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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 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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9 <requirement type="package" version="0.1.12b">vcftools</requirement>
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10 </requirements>
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11
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12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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13 <stdio>
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14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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15 <exit_code range="1:" level="fatal" />
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16 </stdio>
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17
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18 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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19 <version_command>
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20 <!--
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21 tool_binary -v
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22 -->
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23 </version_command>
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24
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25 <!-- [REQUIRED] The command to execute -->
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26 <command interpreter="bash">
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27 calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step
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28 </command>
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29
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30 <!-- [REQUIRED] Input files and tool parameters -->
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31 <inputs>
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32 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
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33 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
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34 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
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35 </inputs>
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36
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37 <!-- [REQUIRED] Output files -->
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38 <outputs>
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39 <data name="fileout" type="data" format="txt" label="${fileout_label}" />
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40 <data name="fileout_bysample" type="data" format="txt" label="${fileout_label}.by_sample" />
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
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46 <param name="step" value="20000" />
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47 <output name="fileout" file="SNPden-result.txt" />
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48 <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
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49 </test>
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50 <!-- [HELP] Multiple tests can be defined with different parameters -->
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51 <!--
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52 <test>
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53 </test>
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54 -->
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55 </tests>
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56
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57 <!-- [OPTIONAL] Help displayed in Galaxy -->
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58 <help>
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59
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60 .. class:: infomark
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61
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62 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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63
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64 | **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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65
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66
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67 .. class:: infomark
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68
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69 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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70
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71 .. class:: infomark
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72
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73 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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74
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75 ---------------------------------------------------
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76
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77
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78
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79 =============
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80 SNP densities
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81 =============
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82
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83 -----------
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84 Description
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85 -----------
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86
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87 Calculate SNP densities along chromosome from a VCF file
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88
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89
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90 -----------------
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91 Workflow position
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92 -----------------
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93
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94 **Upstream tool**
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95
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96 =============== ====================== ===========
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97 Name output file(s) format
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98 =============== ====================== ===========
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99 =============== ====================== ===========
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100
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101
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102 ----------
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103 Input file
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104 ----------
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105
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106 VCF file
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107 File with SNPs
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108
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109
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110 ----------
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111 Parameters
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112 ----------
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113
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114 Step
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115 Step in bp for the window to calculate SNP density
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116
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117 Output name
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118 Output base name for the two ouput files
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119
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120
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121 ------------
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122 Output files
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123 ------------
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124
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125 Output_name
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126 Tabular file with SNP density in each postion
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127
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128 Output_name.by_sample
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129 Tabular file with SNP density for each sample
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130
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131
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132 ---------------------------------------------------
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133
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134 ---------------
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135 Working example
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136 ---------------
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137
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138 Input files
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139 ===========
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140
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141 vcf file
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142 -----------
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143
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144 ::
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145
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146 #fileformat=VCFv4.1
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147 #FILTER=<ID=LowQual,Description="Low quality">
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148 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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149 [...]
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150 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
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151 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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152
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153 Parameters
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154 ==========
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155
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156 Step -> 200000
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157
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158 Output name -> densities
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159
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160
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161 Output files
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162 ============
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163
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164 densities
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165 ---------
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166
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167 ::
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168
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169 Chromosome Position SNPs
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170 chr1 200000 355
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171 chr1 400000 228
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172 chr1 600000 63
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173 chr1 800000 191
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174
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175
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176 densities.by_sample
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177 -------------------
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178
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179 ::
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180
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181 Chromosome BA58 BA59 BD54
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182 chr1 220 197 225
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183 chr1 130 119 133
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184 chr1 43 43 40
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185 chr1 139 167 141
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186
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187 </help>
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188 <citations>
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189 <!-- [HELP] As DOI or BibTex entry -->
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190 <citation type="bibtex">@article{Dereeper03062015,
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191 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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192 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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193 year = {2015},
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194 doi = {10.1093/nar/gkv351},
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195 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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196 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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197 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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198 journal = {Nucleic Acids Research}
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199 }
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200
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201 </citation>
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202
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203 </citations>
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204 </tool>
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