annotate MDSplot/mdsplot.xml @ 10:c6640c49fd01 draft

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1 <tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0">
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> IBS matrix / multi-dimensional scaling</description>
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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="1.6.924">perl-bioperl</requirement>
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10 <requirement type="package" version="1.90b4">plink</requirement>
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11 </requirements>
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13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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14 <stdio>
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15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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16 <exit_code range="1:" level="fatal" />
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17 </stdio>
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18
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20 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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21 <version_command>
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22 <!--
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23 tool_binary -v
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24 -->
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25 </version_command>
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26
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27 <!-- [REQUIRED] The command to execute -->
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28 <command interpreter="bash">
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29 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups
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30 </command>
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31
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32 <!-- [REQUIRED] Input files and tool parameters -->
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33 <inputs>
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34 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
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35 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
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36 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/>
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37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
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38 </inputs>
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39
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40 <!-- [REQUIRED] Output files -->
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41 <outputs>
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42 <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" />
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43 <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" />
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44 <data name="fileout_log" format="txt" label="${fileout_label}.log" />
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45 </outputs>
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46
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47 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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48 <tests>
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49 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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50 <test>
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51 <param name="fileped" value="MDSplot-input.ped" />
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52 <param name="filemap" value="MDSplot-input.map" />
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53 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" />
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54 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" />
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55 </test>
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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><![CDATA[
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62 .. class:: infomark
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63
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64 MDS plot is done with PLINK.
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65 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)
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67 | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007.
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68 | **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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70 .. class:: infomark
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71
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72 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
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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 alexis.dereeper@ird.fr
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78 ---------------------------------------------------
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80 ========
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81 MDS plot
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82 ========
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84 -----------
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85 Description
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86 -----------
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88 | MDS plot compute an IBS matrix and a multi-dimensional scaling.
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89 |
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90 | MDS plot is done with PLINK
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91 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
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92 | For further informations, please visit the PLINK website_.
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96 .. _website: https://www.cog-genomics.org/plink
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97
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98 ------------
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99 Dependencies
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100 ------------
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101 PLINK
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102 plink_ 1.90b4, Conda version
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103 Bioperl
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104 perl-bioperl_ 1.6.924, Conda version
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105
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106 .. _plink: https://anaconda.org/bioconda/plink
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107 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
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108
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109 -----------
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110 Input files
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111 -----------
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112
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113 PED file
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114 PED file usually from VCF tools
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116 MAP file
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117 4 columns tabular file: chromosome, snp id, genetic distance, bp position
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119
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120 ---------
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121 Parameter
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122 ---------
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124 Output name
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125 Output base name for the ouput files
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128 ------------
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129 Output files
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130 ------------
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132 Output_name.ibs_matrix.txt
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133 Tabular file with IBS matrix
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135 Output_name.mds_plot.txt
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136 File to construct mds plot
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138 Output_name.log
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139 Log file
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141 ---------------------------------------------------
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143 ---------------
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144 Working example
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145 ---------------
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147 Input files
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148 ===========
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150 PED file
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151 -----------
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153 ::
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155 IRAT112 1 0 0 1 1 1 1 4 4 ...
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156 IAC25 1 0 0 1 1 1 1 4 4 ...
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157 CIRAD409 1 0 0 1 1 3 3 1 1 ...
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160 MAP file
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161 -----------
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163 ::
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165 Chr1 Chr1:4299 0 4299
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166 Chr1 Chr1:26710 0 26710
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167 Chr1 Chr1:56184 0 56184
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168 Chr1 Chr1:93272 0 93272
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171
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172 Parameter
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173 =========
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175 Output name -> densities
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178 Output files
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179 ============
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181 densities.ibs_matrix.txt
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182 ------------------------
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184 ::
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186 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ...
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187 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ...
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188 IAC25 0.93691 1 0.958768 0.723299 0.965723 ...
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191 densities.mds_plot.txt
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192 ----------------------
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194 ::
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196 IRAT112 -0.0969382 0.0376036
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197 IAC25 -0.0918126 0.0501177
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201 ]]></help>
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202 <citations>
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203 <!-- [HELP] As DOI or BibTex entry -->
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204 <citation type="bibtex">@article{Dereeper03062015,
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205 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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206 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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207 year = {2015},
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208 doi = {10.1093/nar/gkv351},
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209 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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210 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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211 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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212 journal = {Nucleic Acids Research}
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213 }
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215 </citation>
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217 </citations>
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219 </tool>