Mercurial > repos > dereeper > sniplay
annotate MDSplot/mdsplot.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
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| date | Mon, 16 Apr 2018 09:00:24 -0400 |
| parents | 6bf69b40365c |
| children | 15b23cdde685 |
| rev | line source |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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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> | |
| 8 | 9 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
| 10 <requirement type="package" version="1.90b4">plink</requirement> | |
| 3 | 11 </requirements> |
| 4 | 12 |
| 13 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 14 <stdio> | |
| 15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 16 <exit_code range="1:" level="fatal" /> | |
| 17 </stdio> | |
| 18 | |
| 3 | 19 |
| 20 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
| 21 <version_command> | |
| 22 <!-- | |
| 23 tool_binary -v | |
| 24 --> | |
| 25 </version_command> | |
| 26 | |
| 27 <!-- [REQUIRED] The command to execute --> | |
| 28 <command interpreter="bash"> | |
| 8 | 29 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups |
| 3 | 30 </command> |
| 31 | |
| 32 <!-- [REQUIRED] Input files and tool parameters --> | |
| 33 <inputs> | |
| 34 <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> | |
| 35 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> | |
| 8 | 36 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/> |
| 3 | 37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> |
| 38 </inputs> | |
| 39 | |
| 40 <!-- [REQUIRED] Output files --> | |
| 41 <outputs> | |
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42 <data name="fileout_matrix" format="txt" label="${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" /> |
| 3 | 45 </outputs> |
| 46 | |
| 47 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 48 <tests> | |
| 49 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 50 <test> | |
| 4 | 51 <param name="fileped" value="MDSplot-input.ped" /> |
| 52 <param name="filemap" value="MDSplot-input.map" /> | |
| 53 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> | |
| 54 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> | |
| 3 | 55 </test> |
| 56 </tests> | |
| 57 | |
| 58 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
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59 <help><![CDATA[ |
| 3 | 60 |
| 61 | |
| 62 .. class:: infomark | |
| 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) |
| 3 | 66 |
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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). |
| 3 | 69 |
| 70 .. class:: infomark | |
| 71 | |
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72 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 3 | 73 |
| 74 .. class:: infomark | |
| 75 | |
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76 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 3 | 77 |
| 78 --------------------------------------------------- | |
| 79 | |
| 80 ======== | |
| 81 MDS plot | |
| 82 ======== | |
| 83 | |
| 84 ----------- | |
| 85 Description | |
| 86 ----------- | |
| 87 | |
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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_. |
| 3 | 93 |
| 94 | |
| 95 | |
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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 ----------- |
| 3 | 112 |
| 113 PED file | |
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114 PED file usually from VCF tools |
| 3 | 115 |
| 116 MAP file | |
| 117 4 columns tabular file: chromosome, snp id, genetic distance, bp position | |
| 118 | |
| 119 | |
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120 --------- |
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121 Parameter |
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122 --------- |
| 3 | 123 |
| 124 Output name | |
| 125 Output base name for the ouput files | |
| 126 | |
| 127 | |
| 128 ------------ | |
| 129 Output files | |
| 130 ------------ | |
| 131 | |
| 132 Output_name.ibs_matrix.txt | |
| 133 Tabular file with IBS matrix | |
| 134 | |
| 135 Output_name.mds_plot.txt | |
| 136 File to construct mds plot | |
| 137 | |
| 138 Output_name.log | |
| 139 Log file | |
| 140 | |
| 141 --------------------------------------------------- | |
| 142 | |
| 143 --------------- | |
| 144 Working example | |
| 145 --------------- | |
| 146 | |
| 147 Input files | |
| 148 =========== | |
| 149 | |
| 150 PED file | |
| 151 ----------- | |
| 152 | |
| 153 :: | |
| 154 | |
| 155 IRAT112 1 0 0 1 1 1 1 4 4 ... | |
| 156 IAC25 1 0 0 1 1 1 1 4 4 ... | |
| 157 CIRAD409 1 0 0 1 1 3 3 1 1 ... | |
| 158 | |
| 159 | |
| 160 MAP file | |
| 161 ----------- | |
| 162 | |
| 163 :: | |
| 164 | |
| 165 Chr1 Chr1:4299 0 4299 | |
| 166 Chr1 Chr1:26710 0 26710 | |
| 167 Chr1 Chr1:56184 0 56184 | |
| 168 Chr1 Chr1:93272 0 93272 | |
| 169 | |
| 170 | |
| 171 | |
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172 Parameter |
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173 ========= |
| 3 | 174 |
| 175 Output name -> densities | |
| 176 | |
| 177 | |
| 178 Output files | |
| 179 ============ | |
| 180 | |
| 181 densities.ibs_matrix.txt | |
| 182 ------------------------ | |
| 183 | |
| 184 :: | |
| 185 | |
| 186 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ... | |
| 187 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ... | |
| 188 IAC25 0.93691 1 0.958768 0.723299 0.965723 ... | |
| 189 | |
| 190 | |
| 191 densities.mds_plot.txt | |
| 192 ---------------------- | |
| 193 | |
| 194 :: | |
| 195 | |
| 196 IRAT112 -0.0969382 0.0376036 | |
| 197 IAC25 -0.0918126 0.0501177 | |
| 198 | |
| 199 | |
| 200 | |
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201 ]]></help> |
| 3 | 202 <citations> |
| 203 <!-- [HELP] As DOI or BibTex entry --> | |
| 204 <citation type="bibtex">@article{Dereeper03062015, | |
| 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}, | |
| 206 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 207 year = {2015}, | |
| 208 doi = {10.1093/nar/gkv351}, | |
| 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.}, | |
| 210 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 211 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 212 journal = {Nucleic Acids Research} | |
| 213 } | |
| 214 | |
| 215 </citation> | |
| 216 | |
| 217 </citations> | |
| 218 | |
| 219 </tool> |