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comparison MDSplot/mdsplot.xml @ 3:345f88a8f483 draft

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author dereeper
date Fri, 10 Jul 2015 10:38:43 -0400
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2:feb40a9a8eae 3:345f88a8f483
1 <tool id="sniplay_mdsplot" name="MDS plot" version="1.1.1">
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>
9 <requirement type="package" version="1.07">plink</requirement>
10 </requirements>
11
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
13 <version_command>
14 <!--
15 tool_binary -v
16 -->
17 </version_command>
18
19 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="bash">
21 mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log
22 </command>
23
24 <!-- [REQUIRED] Input files and tool parameters -->
25 <inputs>
26 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
27 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
28 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
29 </inputs>
30
31 <!-- [REQUIRED] Output files -->
32 <outputs>
33 <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
34 <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
35 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
36 </outputs>
37
38 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
39 <stdio>
40 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
41 <exit_code range="1:" level="fatal" />
42 </stdio>
43
44 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
45 <tests>
46 <!-- [HELP] Test files have to be in the ~/test-data directory -->
47
48 <test>
49 <param name="fileped" value="input.ped" />
50 <param name="filemap" value="input.map" />
51 <output name="fileout_matrix" file="output.ibs_matrix.txt" />
52 <output name="fileout_plot" file="output.mds_plot.txt" />
53 <output name="fileout_log" file="output.log" />
54 </test>
55
56 <!-- [HELP] Multiple tests can be defined with different parameters -->
57 <!--
58 <test>
59 </test>
60 -->
61 </tests>
62
63 <!-- [OPTIONAL] Help displayed in Galaxy -->
64 <help>
65
66
67 .. class:: infomark
68
69 **Authors** plink_
70
71 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
72
73 | "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.
74
75
76 .. class:: infomark
77
78 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
79
80 .. class:: infomark
81
82 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
83
84 .. class:: infomark
85
86 **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).
87
88 ---------------------------------------------------
89
90
91
92 ========
93 MDS plot
94 ========
95
96 -----------
97 Description
98 -----------
99
100 Compute an IBS matrix and a multi-dimensional scaling.
101
102
103 -----------------
104 Workflow position
105 -----------------
106
107 **Upstream tool**
108
109 =============== ========================== ===============
110 Name output file(s) format
111 =============== ========================== ===============
112 VCFtools Filter PED and MAP file tabular and MAP
113 =============== ========================== ===============
114
115
116
117 ----------
118 Input file
119 ----------
120
121 PED file
122
123 MAP file
124 4 columns tabular file: chromosome, snp id, genetic distance, bp position
125
126
127 ----------
128 Parameters
129 ----------
130
131 Output name
132 Output base name for the ouput files
133
134
135 ------------
136 Output files
137 ------------
138
139 Output_name.ibs_matrix.txt
140 Tabular file with IBS matrix
141
142 Output_name.mds_plot.txt
143 File to construct mds plot
144
145 Output_name.log
146 Log file
147
148 ------------
149 Dependencies
150 ------------
151 plink
152 version 1.07
153
154 ---------------------------------------------------
155
156 ---------------
157 Working example
158 ---------------
159
160 Input files
161 ===========
162
163 PED file
164 -----------
165
166 ::
167
168 IRAT112 1 0 0 1 1 1 1 4 4 ...
169 IAC25 1 0 0 1 1 1 1 4 4 ...
170 CIRAD409 1 0 0 1 1 3 3 1 1 ...
171
172
173 MAP file
174 -----------
175
176 ::
177
178 Chr1 Chr1:4299 0 4299
179 Chr1 Chr1:26710 0 26710
180 Chr1 Chr1:56184 0 56184
181 Chr1 Chr1:93272 0 93272
182
183
184
185 Parameters
186 ==========
187
188 Output name -> densities
189
190
191 Output files
192 ============
193
194 densities.ibs_matrix.txt
195 ------------------------
196
197 ::
198
199 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ...
200 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ...
201 IAC25 0.93691 1 0.958768 0.723299 0.965723 ...
202
203
204 densities.mds_plot.txt
205 ----------------------
206
207 ::
208
209 IRAT112 -0.0969382 0.0376036
210 IAC25 -0.0918126 0.0501177
211
212
213
214 </help>
215 <citations>
216 <!-- [HELP] As DOI or BibTex entry -->
217 <citation type="bibtex">@article{Dereeper03062015,
218 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},
219 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
220 year = {2015},
221 doi = {10.1093/nar/gkv351},
222 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.},
223 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
224 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
225 journal = {Nucleic Acids Research}
226 }
227
228 </citation>
229
230 </citations>
231
232 </tool>