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1 <tool id="sniplay_density" name="SNP density" version="2.0.0">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Calculate SNP densities along chromosome from a VCF input</description>
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5
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6
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7 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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8 <requirements>
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9 <requirement type="binary">perl</requirement>
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10 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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11 <requirement type="package" version="0.1.14">vcftools</requirement>
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12 <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement>
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13 </requirements>
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14
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15 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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16 <stdio>
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17 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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18 <exit_code range="1:" level="fatal" />
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19 </stdio>
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20
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21 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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22 <version_command>
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23 <!--
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24 tool_binary -v
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25 -->
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26 </version_command>
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27
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28 <!-- [REQUIRED] The command to execute -->
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29 <command interpreter="bash">
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30 calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step
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31 </command>
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32
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33 <!-- [REQUIRED] Input files and tool parameters -->
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34 <inputs>
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35 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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36 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
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37 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
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38 </inputs>
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39
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40 <!-- [REQUIRED] Output files -->
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41 <outputs>
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42 <data name="fileout" format="txt" label="${fileout_label}" />
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43 <data name="fileout_bysample" format="txt" label="${fileout_label}.by_sample" />
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
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49 <param name="step" value="20000" />
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50 <output name="fileout" file="SNPden-result.txt" />
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51 <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
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52 </test>
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53 <!-- [HELP] Multiple tests can be defined with different parameters -->
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54 <!--
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55 <test>
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56 </test>
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57 -->
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58 </tests>
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59
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60 <!-- [OPTIONAL] Help displayed in Galaxy -->
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61 <help>
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62
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63 .. class:: infomark
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64
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65 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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66
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67 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
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68
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69
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70 .. class:: infomark
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71
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72 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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73
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74 .. class:: infomark
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75
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76 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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77
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78 ---------------------------------------------------
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79
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80
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81
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82 =============
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83 SNP densities
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84 =============
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85
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86 -----------
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87 Description
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88 -----------
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89
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90 Calculate SNP densities along chromosome from a VCF file
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91
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92
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93 -----------------
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94 Workflow position
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95 -----------------
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96
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97 **Upstream tool**
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98
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99 =============== ====================== ===========
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100 Name output file(s) format
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101 =============== ====================== ===========
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102 =============== ====================== ===========
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103
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104
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105 ----------
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106 Input file
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107 ----------
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108
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109 VCF file
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110 File with SNPs
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111
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112
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113 ----------
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114 Parameters
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115 ----------
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116
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117 Step
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118 Step in bp for the window to calculate SNP density
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119
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120 Output name
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121 Output base name for the two ouput files
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122
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123
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124 ------------
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125 Output files
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126 ------------
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127
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128 Output_name
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129 Tabular file with SNP density in each postion
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130
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131 Output_name.by_sample
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132 Tabular file with SNP density for each sample
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133
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134
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135 ---------------------------------------------------
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136
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137 ---------------
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138 Working example
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139 ---------------
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140
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141 Input files
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142 ===========
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143
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144 vcf file
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145 -----------
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146
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147 ::
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148
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149 #fileformat=VCFv4.1
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150 #FILTER=<ID=LowQual,Description="Low quality">
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151 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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152 [...]
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153 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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154 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0
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155
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156 Parameters
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157 ==========
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158
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159 Step -> 200000
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160
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161 Output name -> densities
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162
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163
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164 Output files
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165 ============
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166
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167 densities
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168 ---------
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169
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170 ::
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171
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172 Chromosome Position SNPs
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173 chr1 200000 355
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174 chr1 400000 228
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175 chr1 600000 63
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176 chr1 800000 191
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177
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178
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179 densities.by_sample
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180 -------------------
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181
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182 ::
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183
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184 Chromosome BA58 BA59 BD54
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185 chr1 220 197 225
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186 chr1 130 119 133
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187 chr1 43 43 40
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188 chr1 139 167 141
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189
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190 </help>
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191 <citations>
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192 <!-- [HELP] As DOI or BibTex entry -->
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193 <citation type="bibtex">@article{Dereeper03062015,
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194 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
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195 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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196 year = {2015},
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197 doi = {10.1093/nar/gkv351},
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198 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
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199 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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200 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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201 journal = {Nucleic Acids Research}
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202 }
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203
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204 </citation>
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205
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206 </citations>
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207 </tool>
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