Mercurial > repos > dereeper > sniplay
annotate MDSplot/mdsplot.xml @ 12:88748d846a20 draft
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| author | dereeper |
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| date | Tue, 14 Aug 2018 08:21:55 -0400 |
| parents | 15b23cdde685 |
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1 <tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0"> |
| 3 | 2 |
| 3 <!-- [REQUIRED] Tool description displayed after the tool name --> | |
| 4 <description> IBS matrix / multi-dimensional scaling</description> | |
| 5 | |
| 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | |
| 7 <requirements> | |
| 8 <requirement type="binary">perl</requirement> | |
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9 <requirement type="package">rsync</requirement> |
| 8 | 10 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
| 11 <requirement type="package" version="1.90b4">plink</requirement> | |
| 3 | 12 </requirements> |
| 4 | 13 |
| 14 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 15 <stdio> | |
| 16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 17 <exit_code range="1:" level="fatal" /> | |
| 18 </stdio> | |
| 19 | |
| 3 | 20 |
| 21 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
| 22 <version_command> | |
| 23 <!-- | |
| 24 tool_binary -v | |
| 25 --> | |
| 26 </version_command> | |
| 27 | |
| 28 <!-- [REQUIRED] The command to execute --> | |
| 29 <command interpreter="bash"> | |
| 8 | 30 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups |
| 3 | 31 </command> |
| 32 | |
| 33 <!-- [REQUIRED] Input files and tool parameters --> | |
| 34 <inputs> | |
| 35 <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> | |
| 36 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> | |
| 8 | 37 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/> |
| 3 | 38 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> |
| 39 </inputs> | |
| 40 | |
| 41 <!-- [REQUIRED] Output files --> | |
| 42 <outputs> | |
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43 <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" /> |
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44 <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" /> |
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45 <data name="fileout_log" format="txt" label="${fileout_label}.log" /> |
| 3 | 46 </outputs> |
| 47 | |
| 48 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 49 <tests> | |
| 50 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 51 <test> | |
| 4 | 52 <param name="fileped" value="MDSplot-input.ped" /> |
| 53 <param name="filemap" value="MDSplot-input.map" /> | |
| 54 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> | |
| 55 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> | |
| 3 | 56 </test> |
| 57 </tests> | |
| 58 | |
| 59 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
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60 <help><![CDATA[ |
| 3 | 61 |
| 62 | |
| 63 .. class:: infomark | |
| 64 | |
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65 MDS plot is done with PLINK. |
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66 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) |
| 3 | 67 |
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68 | **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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69 | **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). |
| 3 | 70 |
| 71 .. class:: infomark | |
| 72 | |
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73 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 3 | 74 |
| 75 .. class:: infomark | |
| 76 | |
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77 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 3 | 78 |
| 79 --------------------------------------------------- | |
| 80 | |
| 81 ======== | |
| 82 MDS plot | |
| 83 ======== | |
| 84 | |
| 85 ----------- | |
| 86 Description | |
| 87 ----------- | |
| 88 | |
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89 | MDS plot compute an IBS matrix and a multi-dimensional scaling. |
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90 | |
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91 | MDS plot is done with PLINK |
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92 | 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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93 | For further informations, please visit the PLINK website_. |
| 3 | 94 |
| 95 | |
| 96 | |
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97 .. _website: https://www.cog-genomics.org/plink |
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98 |
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99 ------------ |
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100 Dependencies |
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101 ------------ |
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102 PLINK |
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103 plink_ 1.90b4, Conda version |
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104 Bioperl |
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105 perl-bioperl_ 1.6.924, Conda version |
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106 Rsync |
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107 rsync_, Conda version |
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108 |
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109 |
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110 .. _plink: https://anaconda.org/bioconda/plink |
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111 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
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112 .. _rsync: https://anaconda.org/conda-forge/rsync |
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113 |
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114 ----------- |
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115 Input files |
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116 ----------- |
| 3 | 117 |
| 118 PED file | |
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119 PED file usually from VCF tools |
| 3 | 120 |
| 121 MAP file | |
| 122 4 columns tabular file: chromosome, snp id, genetic distance, bp position | |
| 123 | |
| 124 | |
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125 --------- |
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126 Parameter |
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127 --------- |
| 3 | 128 |
| 129 Output name | |
| 130 Output base name for the ouput files | |
| 131 | |
| 132 | |
| 133 ------------ | |
| 134 Output files | |
| 135 ------------ | |
| 136 | |
| 137 Output_name.ibs_matrix.txt | |
| 138 Tabular file with IBS matrix | |
| 139 | |
| 140 Output_name.mds_plot.txt | |
| 141 File to construct mds plot | |
| 142 | |
| 143 Output_name.log | |
| 144 Log file | |
| 145 | |
| 146 --------------------------------------------------- | |
| 147 | |
| 148 --------------- | |
| 149 Working example | |
| 150 --------------- | |
| 151 | |
| 152 Input files | |
| 153 =========== | |
| 154 | |
| 155 PED file | |
| 156 ----------- | |
| 157 | |
| 158 :: | |
| 159 | |
| 160 IRAT112 1 0 0 1 1 1 1 4 4 ... | |
| 161 IAC25 1 0 0 1 1 1 1 4 4 ... | |
| 162 CIRAD409 1 0 0 1 1 3 3 1 1 ... | |
| 163 | |
| 164 | |
| 165 MAP file | |
| 166 ----------- | |
| 167 | |
| 168 :: | |
| 169 | |
| 170 Chr1 Chr1:4299 0 4299 | |
| 171 Chr1 Chr1:26710 0 26710 | |
| 172 Chr1 Chr1:56184 0 56184 | |
| 173 Chr1 Chr1:93272 0 93272 | |
| 174 | |
| 175 | |
| 176 | |
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177 Parameter |
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178 ========= |
| 3 | 179 |
| 180 Output name -> densities | |
| 181 | |
| 182 | |
| 183 Output files | |
| 184 ============ | |
| 185 | |
| 186 densities.ibs_matrix.txt | |
| 187 ------------------------ | |
| 188 | |
| 189 :: | |
| 190 | |
| 191 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ... | |
| 192 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ... | |
| 193 IAC25 0.93691 1 0.958768 0.723299 0.965723 ... | |
| 194 | |
| 195 | |
| 196 densities.mds_plot.txt | |
| 197 ---------------------- | |
| 198 | |
| 199 :: | |
| 200 | |
| 201 IRAT112 -0.0969382 0.0376036 | |
| 202 IAC25 -0.0918126 0.0501177 | |
| 203 | |
| 204 | |
| 205 | |
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206 ]]></help> |
| 3 | 207 <citations> |
| 208 <!-- [HELP] As DOI or BibTex entry --> | |
| 209 <citation type="bibtex">@article{Dereeper03062015, | |
| 210 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}, | |
| 211 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 212 year = {2015}, | |
| 213 doi = {10.1093/nar/gkv351}, | |
| 214 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.}, | |
| 215 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 216 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 217 journal = {Nucleic Acids Research} | |
| 218 } | |
| 219 | |
| 220 </citation> | |
| 221 | |
| 222 </citations> | |
| 223 | |
| 224 </tool> |