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comparison biosigner_config.xml @ 2:b2414be87d4b draft

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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
author ethevenot
date Sat, 06 Aug 2016 12:17:12 -0400
parents 4ff502a46189
children fa80bd02055f
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1:4ff502a46189 2:b2414be87d4b
1 <tool id="biosigner" name="Biosigner" version="2.2.4"> 1 <tool id="biosigner" name="Biosigner" version="2.2.6">
2 <description>Molecular signature discovery from omics data</description> 2 <description>Molecular signature discovery from omics data</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2.2">R</requirement> 5 <requirement type="package" version="3.2.2">R</requirement>
6 <requirement type="package">r-batch</requirement> 6 <requirement type="package">r-batch</requirement>
7 <requirement type="package">bioconductor-biosigner</requirement> 7 <requirement type="package">bioconductor-biosigner</requirement>
8 </requirements> 8 </requirements>
9 9
10 <command><![CDATA[ 10 <stdio>
11 $__tool_directory__/biosigner_wrapper.R 11 <exit_code range="1:" level="fatal" />
12 12 </stdio>
13 dataMatrix_in "$dataMatrix_in" 13
14 sampleMetadata_in "$sampleMetadata_in" 14 <command><![CDATA[
15 variableMetadata_in "$variableMetadata_in" 15 Rscript $__tool_directory__/biosigner_wrapper.R
16 16
17 respC "$respC" 17 dataMatrix_in "$dataMatrix_in"
18 18 sampleMetadata_in "$sampleMetadata_in"
19 #if $advCpt.opcC == "full" 19 variableMetadata_in "$variableMetadata_in"
20 methodC "$advCpt.methodC" 20
21 bootI "$advCpt.bootI" 21 respC "$respC"
22 tierC "$advCpt.tierC" 22
23 pvalN "$advCpt.pvalN" 23 #if $advCpt.opcC == "full"
24 seedI "$advCpt.seedI" 24 methodC "$advCpt.methodC"
25 #end if 25 bootI "$advCpt.bootI"
26 26 tierC "$advCpt.tierC"
27 variableMetadata_out "$variableMetadata_out" 27 pvalN "$advCpt.pvalN"
28 figure_tier "$figure_tier" 28 seedI "$advCpt.seedI"
29 figure_boxplot "$figure_boxplot" 29 #end if
30 information "$information" 30
31 ]]></command> 31 variableMetadata_out "$variableMetadata_out"
32 32 figure_tier "$figure_tier"
33 <inputs> 33 figure_boxplot "$figure_boxplot"
34 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> 34 information "$information"
35 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> 35 ]]></command>
36 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> 36
37 <param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., 'case' and 'control')" /> 37 <inputs>
38 38 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
39 <conditional name="advCpt"> 39 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
40 <param name="opcC" type="select" label="Advanced computational parameters" > 40 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
41 <option value="default" selected="true">Use default</option> 41 <param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., 'case' and 'control')" />
42 <option value="full">Full parameter list</option> 42
43 </param> 43 <conditional name="advCpt">
44 <when value="default"/> 44 <param name="opcC" type="select" label="Advanced computational parameters" >
45 <when value="full"> 45 <option value="default" selected="true">Use default</option>
46 <param name="methodC" label="Classification method(s)" type="select" help=""> 46 <option value="full">Full parameter list</option>
47 <option value="all" selected="true">all</option> 47 </param>
48 <option value="plsda">PLS-DA</option> 48 <when value="default"/>
49 <option value="randomforest">Random Forest</option> 49 <when value="full">
50 <option value="svm">SVM</option> 50 <param name="methodC" label="Classification method(s)" type="select" help="">
51 </param> 51 <option value="all" selected="true">all</option>
52 <param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/> 52 <option value="plsda">PLS-DA</option>
53 <param name="tierC" label="Selection tier(s)" type="select" help=""> 53 <option value="randomforest">Random Forest</option>
54 <option value="S" selected="true">S</option> 54 <option value="svm">SVM</option>
55 <option value="A">S+A</option> 55 </param>
56 </param> 56 <param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/>
57 <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/> 57 <param name="tierC" label="Selection tier(s)" type="select" help="">
58 <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/> 58 <option value="S" selected="true">S</option>
59 </when> 59 <option value="A">S+A</option>
60 </conditional> 60 </param>
61 61 <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/>
62 <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/>
63 </when>
64 </conditional>
62 </inputs> 65 </inputs>
63 66
64 <outputs> 67 <outputs>
65 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 68 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
66 <data name="figure_tier" label="${tool.name}__figure-tier.pdf" format="pdf"/> 69 <data name="figure_tier" label="${tool.name}__figure-tier.pdf" format="pdf"/>
67 <data name="figure_boxplot" label="${tool.name}__figure-boxplot.pdf" format="pdf"/> 70 <data name="figure_boxplot" label="${tool.name}__figure-boxplot.pdf" format="pdf"/>
68 <data name="information" label="${tool.name}__information.txt" format="txt"/> 71 <data name="information" label="${tool.name}__information.txt" format="txt"/>
69 </outputs> 72 </outputs>
70 73
71 <tests> 74 <tests>
72 <test> 75 <test>
73 <param name="dataMatrix_in" value="dataMatrix.tsv"/> 76 <param name="dataMatrix_in" value="dataMatrix.tsv"/>
74 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/> 77 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
75 <param name="variableMetadata_in" value="variableMetadata.tsv"/> 78 <param name="variableMetadata_in" value="variableMetadata.tsv"/>
76 <param name="respC" value="gender"/> 79 <param name="respC" value="gender"/>
77 <param name="opcC" value="full"/> 80 <param name="opcC" value="full"/>
78 <param name="methodC" value="all"/> 81 <param name="methodC" value="all"/>
79 <param name="bootI" value="5"/> 82 <param name="bootI" value="5"/>
80 <param name="tierC" value="S"/> 83 <param name="tierC" value="S"/>
81 <param name="pvalN" value="0.05"/> 84 <param name="pvalN" value="0.05"/>
82 <param name="seedI" value="123"/> 85 <param name="seedI" value="123"/>
83 <output name="variableMetadata_out" file="variableMetadata.out"/> 86 <output name="variableMetadata_out" file="variableMetadata.out"/>
84 </test> 87 </test>
85 </tests> 88 </tests>
86 89
87 <help> 90 <help>
88 91
89 .. class:: infomark 92 .. class:: infomark
90 93
91 **Author** Philippe Rinaudo and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr) 94 **Author** Philippe Rinaudo and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)
94 97
95 .. class:: infomark 98 .. class:: infomark
96 99
97 **Please cite** 100 **Please cite**
98 101
99 Philippe Rinaudo, Christophe Junot and Etienne A. Thevenot. *biosigner*: A new method for the discovery of restricted and stable molecular signatures from omics data. *submitted*. 102 Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2016). *biosigner*: a new method for the discovery of significant molecular signatures from omics data. *Frontiers in Molecular Biosciences*, **3** (http://dx.doi.org/10.3389/fmolb.2016.00026).
100 103
101 --------------------------------------------------- 104 ---------------------------------------------------
102 105
103 .. class:: infomark 106 .. class:: infomark
104 107
105 **R package** 108 **R package**
106 109
107 The *biosigner* package has been submitted to the bioconductor repository (http://bioconductor.org/packages/biosigner). 110 The *biosigner* package is available from the bioconductor repository (http://bioconductor.org/packages/biosigner).
108 111
109 --------------------------------------------------- 112 ---------------------------------------------------
110 113
111 .. class:: infomark 114 .. class:: infomark
112 115
241 244
242 --------------- 245 ---------------
243 Working example 246 Working example
244 --------------- 247 ---------------
245 248
246 See the **W4M00003_diaplasma** in the **Shared Data/Published Histories** menu 249 See the **W4M00001a_sacurine-subset-statistics** and **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
247 250
248 251
249 252
250 Figure output 253 Figure output
251 ============= 254 =============
257 260
258 ---- 261 ----
259 NEWS 262 NEWS
260 ---- 263 ----
261 264
265 CHANGES IN VERSION 2.2.6
266 ========================
267
268 INTERNAL MODIFICATIONS
269
270 Minor internal modifications
271
272 CHANGES IN VERSION 2.2.4
273 ========================
274
275 INTERNAL MODIFICATIONS
276
277 Creating additional files for planemo and travis running and installation validation
278
262 CHANGES IN VERSION 2.2.2 279 CHANGES IN VERSION 2.2.2
263 ======================== 280 ========================
264 281
282 INTERNAL MODIFICATIONS
283
265 Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3) 284 Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)
266 285
267 CHANGES IN VERSION 2.2.1 286 CHANGES IN VERSION 2.2.1
268 ======================== 287 ========================
269 288
289 NEW FEATURE
290
270 Creation of the tool 291 Creation of the tool
271 292
272 </help> 293 </help>
273 294
274 <citations/> 295 <citations>
296 <citation type="bibtex">@Article{Rinaudo2016,
297 Title = {biosigner: a new method for the discovery of significant molecular signatures from omics data},
298 Author = {Rinaudo, Philippe and Boudah, Samia and Junot, Christophe and Thevenot, Etienne A},
299 Journal = {Frontiers in Molecular Biosciences},
300 Year = {2016},
301 Pages = {--},
302 Volume = {3},
303 Doi = {10.3389/fmolb.2016.00026}
304 }</citation>
305 <citation type="doi">10.1093/bioinformatics/btu813</citation>
306 </citations>
275 307
276 </tool> 308 </tool>