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comparison MDSplot/mdsplot.xml @ 10:c6640c49fd01 draft

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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 09:00:24 -0400
parents 6bf69b40365c
children 15b23cdde685
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9:98c37a5d67f4 10:c6640c49fd01
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},