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comparison MDSplot/mdsplot.xml @ 19:a0a95688cf17 draft

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author dereeper
date Thu, 26 Feb 2015 16:09:14 -0500
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18:7ba803afa41b 19:a0a95688cf17
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="0.1.13">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 .. class:: infomark
67
68 **Authors**
69
70 ---------------------------------------------------
71
72 .. class:: infomark
73
74 **Please cite** If you use this tool, please cite dereeper et al. 2015 in prep.
75
76 ---------------------------------------------------
77
78 ========
79 MDS plot
80 ========
81
82 -----------
83 Description
84 -----------
85
86 Compute an IBS matrix and a multi-dimensional scaling.
87
88
89 -----------------
90 Workflow position
91 -----------------
92
93 **Upstream tools**
94
95 =========== ========================== =======
96 Name output file(s) format
97 =========== ========================== =======
98 =========== ========================== =======
99
100
101 **Downstream tools**
102
103 =========== ========================== =======
104 Name output file(s) format
105 =========== ========================== =======
106 =========== ========================== =======
107
108
109 ----------
110 Input file
111 ----------
112
113 PED file
114
115 MAP file
116 4 columns tabular file: chromosome, snp id, genetic distance, bp position
117
118
119 ----------
120 Parameters
121 ----------
122
123 Output name
124 Output base name for the ouput files
125
126
127 ------------
128 Output files
129 ------------
130
131 Output_name.ibs_matrix.txt
132 Tabular file with IBS matrix
133
134 Output_name.mds_plot.txt
135 File to construct mds plot
136
137 Output_name.log
138 Log file
139
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
172 Parameters
173 ==========
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
201 </help>
202
203 </tool>