Mercurial > repos > dereeper > sniplay
comparison 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 |
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9:98c37a5d67f4 | 10:c6640c49fd01 |
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1 <tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0"> | 1 <tool id="sniplay_mdsplot" name="PLINK: MDS plot" version="2.0.0"> |
2 | 2 |
3 <!-- [REQUIRED] Tool description displayed after the tool name --> | 3 <!-- [REQUIRED] Tool description displayed after the tool name --> |
4 <description> IBS matrix / multi-dimensional scaling</description> | 4 <description> IBS matrix / multi-dimensional scaling</description> |
5 | 5 |
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> |
37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> | 37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" /> |
38 </inputs> | 38 </inputs> |
39 | 39 |
40 <!-- [REQUIRED] Output files --> | 40 <!-- [REQUIRED] Output files --> |
41 <outputs> | 41 <outputs> |
42 <data name="fileout_matrix" type="data" format="txt" label="${fileout_label}.ibs_matrix.txt" /> | 42 <data name="fileout_matrix" format="txt" label="${fileout_label}.ibs_matrix.txt" /> |
43 <data name="fileout_plot" type="data" format="txt" label="${fileout_label}.mds_plot.txt" /> | 43 <data name="fileout_plot" format="txt" label="${fileout_label}.mds_plot.txt" /> |
44 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> | 44 <data name="fileout_log" format="txt" label="${fileout_label}.log" /> |
45 </outputs> | 45 </outputs> |
46 | 46 |
47 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | 47 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> |
48 <tests> | 48 <tests> |
49 <!-- [HELP] Test files have to be in the ~/test-data directory --> | 49 <!-- [HELP] Test files have to be in the ~/test-data directory --> |
50 | |
51 <test> | 50 <test> |
52 <param name="fileped" value="MDSplot-input.ped" /> | 51 <param name="fileped" value="MDSplot-input.ped" /> |
53 <param name="filemap" value="MDSplot-input.map" /> | 52 <param name="filemap" value="MDSplot-input.map" /> |
54 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> | 53 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> |
55 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> | 54 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> |
56 </test> | 55 </test> |
57 | |
58 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
59 <!-- | |
60 <test> | |
61 </test> | |
62 --> | |
63 </tests> | 56 </tests> |
64 | 57 |
65 <!-- [OPTIONAL] Help displayed in Galaxy --> | 58 <!-- [OPTIONAL] Help displayed in Galaxy --> |
66 <help> | 59 <help><![CDATA[ |
67 | 60 |
68 | 61 |
69 .. class:: infomark | 62 .. class:: infomark |
70 | 63 |
71 **Authors** plink_ | 64 MDS plot is done with PLINK. |
72 | 65 **Authors** PLINK: Shaun Purcell (https://www.cog-genomics.org/plink) |
73 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/ | 66 |
74 | 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. |
75 | "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. | 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). |
76 | |
77 | 69 |
78 .. class:: infomark | 70 .. class:: infomark |
79 | 71 |
80 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. | 72 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
81 | 73 |
82 .. class:: infomark | 74 .. class:: infomark |
83 | 75 |
84 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr | 76 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
85 | |
86 .. class:: infomark | |
87 | |
88 **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). | |
89 | 77 |
90 --------------------------------------------------- | 78 --------------------------------------------------- |
91 | |
92 | |
93 | 79 |
94 ======== | 80 ======== |
95 MDS plot | 81 MDS plot |
96 ======== | 82 ======== |
97 | 83 |
98 ----------- | 84 ----------- |
99 Description | 85 Description |
100 ----------- | 86 ----------- |
101 | 87 |
102 Compute an IBS matrix and a multi-dimensional scaling. | 88 | MDS plot compute an IBS matrix and a multi-dimensional scaling. |
103 | 89 | |
104 | 90 | MDS plot is done with PLINK |
105 ----------------- | 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. |
106 Workflow position | 92 | For further informations, please visit the PLINK website_. |
107 ----------------- | 93 |
108 | 94 |
109 **Upstream tool** | 95 |
110 | 96 .. _website: https://www.cog-genomics.org/plink |
111 =============== ========================== =============== | 97 |
112 Name output file(s) format | 98 ------------ |
113 =============== ========================== =============== | 99 Dependencies |
114 VCFtools Filter PED and MAP file tabular and MAP | 100 ------------ |
115 =============== ========================== =============== | 101 PLINK |
116 | 102 plink_ 1.90b4, Conda version |
117 | 103 Bioperl |
118 | 104 perl-bioperl_ 1.6.924, Conda version |
119 ---------- | 105 |
120 Input file | 106 .. _plink: https://anaconda.org/bioconda/plink |
121 ---------- | 107 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
108 | |
109 ----------- | |
110 Input files | |
111 ----------- | |
122 | 112 |
123 PED file | 113 PED file |
114 PED file usually from VCF tools | |
124 | 115 |
125 MAP file | 116 MAP file |
126 4 columns tabular file: chromosome, snp id, genetic distance, bp position | 117 4 columns tabular file: chromosome, snp id, genetic distance, bp position |
127 | 118 |
128 | 119 |
129 ---------- | 120 --------- |
130 Parameters | 121 Parameter |
131 ---------- | 122 --------- |
132 | 123 |
133 Output name | 124 Output name |
134 Output base name for the ouput files | 125 Output base name for the ouput files |
135 | 126 |
136 | 127 |
144 Output_name.mds_plot.txt | 135 Output_name.mds_plot.txt |
145 File to construct mds plot | 136 File to construct mds plot |
146 | 137 |
147 Output_name.log | 138 Output_name.log |
148 Log file | 139 Log file |
149 | |
150 ------------ | |
151 Dependencies | |
152 ------------ | |
153 plink | |
154 version 1.07 | |
155 | 140 |
156 --------------------------------------------------- | 141 --------------------------------------------------- |
157 | 142 |
158 --------------- | 143 --------------- |
159 Working example | 144 Working example |
182 Chr1 Chr1:56184 0 56184 | 167 Chr1 Chr1:56184 0 56184 |
183 Chr1 Chr1:93272 0 93272 | 168 Chr1 Chr1:93272 0 93272 |
184 | 169 |
185 | 170 |
186 | 171 |
187 Parameters | 172 Parameter |
188 ========== | 173 ========= |
189 | 174 |
190 Output name -> densities | 175 Output name -> densities |
191 | 176 |
192 | 177 |
193 Output files | 178 Output files |
211 IRAT112 -0.0969382 0.0376036 | 196 IRAT112 -0.0969382 0.0376036 |
212 IAC25 -0.0918126 0.0501177 | 197 IAC25 -0.0918126 0.0501177 |
213 | 198 |
214 | 199 |
215 | 200 |
216 </help> | 201 ]]></help> |
217 <citations> | 202 <citations> |
218 <!-- [HELP] As DOI or BibTex entry --> | 203 <!-- [HELP] As DOI or BibTex entry --> |
219 <citation type="bibtex">@article{Dereeper03062015, | 204 <citation type="bibtex">@article{Dereeper03062015, |
220 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}, | 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}, |
221 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | 206 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, |