Mercurial > repos > ethevenot > univariate

annotate univariate_config.xml @ 2:09799fc16bc6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents fdefbc780d2e
children 140290de7986
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
1 <tool id="Univariate" name="Univariate" version="2.1.4">
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
2 <description>Univariate statistics</description>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
3
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
4 <requirements>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
5 <requirement type="package" version="3.2.2">R</requirement>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
6 <requirement type="package">r-batch</requirement>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
7 <requirement type="package">r-PMCMR</requirement>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
8 </requirements>
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
9
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
10 <stdio>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
11 <exit_code range="1:" level="fatal" />
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
12 </stdio>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
13
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
14 <command><![CDATA[
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
15 Rscript $__tool_directory__/univariate_wrapper.R
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
16
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
17 dataMatrix_in "$dataMatrix_in"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
18 sampleMetadata_in "$sampleMetadata_in"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
19 variableMetadata_in "$variableMetadata_in"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
20
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
21 facC "$facC"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
22 tesC "$tesC"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
23 adjC "$adjC"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
24 thrN "$thrN"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
25
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
26 variableMetadata_out "$variableMetadata_out"
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
27 information "$information"
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
28 ]]></command>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
29 <inputs>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
30 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
31 <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" />
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
32 <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" />
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
33 <param name="facC" label="Factor of interest" type="text" help="Name of the column of the sample metadata table corresponding to the qualitative or quantitative variable"/>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
34 <param name="tesC" label="Test" type="select" help="">
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
35 <option value="ttest">ttest (qualitative, 2 levels)</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
36 <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
37 <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
38 <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
39 <option value="pearson">Pearson correlation test (quantitative)</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
40 <option value="spearman">Spearman correlation rank test (quantitative)</option>
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
41 </param>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
42 <param name="adjC" label="Method for multiple testing correction" type="select" help="">
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
43 <option value="fdr">fdr</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
44 <option value="BH">BH</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
45 <option value="bonferroni">bonferroni</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
46 <option value="BY">BY</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
47 <option value="hochberg">hochberg</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
48 <option value="holm">holm</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
49 <option value="hommel">hommel</option>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
50 <option value="none">none</option>
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
51 </param>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
52 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
53 </inputs>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
54
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
55 <outputs>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
56 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
57 <data name="information" label="${tool.name}_information.txt" format="txt"/>
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
58 </outputs>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
59
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
60 <tests>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
61 <test>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
62 <param name="dataMatrix_in" value="dataMatrix.tsv"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
63 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
64 <param name="variableMetadata_in" value="variableMetadata.tsv"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
65 <param name="facC" value="ageGroup"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
66 <param name="tesC" value="kruskal"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
67 <param name="adjC" value="fdr"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
68 <param name="thrN" value="0.05"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
69 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
70 </test>
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
71 </tests>
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
72
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
73 <help>
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
74
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
75 .. class:: infomark
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
76
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
77 | **Tool update: See the 'NEWS' section at the bottom of the page**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
78
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
79 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
80
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
81 .. class:: infomark
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
82
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
83 **Authors**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
84
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
85 | **Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr)** and **Etienne Thevenot (etienne.thevenot@cea.fr)** wrote this wrapper of R univariate statistical tests.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
86 | MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
87
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
88 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
89
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
90 .. class:: infomark
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
91
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
92 **Please cite**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
93
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
94 R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
95
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
96 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
97
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
98 .. class:: infomark
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
99
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
100 **References**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
101
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
102 | Benjamini Y. and Hochberg Y. (1995). Controlling the false discovery rate: a practical and powerful approach for multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
103 | Dalgaard P. (2002). Introductory statistics with R. Springer.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
104 | Kvam P. and Vidakovic B. (2007). Nonparametric statistics with applications to science and engineering. Wiley.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
105 | Van Belle G., Fisher L., Heagerty P. and Lumley T. (2004). Biostatistics - a methodology for the health sciences. Wiley.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
106 | Pohlert T. (2015). PMCMR: Calculate pairwise multiple comparisons of mean rank sums. R package on CRAN.
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
107
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
108 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
109
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
110 =====================
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
111 Univariate statistics
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
112 =====================
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
113
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
114 -----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
115 Description
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
116 -----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
117
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
118 | The module performs two sample tests (t-test and Wilcoxon rank test), analysis of variance and Kruskal-Wallis rank test, and correlation tests (by using either the pearson or the spearman correlation)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
119
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
120 -----------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
121 Workflow position
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
122 -----------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
123
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
124 .. image:: univariate_workflowPositionImage.png
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
125 :width: 584
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
126
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
127 -----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
128 Input files
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
129 -----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
130
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
131 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
132 | File | Format |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
133 +==============================+============+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
134 | 1) Data matrix | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
135 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
136 | 2) Sample metadata | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
137 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
138 | 3) Variable metadata | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
139 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
140
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
141 ----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
142 Parameters
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
143 ----------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
144
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
145 Data matrix file
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
146 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
147 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
148
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
149 Sample metadata file
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
150 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
151 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
152
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
153 Variable metadata file
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
154 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
155 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
156
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
157 Factor
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
158 | Column of the sample metadata table to be used as qualitative factor (t-test, Wilcoxon test, Analysis of variance, Kruskal-Wallis test) or quantitative variable (correlation)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
159 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
160
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
161 Test
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
162 | Depending on the factor of interest (qualitative with 2 or more levels, or quantitative), and on the normality of the sample values (determining whether a parametric or nonparametric test is required), you can choose one of the 6 tests available:
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
163
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
164
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
165 +---------------------------+------------------+----------------------+----------------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
166 | Factor to be tested | Number of levels | Parametric test | Nonparametric test |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
167 +===========================+==================+======================+======================+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
168 | Qualitative | 2 | t-test | Wilcoxon test |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
169 + +------------------+----------------------+----------------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
170 | | > 2 | Analysis of variance | Kruskal-Wallis |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
171 +---------------------------+------------------+----------------------+----------------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
172 | Quantitative | | Pearson correlation | Spearman correlation |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
173 +---------------------------+------------------+----------------------+----------------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
174
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
175 Method for multiple testing correction
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
176 | The 7 methods implemented in the 'p.adjust' R function are available and documented as follows:
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
177 | "The adjustment methods include the Bonferroni correction ("bonferroni") in which the p-values are multiplied by the number of comparisons. Less conservative corrections are also included by Holm (1979) ("holm"), Hochberg (1988) ("hochberg"), Hommel (1988) ("hommel"), Benjamini and Hochberg (1995) ("BH" or its alias "fdr"), and Benjamini and Yekutieli (2001) ("BY"), respectively. A pass-through option ("none") is also included. The set of methods are contained in the p.adjust.methods vector for the benefit of methods that need to have the method as an option and pass it on to p.adjust. The first four methods are designed to give strong control of the family-wise error rate. There seems no reason to use the unmodified Bonferroni correction because it is dominated by Holm's method, which is also valid under arbitrary assumptions. Hochberg's and Hommel's methods are valid when the hypothesis tests are independent or when they are non-negatively associated (Sarkar, 1998; Sarkar and Chang, 1997). Hommel's method is more powerful than Hochberg's, but the difference is usually small and the Hochberg p-values are faster to compute. The "BH" (aka "fdr") and "BY" method of Benjamini, Hochberg, and Yekutieli control the false discovery rate, the expected proportion of false discoveries amongst the rejected hypotheses. The false discovery rate is a less stringent condition than the family-wise error rate, so these methods are more powerful than the others."
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
178 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
179
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
180 (Corrected) p-value significance threshold
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
181 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
182 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
183
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
184
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
185 ------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
186 Output files
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
187 ------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
188
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
189 variableMetadata_out.tabular
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
190 | **variableMetadata** file identical to the file given as argument, except that (at least) three columns have been added:
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
191 | 1) [factor]_[test]_[class'a']-[class'b']_dif or [factor]_[test]_cor: difference of the means (ttest) or the medians (wilcoxon) between the two classes, or 'pearson' or 'spearman' correlations
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
192 | 2) [factor]_[test]_[class'a']-[class'b']_[method] or [factor]_[test]_[method]: adjusted p-values
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
193 | 3) [factor]_[test]_[class'a']-[class'b']_sig or [factor]_[test]_sig: significance (coded as '1' if below the threshold and '0' otherwise)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
194 | In the case of 'anova' and 'kruskal', the columns 2) and 3) appear first to give the results from the ANOVA or Kruskal Wallis test, and, when these tests are significant, the results of the pairwise comparisons are reported in additional columns (otherwise NA in these columns): in the case of ANOVA, the Tukey HSD post-hoc analysis is used (for each comparison, the difference between means, p value, and significance are provided); in the case of Kruskal Wallis, the Nemenyi is performed (PMCMR package) (for each pairwise comparison, the difference between medians, p value and significance are provided)
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
195 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
196
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
197 information.txt
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
198 | File with all messages and warnings generated during the computation
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
199 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
200
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
201 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
202
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
203 ---------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
204 Working example
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
205 ---------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
206
2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
207 .. class:: infomark
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
208
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
209 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
210
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
211 ---------------------------------------------------
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
212
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
213 ----
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
214 NEWS
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
215 ----
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
216
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
217 CHANGES IN VERSION 2.1.4
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
218 ========================
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
219
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
220 NEW FEATURE
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
221
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
222 Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
223
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
224 INTERNAL MODIFICATIONS
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
225
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
226 Minor internal changes for toolshed export
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
227
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
228 CHANGES IN VERSION 2.1.2
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
229 ========================
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
230
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
231 INTERNAL MODIFICATIONS
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
232
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
233 Minor internal changes for toolshed export
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
234
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
235 CHANGES IN VERSION 2.1.1
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
236 ========================
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
237
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
238 INTERNAL MODIFICATIONS
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
239
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
240 Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples)
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
241
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
242 CHANGES IN VERSION 2.0.1
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
243 ========================
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
244
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
245 NEW FEATURE
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
246
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
247 (corrected) p-value threshold can be set to any value between 0 and 1
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
248
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
249
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
250 </help>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
251
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
252 <citations>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
253 <citation type="bibtex">@Manual{,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
254 title = {R: A Language and Environment for Statistical Computing},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
255 author = {{R Core Team}},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
256 organization = {R Foundation for Statistical Computing},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
257 address = {Vienna, Austria},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
258 year = {2016},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
259 url = {https://www.R-project.org/},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
260 }</citation>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
261 <citation type="bibtex">@Article{Thevenot2015,
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
262 Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
263 Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
264 Journal = {Journal of Proteome Research},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
265 Year = {2015},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
266 Note = {PMID: 26088811},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
267 Number = {8},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
268 Pages = {3322-3335},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
269 Volume = {14},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
270
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
271 Doi = {10.1021/acs.jproteome.5b00354},
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
272 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
273 }</citation>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
274 <citation type="doi">10.1093/bioinformatics/btu813</citation>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
275 </citations>
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
276
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
277
09799fc16bc6 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
ethevenot
parents: 1
diff changeset
278
0
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
279 Input files
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
280 ===========
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
281
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
282 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
283 | **1) copy/paste the values below in three distinct .txt files**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
284 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
285 | **a) File Format: 'tabular'**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
286 | **b) Convert spaces to tabs: 'Yes'**
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
287 |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
288
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
289 **dataMatrix file**::
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
290
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
291 dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
292 HMDB01032 2569204.92420381 6222035.77434915 17070707.9912636 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 4970265.57952158 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
293 HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 3260583.81592376 8932005.5351622 8340827.52597275 9256460.69197759 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
294 HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 6030501.02648005 474901.604069803 2885792.42617652 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
295
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
296
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
297 **sampleMetadata file**::
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
298
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
299 sampleMetadata age ageGrp
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
300 HU_017 41 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
301 HU_021 34 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
302 HU_027 37 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
303 HU_032 38 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
304 HU_041 28 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
305 HU_048 39 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
306 HU_049 50 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
307 HU_050 30 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
308 HU_052 51 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
309 HU_059 81 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
310 HU_060 55 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
311 HU_066 25 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
312 HU_072 47 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
313 HU_077 27 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
314 HU_090 46 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
315 HU_109 32 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
316 HU_110 50 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
317 HU_125 58 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
318 HU_126 45 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
319 HU_131 42 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
320 HU_134 48 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
321 HU_149 35 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
322 HU_150 49 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
323 HU_173 55 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
324 HU_179 33 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
325 HU_180 53 senior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
326 HU_182 43 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
327 HU_202 42 experienced
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
328 HU_204 31 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
329 HU_209 17.5 junior
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
330
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
331
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
332 **variableMetadata file**::
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
333
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
334 variableMetadata name
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
335 HMDB01032 Dehydroepiandrosterone sulfate
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
336 HMDB03072 Quinic acid
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
337 HMDB00792 Sebacic acid
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
338
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
339
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
340 Parameters
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
341 ==========
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
342
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
343 **Factor of interest:** "ageGroup"
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
344
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
345 **Test:** "Kruskal-Wallis rank test (qualitative, > 2 levels)"
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
346
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
347 **Method for multiple testing correction:** "fdr"
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
348
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
349 **(Corrected) p-value significance threshold:** 0.05
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
350
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
351
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
352 Output files
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
353 ============
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
354
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
355 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
356 | File | Format |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
357 +==============================+============+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
358 | 1) dataMatrix | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
359 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
360 | 2) sampleMetadata | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
361 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
362 | 3) variableMetadata | tabular |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
363 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
364 | 4) information | text |
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
365 +------------------------------+------------+
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
366
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
367
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
368 ---------------------------------------------------
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
369
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
370
ef64d3752050 planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit ca0e312e1c986c45310f37effe031f60009fbcab
ethevenot
parents:
diff changeset
371 </tool>