Mercurial > repos > workflow4metabolomics > mixmodel4repeated_measures

annotate mixmodel.xml @ 0:a4d89d47646f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
author workflow4metabolomics
date Mon, 16 May 2022 09:25:01 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
1 <tool id="mixmodel4repeated_measures" name="mixmodel" version="3.1.0" profile="19.01">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
2 <description>ANOVA for repeated measures statistics</description>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
3
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
4 <requirements>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
5 <requirement type="package" version="1.1_27">r-lme4</requirement>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
6 <requirement type="package" version="3.1_3">r-lmertest</requirement>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
7 <requirement type="package" version="3.2_0">r-ggplot2</requirement>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
8 <requirement type="package" version="2.3">r-gridExtra</requirement>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
9 <requirement type="package" version="2.40.0">bioconductor-multtest</requirement>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
10 </requirements>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
11
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
13 Rscript '$__tool_directory__/mixmodel_wrapper.R'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
14
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
15 dataMatrix_in '$dataMatrix_in'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
16 sampleMetadata_in '$sampleMetadata_in'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
17 variableMetadata_in '$variableMetadata_in'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
18
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
19 fixfact '$fixfact'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
20 time '$time'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
21 subject '$subject'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
22 adjC '$adjC'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
23 trf '$trf'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
24 thrN '$thrN'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
25 diaR '$diaR'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
26 dff '$dff'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
27 rounding '${roundchoice.rounding}'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
28 #if $roundchoice.rounding == 'yes' :
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
29 decplaces '${roundchoice.decplaces}'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
30 #end if
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
31
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
32 variableMetadata_out '$variableMetadata_out'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
33 out_graph_pdf '$out_graph_pdf'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
34 out_estim_pdf '$out_estim_pdf'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
35 information '$information'
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
36
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
37 ]]></command>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
38
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
39 <inputs>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
40 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
41 <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" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
42 <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" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
43 <param name="fixfact" label="Fixed Factor of interest" type="text" help="Name of sample metadata column corresponding to the fixed factor (use none if only time factor"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
44 <param name="time" label="Repeated factor (time)" type="text" help="Name of the column of the sample metadata table corresponding to the repeated factor"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
45 <param name="subject" label="Subject factor" type="text" help="Name of the column of the sample metadata table corresponding to the subject factor"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
46 <param name="dff" label="Degrees of freedom method for the F-tests" type="select" help="">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
47 <option value="Satt">Satterthwaite</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
48 <option value="KenR">Kenward-Roger</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
49 </param>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
50 <param name="adjC" label="Method for multiple testing correction" type="select" help="">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
51 <option value="fdr">fdr</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
52 <option value="BH">BH</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
53 <option value="bonferroni">bonferroni</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
54 <option value="BY">BY</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
55 <option value="hochberg">hochberg</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
56 <option value="holm">holm</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
57 <option value="hommel">hommel</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
58 <option value="none">none</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
59 </param>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
60 <param name="trf" label="Log transform of raw data" type="select" help="Transformation of raw data">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
61 <option value="none">none</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
62 <option value="log10">log10</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
63 <option value="log2">log2</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
64 </param>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
65 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
66 <param name="diaR" label="Perform diagnostic of the residuals" type="select" help=" Used to assess the quality of models considering distribution of residuals ">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
67 <option value="yes">yes</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
68 <option value="no">no</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
69 </param>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
70 <conditional name="roundchoice">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
71 <param name="rounding" type="select" label="Rounding the result's numerical columns" help="Should the numerical values generated by this tool be rounded to a chosen number of decimal places?">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
72 <option value="no">No</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
73 <option value="yes">Yes</option>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
74 </param>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
75 <when value="yes">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
76 <param argument="decplaces" type="integer" value="6" label="Number of decimal places for rounding" help="Positive interger" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
77 </when>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
78 <when value="no">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
79 </when>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
80 </conditional>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
81 </inputs>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
82
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
83 <outputs>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
84 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
85 <data name="information" label="${tool.name}_information.txt" format="txt"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
86 <data name="out_estim_pdf" label="${tool.name}_Estimates" format="pdf"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
87 <data name="out_graph_pdf" label="${tool.name}_diagResiduals" format="pdf">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
88 <filter>diaR == 'yes'</filter>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
89 </data>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
90 </outputs>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
91
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
92 <tests>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
93 <test expect_num_outputs="4">
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
94 <param name="dataMatrix_in" value="TwoFactor_dataMatrix.txt" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
95 <param name="sampleMetadata_in" value="TwoFactor_sampleMetadata.txt" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
96 <param name="variableMetadata_in" value="TwoFactor_variableMetadata.txt" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
97 <param name="fixfact" value="phenotype" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
98 <param name="time" value="time" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
99 <param name="subject" value="sujet" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
100 <param name="adjC" value = "none"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
101 <param name="trf" value = "log10"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
102 <param name="thrN" value = "0.01"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
103 <param name="dff" value = "Satt"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
104 <param name="rounding" value = "yes"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
105 <param name="decplaces" value = "6"/>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
106 <output name="variableMetadata_out" value="mixmodel_TwoFactor_variableMetadata.txt" />
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
107 </test>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
108 </tests>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
109
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
110 <help><![CDATA[
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
111 .. class:: infomark
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
112
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
113 **Tool update: See the 'NEWS' section at the bottom of the page**
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
114
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
115 .. class:: infomark
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
116
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
117 **Authors** Natacha Lenuzza and Jean-Francois Martin wrote this wrapper of R repeated measure anova statistical tests.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
118 **Maintainers** Melanie Petera and Marie Tremblay-Franco (INRAE-MetaboHUB)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
119
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
120 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr/home.html)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
121
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
122 .. class:: infomark
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
123
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
124 **Please cite**
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
125
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
126 R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
127
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
128 .. class:: infomark
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
129
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
130 **References**
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
131 Kuznetsova A. Brockhoff PB. and Christensen RHB (2017). lmerTest Package: Tests in Linear Mixed Effects Models. Journal of Statistical Software, 82(13), pp. 1–26. doi: 10.18637/jss.v082.i13.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
132 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.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
133
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
134
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
135 =============
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
136 Mixed models
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
137 =============
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
138
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
139 -----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
140 Description
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
141 -----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
142
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
143 The module performs analysis of variance for repeated measures using mixed model
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
144
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
145
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
146 -----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
147 Input files
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
148 -----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
149
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
150 +---------------------------+------------+
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
151 | File | Format |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
152 +===========================+============+
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
153 | 1 : Data matrix | tabular |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
154 +---------------------------+------------+
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
155 | 2 : Sample metadatx | tabular |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
156 +---------------------------+------------+
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
157 | 3 : Variable metadata | tabular |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
158 +---------------------------+------------+
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
159
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
160
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
161 ----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
162 Parameters
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
163 ----------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
164
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
165 Data matrix file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
166 | 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)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
167 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
168
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
169 Sample metadata file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
170 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
171 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
172
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
173 Variable metadata file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
174 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
175 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
176
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
177
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
178 Treatment
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
179 | Name of the fixed factor in the sample metadata file. Use "none" if you have only a time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
180 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
181
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
182 Time
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
183 | Name of the repeated (time) factor in the sample metadata file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
184 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
185
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
186 Subject
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
187 | Name of the subject (on which the repeated measurement id done) in the sample metadata file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
188 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
189
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
190 Degrees of freedom
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
191 | Method to use for degrees of freedom computation
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
192 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
193
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
194 Method for multiple testing correction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
195 | The 7 methods implemented in the 'p.adjust' R function are available and documented as follows:
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
196 | "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."
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
197
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
198
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
199 (Corrected) p-value significance threshold
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
200 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
201 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
202
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
203 Rounding the result's numerical columns
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
204 | This parameter enables the choice of a given number of decimal places to be used to display results' values in the output columns of the variableMetadata that are generated by the tool.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
205 | If set to "Yes", you can indicate the number of decimal places wanted, and all the results' values will be rounded according to this number.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
206 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
207
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
208 ------------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
209 Output files
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
210 ------------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
211
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
212 variableMetadata_out.tabular
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
213 | **variableMetadata** file identical to the file given as argument plus
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
214 | pvalue of Shapiro normality test of the residuals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
215 | pvalues of the main effects and interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
216 | PostHoc test with difference between levels and pvalues of these difference
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
217 |
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
218
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
219 mixedmodel_Estimates
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
220 | A pdf file is created with a graphical representation of differences among levels of factors with a color code for significance and an error bar.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
221 | Plots are only provided for features with at least one significant factor.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
222
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
223
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
224 mixedmodel_diagResiduals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
225 | if Perform diagnostic of the residuals" is set to yes(default) a pdf file is created with a a serie of
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
226 | graphics outputed in order to assess the distribution of residuals to check the adjustment.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
227 | Plots are only provided for features with at least one factor being significant based on the non-corrected p-values.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
228
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
229 information.txt
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
230 | File with all messages and warnings generated during the computation
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
231 | The list of variables with name and a tag if it is significant for at least fixed or repeated factor.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
232
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
233
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
234
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
235 ---------------------------------------------------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
236
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
237 Changelog/News
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
238 --------------
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
239
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
240 **Version 3.1.0 - April 2022**
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
241
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
242 - NEW FEATURE: the tool now can be used without fixed factor by specify "none" in the concerned parameter field.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
243
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
244 - NEW FEATURE: addition of the possibility to choose the degrees of freedom computation method (previously using only the Satterthwaite method).
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
245
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
246 - NEW FEATURE: addition of the possibility to choose the number of decimal places in the variable-metadata numerical columns' output.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
247
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
248
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
249 ]]></help>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
250
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
251 <citations>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
252 <citation type="doi">10.18637/jss.v082.i13.</citation>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
253 <citation type="bibtex">@ARTICLE{fisher,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
254 author = {Benjamini Y. and Hochberg Y.,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
255 title = {Controlling the false discovery rate: a practical and powerful approach for multiple testing. Journal of the Royal Statistical Society},
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
256 journal = {Series B (Methodological)},
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
257 year = {1995},
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
258 volume = {57},
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
259 pages = {289-300}
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
260 }</citation>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
261 <citation type="doi">10.1093/bioinformatics/btu813</citation>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
262 </citations>
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
263
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8
workflow4metabolomics
parents:
diff changeset
264 </tool>