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1 <tool id="sniplay_density" name="SNP density" version="1.2.0">
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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 HapMap</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 </requirements>
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10
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11 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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12 <version_command>
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13 <!--
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14 tool_binary -v
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15 -->
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16 </version_command>
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17
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18 <!-- [REQUIRED] The command to execute -->
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19 <command interpreter="bash">
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20 calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
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21 </command>
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22
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23 <!-- [REQUIRED] Input files and tool parameters -->
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24 <inputs>
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25 <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
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26 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
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27 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />
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28 </inputs>
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29
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30 <!-- [REQUIRED] Output files -->
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31 <outputs>
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32 <data name="fileout" type="data" format="tabular" label="${fileout_label}" />
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33 <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
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34 </outputs>
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35
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36 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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37 <stdio>
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38 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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39 <exit_code range="1:" level="fatal" />
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40 </stdio>
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41
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42 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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43 <tests>
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44 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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45 <!--
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46 <test>
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47 <param name="input" value="input_test.txt" />
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48 <output name="output" file="output_test.txt" />
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49 </test>
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50 -->
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51 <!-- [HELP] Multiple tests can be defined with different parameters -->
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52 <!--
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53 <test>
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54 </test>
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55 -->
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56 </tests>
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57
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58 <!-- [OPTIONAL] Help displayed in Galaxy -->
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59 <help>
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60
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61 .. class:: infomark
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62
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63 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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64
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65 | **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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66
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67
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68 .. class:: infomark
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69
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70 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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71
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72 .. class:: infomark
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73
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74 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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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 =============
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81 SNP densities
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82 =============
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83
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84 -----------
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85 Description
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86 -----------
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87
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88 Calculate SNP densities along chromosome from HapMap
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89
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90
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91 -----------------
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92 Workflow position
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93 -----------------
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94
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95 **Upstream tool**
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96
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97 =============== ====================== ===========
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98 Name output file(s) format
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99 =============== ====================== ===========
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100 VCF to Hapmap Hapmap file hapmap
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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 Input file
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106 ----------
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107
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108 Hapmap file
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109 File with SNPs
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110
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111
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112 ----------
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113 Parameters
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114 ----------
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115
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116 Step
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117 Step in bp for the window to calculate SNP density
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118
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119 Output name
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120 Output base name for the two ouput files
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121
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122
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123 ------------
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124 Output files
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125 ------------
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126
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127 Output_name
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128 Tabular file with SNP density in each postion
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129
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130 Output_name.by_sample
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131 Tabular file with SNP density for each sample
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132
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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 Working example
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138 ---------------
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139
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140 Input files
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141 ===========
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142
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143 hapmap file
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144 -----------
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145
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146 ::
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147
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148 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode ref BA58 BA59 BD54
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149 chr1:1774 [G/T] chr1 1774 Cc01_g00010:47 exon NON_SYNONYMOUS_CODING gCg/gAg A/E 25.0% 4 GG TT TT TT
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150 chr1:1640 [G/A] chr1 1640 Cc01_g00010:127 exon NON_SYNONYMOUS_CODING Ccg/Tcg P/S 37.5% 4 GG GG AA GA
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151 chr1:1629 [A/C] chr1 1629 Cc01_g00010:138 exon SYNONYMOUS_CODING ctT/ctG L/L 37.5% 4 AA CC CC AC
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152 chr1:1628 [C/G] chr1 1628 Cc01_g00010:139 exon NON_SYNONYMOUS_CODING Ggg/Cgg G/R 12.5% 4 CC CC CC CG
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153 chr1:1619 [T/G] chr1 1619 Cc01_g00010:148 exon NON_SYNONYMOUS_CODING Aaa/Caa K/Q 37.5% 4 TT TT GG TG
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154 chr1:1405 [C/T] chr1 1405 Cc01_g00010:362 exon NON_SYNONYMOUS_CODING cGg/cAg R/Q 16.7% 3 CC CC NN CT
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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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