Mercurial > repos > dereeper > sniplay
annotate MDSplot/mdsplot.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
---|---|
date | Mon, 16 Apr 2018 09:00:24 -0400 |
parents | 6bf69b40365c |
children | 15b23cdde685 |
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 | 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 $groups |
3 | 30 </command> |
31 | |
32 <!-- [REQUIRED] Input files and tool parameters --> | |
33 <inputs> | |
34 <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> | |
35 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/> | |
8 | 36 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/> |
3 | 37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> |
38 </inputs> | |
39 | |
40 <!-- [REQUIRED] Output files --> | |
41 <outputs> | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
42 <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" /> |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
43 <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" /> |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
44 <data name="fileout_log" format="txt" label="${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 --> | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
59 <help><![CDATA[ |
3 | 60 |
61 | |
62 .. class:: infomark | |
63 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
64 MDS plot is done with PLINK. |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
65 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) |
3 | 66 |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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. |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
72 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
3 | 73 |
74 .. class:: infomark | |
75 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
88 | MDS plot compute an IBS matrix and a multi-dimensional scaling. |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
89 | |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
90 | MDS plot is done with PLINK |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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. |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
92 | For further informations, please visit the PLINK website_. |
3 | 93 |
94 | |
95 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
96 .. _website: https://www.cog-genomics.org/plink |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
97 |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
98 ------------ |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
99 Dependencies |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
100 ------------ |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
101 PLINK |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
102 plink_ 1.90b4, Conda version |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
103 Bioperl |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
104 perl-bioperl_ 1.6.924, Conda version |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
105 |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
106 .. _plink: https://anaconda.org/bioconda/plink |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
107 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
108 |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
109 ----------- |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
110 Input files |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
111 ----------- |
3 | 112 |
113 PED file | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
120 --------- |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
121 Parameter |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
172 Parameter |
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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 | |
10
c6640c49fd01
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
8
diff
changeset
|
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> |