comparison abims_anova.xml @ 8:a2b19a78306a draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/anova commit 493595bdd63ff88e7b93f22d8a092a70d4f39a05

7:8190dfb5a351

<tool id="abims_anova" name="Anova" version="1.2.0">

    <description>N-way anova. With ou Without interactions</description>

    <requirements>
	<requirement type="package" version="1.1_4">r-batch</requirement>

outputdatapvalue '$varMetaPValue'
outputdatasignif '$dataSignif'
    </command>

    <inputs>
        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
        <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
        <param name="varinfo" type="data" label="Variable Metadata file" format="tabular" help="Tabular file with information about your tested variables. Only used to aggregate generated information." />

        <param name="mode" type="select" help="Perform the anova tests on column/row; for W4M 3-tables format, use 'row'." format="text" optional="true">
            <label>Mode</label>

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Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.



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Input files
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8:a2b19a78306a

<tool id="abims_anova" name="Anova" version="1.2.1">

    <description>N-way anova. With ou Without interactions</description>

    <requirements>
	<requirement type="package" version="1.1_4">r-batch</requirement>

outputdatapvalue '$varMetaPValue'
outputdatasignif '$dataSignif'
    </command>

    <inputs>
        <param name="input" type="data" label="Data Matrix file" format="tabular,csv" help="Matrix of numeric data with headers." />
        <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
        <param name="varinfo" type="data" label="Variable Metadata file" format="tabular" help="Tabular file with information about your tested variables. Only used to aggregate generated information." />

        <param name="mode" type="select" help="Perform the anova tests on column/row; for W4M 3-tables format, use 'row'." format="text" optional="true">
            <label>Mode</label>

-----------

Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.

**Note about sum of squares (SS) calculation of N-way ANOVA in this module.**
This module use R function *manova()* (and thus R function *aov()*) to establish N-way ANOVA. 
Therefore calculated sum of squares are sequential ones (sometimes called "Type I SS"). 
If your design is unbalanced, this may not correspond to the type of hypothesis being of interest. 
Note that you can obtain adjusted sums of squares ("Type II SS") by running several times this module with different orders in factors. 


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Input files
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