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
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176 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
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177 <param name="mincov" value="2" />
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178 <param name="minqual" value="60" />
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179 <param name="outputs" value="outgff,outsum" />
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180 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
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181 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
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182 </test>
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183
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184 <test> <!-- test 2 - fasta ref one snp paired_collection -->
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185 <conditional name="reference_source">
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186 <param name="reference_source_selector" value="history"/>
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187 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
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188 </conditional>
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189 <param name="fastq_input_selector" value="paired_collection" />
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190 <param name="fastq_input">
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191 <collection type="paired">
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192 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
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193 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
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194 </collection>
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195 </param>
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196 <param name="mincov" value="2" />
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197 <param name="minqual" value="60" />
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198 <param name="outputs" value="outgff,outsum" />
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199 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
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200 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
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201 </test>
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202
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203 <test> <!-- test 3 - fasta ref one snp single -->
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204 <conditional name="reference_source">
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205 <param name="reference_source_selector" value="history"/>
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206 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
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207 </conditional>
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208 <param name="fastq_input_selector" value="single" />
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209 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
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210 <param name="mincov" value="2" />
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211 <param name="minqual" value="60" />
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212 <param name="outputs" value="outgff,outsum" />
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213 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
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214 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
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215 </test>
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216
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217 <test> <!-- test 4 - reference source as cached -->
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218 <conditional name="reference_source">
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219 <param name="reference_source_selector" value="cached"/>
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220 <param name="ref_file" value="test_id"/>
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221 </conditional>
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222 <param name="fastq_input_selector" value="single" />
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223 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
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224 <param name="mincov" value="2" />
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225 <param name="minqual" value="60" />
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226 <param name="outputs" value="outgff,outsum" />
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227 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="8" />
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228 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" lines_diff="2"/>
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229 </test>
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230
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231 <test> <!-- test 5 - fasta ref one snp single -->
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232 <conditional name="reference_source">
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233 <param name="reference_source_selector" value="history"/>
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234 <param name="ref_file" value="reference.fasta" ftype="fasta"/>
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235 </conditional>
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236 <conditional name="fastq_input">
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237 <param name="fastq_input_selector" value="contigs" />
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238 <param name="fasta_input" value="contigs.fasta" ftype="fasta" />
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239 </conditional>
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240 <param name="mincov" value="2" />
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241 <param name="minqual" value="60" />
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242 <param name="outputs" value="outgff,outsum" />
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243 <output name="snpsum" ftype="tabular" file="d_fna_ref_mincov_1_minqual_60.snps.txt" lines_diff="6" />
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244 <output name="snpgff" ftype="gff3" file="d_fna_ref_mincov_1_minqual_60.snps.gff" lines_diff="2"/>
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245 </test>
0
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246 </tests>
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247
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248
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249 <help><![CDATA[
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250
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251 **Snippy @VERSION@**
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252
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253 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).
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254
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255 **Author**
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256
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257 Torsten Seemann
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258
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259 **Inputs**
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260
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261 - NGS Reads in fastq format (single or paired end)
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262 - Reference file in either fasta or genbank format
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263
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264 If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.
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265
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266 **Advanced options**
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267
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268 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
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269
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270 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
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271
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272 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
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273
2
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274 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
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275
0
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276 - rgid - String - Use this @RG ID: in the BAM header (default '')
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277
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278 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
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279
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280 **Further information**
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281
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282 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
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283
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284 ]]> </help>
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285 <expand macro="citations"/>
0
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286
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287 </tool>