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annotate snippy.xml @ 25:ae9dffe91f20 draft

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author dfornika
date Tue, 18 Jun 2019 16:08:43 -0400
parents 542d3c3d5a6e
children 15d5dd95daf2
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1 <tool id="snippy" name="snippy" version="@VERSION@+galaxy3">
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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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13 #import re
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14 #if str( $fastq_input.fastq_input_selector ) == "paired"
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15 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
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16 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
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17 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
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18 #elif str( $fastq_input.fastq_input_selector ) == "single"
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19 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
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20 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
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21 #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
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22 #end if
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23
0
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24 #if $ref.is_of_type("fasta")
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25 cp '$ref' 'ref.fna' &&
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26 #end if
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27 #if $ref.is_of_type("genbank")
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28 cp '$ref' 'ref.gbk' &&
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29 #end if
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30 snippy
25
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31 --outdir '$dir_name'
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32 --cpus \${GALAXY_SLOTS:-1}
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33 --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
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34 #if $ref.is_of_type("fasta")
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35 --ref 'ref.fna'
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36 #end if
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37 #if $ref.is_of_type("genbank")
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38 --ref 'ref.gbk'
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39 #end if
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40 --mapqual $adv.mapqual
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41 --mincov $adv.mincov
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42 --minfrac $adv.minfrac
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43 --minqual $adv.minqual
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44 #if $adv.rgid
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45 --rgid '$adv.rgid'
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46 #end if
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47 #if $adv.bwaopt
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48 --bwaopt '$adv.bwaopt'
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49 #end if
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51 #if str( $fastq_input.fastq_input_selector ) == "paired"
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52 --R1 '$fastq_input.fastq_input1'
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53 --R2 '$fastq_input.fastq_input2'
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54 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
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55 --R1 '$fastq_input.fastq_input.forward'
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56 --R2 '$fastq_input.fastq_input.reverse'
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57 #elif str( $fastq_input.fastq_input_selector ) == "single"
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58 --se '$fastq_input.fastq_input_single'
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59 #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
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60 --peil '$fastq_input.fastq_input_interleaved'
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61 #end if
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62
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63 &&
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64
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65 tar -czf out.tgz ${dir_name}
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66 #if "outcon" in str($outputs) and $adv.rename_cons
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67 && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
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68 #end if
0
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71 ]]></command>
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73 <inputs>
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74
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75 <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />
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76
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77 <conditional name="fastq_input">
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78 <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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79 <option value="paired">Paired</option>
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80 <option value="single">Single</option>
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81 <option value="paired_collection">Paired Collection</option>
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82 <option value="paired_iv">Paired Interleaved</option>
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83 </param>
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84 <when value="paired">
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85 <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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86 <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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87 </when>
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88 <when value="single">
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89 <param name="fastq_input_single" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
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90 </when>
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91 <when value="paired_collection">
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92 <param name="fastq_input" 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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93 </when>
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94 <when value="paired_iv">
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95 <param name="fastq_input_interleaved" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
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96 </when>
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97 </conditional>
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98
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99 <section name="adv" title="Advanced parameters" expanded="false">
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100 <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
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101 <param name="mincov" type="integer" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
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102 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
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103 <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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104 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
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105 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
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106 <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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107 </section>
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108
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109 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
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110 <option value="outvcf" selected="True">The final annotated variants in VCF format</option>
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111 <option value="outgff" selected="False">The variants in GFF3 format</option>
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112 <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option>
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113 <option value="outsum" selected="False">A summary of the samples and mapping</option>
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114 <option value="outlog" selected="False">A log file with the commands run and their outputs</option>
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115 <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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116 <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option>
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117 <option value="outdep" selected="False">Output of samtools depth for the .bam file</option>
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118 <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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119 <option value="outzip" selected="True">Zipped files needed for input into snippy-core</option>
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120 </param>
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121
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122 </inputs>
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123
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124 <outputs>
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125
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126 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="${dir_name}/snps.vcf">
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127 <filter>outputs and 'outvcf' in outputs</filter>
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128 </data>
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129 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="${dir_name}/snps.gff">
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130 <filter>outputs and 'outgff' in outputs</filter>
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131 </data>
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132 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="${dir_name}/snps.tab">
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133 <filter>outputs and 'outtab' in outputs</filter>
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134 </data>
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135 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="${dir_name}/snps.txt">
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136 <filter>outputs and 'outsum' in outputs</filter>
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137 </data>
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138 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="${dir_name}/snps.log">
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139 <filter>outputs and 'outlog' in outputs</filter>
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140 </data>
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141 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="${dir_name}/snps.aligned.fa">
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142 <filter>outputs and 'outaln' in outputs</filter>
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143 </data>
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144 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="${dir_name}/snps.consensus.fa">
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145 <filter>outputs and 'outcon' in outputs</filter>
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146 </data>
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147 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="${dir_name}/snps.depth">
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148 <filter>outputs and 'outdep' in outputs</filter>
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149 </data>
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150 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="${dir_name}/snps.bam">
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151 <filter>outputs and 'outbam' in outputs</filter>
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152 </data>
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153 <data format="tar" name="outdir" label="${tool.name} on ${on_string} dir for snippy core" from_work_dir="out.tgz">
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154 <filter>outputs and 'outzip' in outputs</filter>
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155 </data>
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156
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157 </outputs>
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158
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159 <tests>
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160
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161 <test> <!-- test 0 - fasta ref no snps -->
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162 <param name="ref" value="reference.fasta" ftype="fasta" />
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163 <param name="fastq_input_selector" value="paired" />
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164 <param name="fastq_input1" ftype="fastqsanger" value="a_1.fastq" />
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165 <param name="fastq_input2" ftype="fastqsanger" value="a_2.fastq" />
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166 <param name="mincov" value="2" />
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167 <param name="minqual" value="60" />
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168 <param name="outputs" value="outgff,outsum" />
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169 <output name="snpsum" ftype="tabular" file="a_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
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170 <output name="snpgff" ftype="gff3" file="a_fna_ref_mincov_2_minqual_60.snps.gff" />
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171 </test>
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172
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173 <test> <!-- test 1 - fasta ref one snp -->
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174 <param name="ref" value="reference.fasta" ftype="fasta" />
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175 <param name="fastq_input_selector" value="paired" />
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176 <param name="fastq_input1" ftype="fastqsanger" value="b_1.fastq" />
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177 <param name="fastq_input2" ftype="fastqsanger" value="b_2.fastq" />
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178 <param name="mincov" value="2" />
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179 <param name="minqual" value="60" />
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180 <param name="outputs" value="outgff,outsum" />
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181 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
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182 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
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183 </test>
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184
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185 <test> <!-- test 2 - fasta ref one snp paired_collection -->
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186 <param name="ref" value="reference.fasta" ftype="fasta" />
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187 <param name="fastq_input_selector" value="paired_collection" />
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188 <param name="fastq_input">
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189 <collection type="paired">
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190 <element name="forward" ftype="fastqsanger" value="b_1.fastq" />
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191 <element name="reverse" ftype="fastqsanger" value="b_2.fastq" />
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192 </collection>
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193 </param>
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194 <param name="mincov" value="2" />
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195 <param name="minqual" value="60" />
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196 <param name="outputs" value="outgff,outsum" />
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197 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
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198 <output name="snpgff" ftype="gff3" file="b_fna_ref_mincov_2_minqual_60.snps.gff" />
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199 </test>
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200
22
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201 <test> <!-- test 3 - fasta ref one snp single -->
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202 <param name="ref" value="reference.fasta" ftype="fasta" />
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203 <param name="fastq_input_selector" value="single" />
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204 <param name="fastq_input_single" value="b_2.fastq" ftype="fastqsanger" />
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205 <param name="mincov" value="2" />
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206 <param name="minqual" value="60" />
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207 <param name="outputs" value="outgff,outsum" />
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208 <output name="snpsum" ftype="tabular" file="b_fna_ref_mincov_2_minqual_60.snps.txt" lines_diff="6" />
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209 <output name="snpgff" ftype="gff3" file="b_2_fna_ref_mincov_2_minqual_60.snps.gff" />
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210 </test>
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211 </tests>
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212
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213
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214 <help><![CDATA[
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215
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216 **Snippy @VERSION@**
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217
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218 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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219
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220 **Author**
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221
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222 Torsten Seemann
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223
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224 **Inputs**
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225
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226 - NGS Reads in fastq format (single or paired end)
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227 - Reference file in either fasta or genbank format
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228
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229 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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230
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231 **Advanced options**
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232
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233 - mapping quality - Integer - Minimum mapping quality to allow (default '60')
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234
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235 - minimum coverage - Integer - Minimum coverage of variant site (default '10')
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236
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237 - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
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238
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239 - minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
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240
0
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241 - rgid - String - Use this @RG ID: in the BAM header (default '')
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242
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243 - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')
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244
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245 **Further information**
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246
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247 For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy
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248
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249 ]]></help>
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250 <expand macro="citations"/>
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251
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252 </tool>