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1 <tool id="cpo_snippy" name="CPO_Snippy" version="3.2">
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2 <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description>
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1
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3 <requirements>
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4 <requirement type="package" version="3.2">snippy</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9
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10 <command>
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11 <![CDATA[
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12 snippy
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13 --outdir out
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14 --cpus "\${GALAXY_SLOTS:-1}"
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15 --ref $ref
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16 $cleanup
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17 #if str( $advanced.is_advanced ) == "advanced"
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18 --mapqual $advanced.mapqual
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19 --mincov $advanced.mincov
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20 --minfrac $advanced.minfrac
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21 #if $advanced.rgid
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22 --rgid $advanced.rgid
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23 #end if
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24 #if $advanced.bwaopt
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25 --bwaopt $advanced.bwaopt
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26 #end if
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27 #end if
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28 --ctgs $input
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29
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30 &&
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31
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32 gunzip out/snps.depth.gz
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33
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34 &&
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35
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36 #import re
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12
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37 #set $dir_name = ($input.element_identifier)
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38 mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
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39
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40 tar -czf out.tgz ${dir_name}
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1
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41
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42
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43 ]]>
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44 </command>
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45 <inputs>
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46
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47 <param name="ref" type="data" format="fasta" label="Reference Fasta" />
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48 <param name="input" type="data" format="fasta" label="assembled contigs"/>
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49 <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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50 <conditional name="advanced">
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51 <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings">
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52 <option value="advanced">Show advanced settings</option>
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53 <option value="simple" selected="true">Hide advanced settings</option>
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54 </param>
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55 <when value="advanced">
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56 <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" />
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57 <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" />
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58 <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" />
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59 <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
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60 <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
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61 </when>
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62 <when value="simple">
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63
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64 </when>
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65 </conditional>
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66 </inputs>
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67 <outputs>
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68 <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/>
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69 <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/>
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70 <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/>
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71 <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/>
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72 <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/>
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73 <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/>
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74 <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/>
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75 <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/>
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76 <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
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77 <filter>cleanup is False</filter>
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78 </data>
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79 <data format="zip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.tgz" />
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80 </outputs>
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81
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82 <tests>
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83 <test>
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84 <param name="ref_type_selector" value="fasta" />
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85 <param name="ref" value="Ecoli.fna" ftype="fasta" />
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86 <param name="fastq_input_selector" value="paired" />
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87 <param name="fastq_input1" ftype="fastq" value="reads_1.fq" />
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88 <param name="fastq_input2" ftype="fastq" value="reads_2.fq" />
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89 <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" />
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90 </test>
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91 </tests>
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92
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93
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94 <help>
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95 <![CDATA[
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96 Synopsis:
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97 snippy 3.0 - fast bacterial variant calling from NGS reads
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98
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99 Author:
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100 Torsten Seemann <torsten.seemann@gmail.com>
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101
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102 Usage:
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103 snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>
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104
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105 snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>
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106
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107 snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>
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108
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109 Options:
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110 --help This help
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111
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112 --version Print version and exit
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113
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114 --citation Print citation for referencing snippy
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115
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116 --quiet No screen output (default OFF)
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117
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118 --cpus [N] Maximum number of CPU cores to use (default '8')
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119
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120 --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')
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121
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122 --outdir [X] Output folder (default '')
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123
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124 --prefix [X] Prefix for output files (default 'snps')
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125
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126 --force Force overwrite of existing output folder (default OFF)
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127
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128 --pe1|R1|left [X] Reads, paired-end R1 (left) (default '')
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129
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130 --pe2|R2|right [X] Reads, paired-end R2 (right) (default '')
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131
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132 --se|single [X] Single-end reads (default '')
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133
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134 --peil [X] Reads, paired-end R1/R2 interleaved (default '')
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135
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136 --mapqual [n.n] Minimum mapping quality to allow (default '60')
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137
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138 --mincov [N] Minimum coverage of variant site (default '10')
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139
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140 --minfrac [n.n] Minumum proportion for variant evidence (default '0.9')
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141
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142 --report Produce long report with visual alignment (slow) (default OFF)
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143
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144 --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF)
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145
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146 --rgid [X] Use this @RG ID: in the BAM header (default '')
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147
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148 --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')
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149
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150 ]]>
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151 </help>
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152 <citations>
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153 <citation type="bibtex">
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154 @UNPUBLISHED{Seemann2013,
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155 author = "Seemann T",
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156 title = "snippy: fast bacterial variant calling from NGS reads",
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157 year = "2015",
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158 note = "https://github.com/tseemann/snippy"}
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159 </citation>
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160 </citations>
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161
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162
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163 </tool> |
