annotate MDSplot/mdsplot.xml @ 15:31c23d943c29 draft default tip

Uploaded
author dereeper
date Tue, 08 Jan 2019 08:47:56 -0500
parents 15b23cdde685
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
1 <tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0">
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
2
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
4 <description> IBS matrix / multi-dimensional scaling</description>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
5
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
7 <requirements>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
8 <requirement type="binary">perl</requirement>
11
15b23cdde685 planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
dereeper
parents: 10
diff changeset
9 <requirement type="package">rsync</requirement>
8
6bf69b40365c Uploaded
dereeper
parents: 5
diff changeset
10 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6bf69b40365c Uploaded
dereeper
parents: 5
diff changeset
11 <requirement type="package" version="1.90b4">plink</requirement>
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
12 </requirements>
4
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
13
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
14 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
15 <stdio>
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
17 <exit_code range="1:" level="fatal" />
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
18 </stdio>
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
19
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
20
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
21 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
22 <version_command>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
23 <!--
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
24 tool_binary -v
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
25 -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
26 </version_command>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
27
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
28 <!-- [REQUIRED] The command to execute -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
29 <command interpreter="bash">
8
6bf69b40365c Uploaded
dereeper
parents: 5
diff changeset
30 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
31 </command>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
32
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
33 <!-- [REQUIRED] Input files and tool parameters -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
34 <inputs>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
35 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
36 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
8
6bf69b40365c Uploaded
dereeper
parents: 5
diff changeset
37 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/>
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
38 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
39 </inputs>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
40
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
41 <!-- [REQUIRED] Output files -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
42 <outputs>
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
43 <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" />
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
44 <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" />
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
45 <data name="fileout_log" format="txt" label="${fileout_label}.log" />
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
46 </outputs>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
47
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
48 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
49 <tests>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
50 <!-- [HELP] Test files have to be in the ~/test-data directory -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
51 <test>
4
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
52 <param name="fileped" value="MDSplot-input.ped" />
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
53 <param name="filemap" value="MDSplot-input.map" />
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
54 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" />
10627af23f10 planemo upload
gandres
parents: 3
diff changeset
55 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" />
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
56 </test>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
57 </tests>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
58
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
59 <!-- [OPTIONAL] Help displayed in Galaxy -->
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
60 <help><![CDATA[
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
61
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
62
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
63 .. class:: infomark
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
64
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
65 MDS plot is done with PLINK.
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
66 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink)
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
67
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
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.
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
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
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
70
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
71 .. class:: infomark
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
72
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
73 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
74
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
75 .. class:: infomark
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
76
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
77 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
78
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
79 ---------------------------------------------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
80
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
81 ========
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
82 MDS plot
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
83 ========
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
84
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
85 -----------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
86 Description
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
87 -----------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
88
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
89 | MDS plot compute an IBS matrix and a multi-dimensional scaling.
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
90 |
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
91 | MDS plot is done with PLINK
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
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.
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
93 | For further informations, please visit the PLINK website_.
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
94
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
95
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
96
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
97 .. _website: https://www.cog-genomics.org/plink
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
98
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
99 ------------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
100 Dependencies
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
101 ------------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
102 PLINK
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
103 plink_ 1.90b4, Conda version
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
104 Bioperl
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
105 perl-bioperl_ 1.6.924, Conda version
11
15b23cdde685 planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
dereeper
parents: 10
diff changeset
106 Rsync
15b23cdde685 planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
dereeper
parents: 10
diff changeset
107 rsync_, Conda version
15b23cdde685 planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
dereeper
parents: 10
diff changeset
108
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
109
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
110 .. _plink: https://anaconda.org/bioconda/plink
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
111 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
11
15b23cdde685 planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty
dereeper
parents: 10
diff changeset
112 .. _rsync: https://anaconda.org/conda-forge/rsync
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
113
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
114 -----------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
115 Input files
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
116 -----------
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
117
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
118 PED file
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
119 PED file usually from VCF tools
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
120
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
121 MAP file
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
122 4 columns tabular file: chromosome, snp id, genetic distance, bp position
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
123
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
124
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
125 ---------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
126 Parameter
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
127 ---------
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
128
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
129 Output name
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
130 Output base name for the ouput files
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
131
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
132
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
133 ------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
134 Output files
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
135 ------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
136
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
137 Output_name.ibs_matrix.txt
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
138 Tabular file with IBS matrix
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
139
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
140 Output_name.mds_plot.txt
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
141 File to construct mds plot
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
142
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
143 Output_name.log
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
144 Log file
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
145
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
146 ---------------------------------------------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
147
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
148 ---------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
149 Working example
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
150 ---------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
151
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
152 Input files
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
153 ===========
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
154
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
155 PED file
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
156 -----------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
157
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
158 ::
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
159
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
160 IRAT112 1 0 0 1 1 1 1 4 4 ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
161 IAC25 1 0 0 1 1 1 1 4 4 ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
162 CIRAD409 1 0 0 1 1 3 3 1 1 ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
163
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
164
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
165 MAP file
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
166 -----------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
167
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
168 ::
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
169
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
170 Chr1 Chr1:4299 0 4299
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
171 Chr1 Chr1:26710 0 26710
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
172 Chr1 Chr1:56184 0 56184
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
173 Chr1 Chr1:93272 0 93272
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
174
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
175
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
176
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
177 Parameter
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
178 =========
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
179
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
180 Output name -> densities
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
181
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
182
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
183 Output files
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
184 ============
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
185
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
186 densities.ibs_matrix.txt
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
187 ------------------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
188
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
189 ::
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
190
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
191 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
192 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
193 IAC25 0.93691 1 0.958768 0.723299 0.965723 ...
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
194
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
195
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
196 densities.mds_plot.txt
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
197 ----------------------
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
198
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
199 ::
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
200
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
201 IRAT112 -0.0969382 0.0376036
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
202 IAC25 -0.0918126 0.0501177
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
203
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
204
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
205
10
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 8
diff changeset
206 ]]></help>
3
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
207 <citations>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
208 <!-- [HELP] As DOI or BibTex entry -->
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
209 <citation type="bibtex">@article{Dereeper03062015,
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
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},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
211 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
212 year = {2015},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
213 doi = {10.1093/nar/gkv351},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
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.},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
215 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
216 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
217 journal = {Nucleic Acids Research}
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
218 }
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
219
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
220 </citation>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
221
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
222 </citations>
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
223
345f88a8f483 Uploaded
dereeper
parents:
diff changeset
224 </tool>