annotate anova_fixed.xml @ 2:caba07f41453 draft default tip

"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"

<tool id="secimtools_anova_fixed" name="Analysis of Variance (ANOVA) Fixed Effects Model"  version="@WRAPPER_VERSION@">
    <description>- Perform a multi-way ANOVA with covariates and fixed effects.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
anova_fixed.py
--input $input
--design $design
--ID $uniqID
--factors "$factor"
--factorTypes $factorTypes
--out $results_table
--flags $flags_table
--fig $qq_plots
--fig2 $volcano_plots
#if $interactions
    --interactions
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note: you need a 'sampleID' column. If not-tab separated, see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature Identifier" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
        <param name="factor" type="text" size="30" value="" label="Group(s)/Treatment(s)" help="Name of the column(s) (comma separated) in your design file that you want to use for ANOVA (ie. treatment1,treatment2,weight)."/>
        <param name="factorTypes" type="text" size="30" value="" label=" Type of Group(s)/Treatment(s)" help="Type of data in your treatment columns: 'C' for Categorical and 'N' for numerical.  Match the order the groups used. (ie. C,C,N)."/>
        <param name="interactions" type="boolean" label="Calculate ANOVA with interactions" help="If 'Yes', the ANOVA program will output the interactions."/>
    </inputs>
    <outputs>
        <data format="tabular" name="results_table" label="${tool.name} on ${on_string}: Results Table"/>
        <data format="tabular" name="flags_table" label="${tool.name} on ${on_string}: Flags Table"/>
        <data format="pdf" name="qq_plots" label="${tool.name} on ${on_string}: QQ Plots"/>
        <data format="pdf" name="volcano_plots" label="${tool.name} on ${on_string}: Volcano Plots"/>
    </outputs>
    <tests>
        <test>
            <param name="input"       value="ST000006_data.tsv"/>
            <param name="design"      value="ST000006_design.tsv"/>
            <param name="uniqID"      value="Retention_Index" />
            <param name="factor"      value="White_wine_type_and_source" />
            <param name="factorTypes" value="C" />
            <output name="results_table" file="ST000006_anova_fixed_with_group_summary.tsv" />
            <output name="flags_table"   file="ST000006_anova_fixed_with_group_flags.tsv" />
            <output name="qq_plots"      file="ST000006_anova_fixed_with_group_qq_plots.pdf" compare="sim_size" delta="10000" />
            <output name="volcano_plots" file="ST000006_anova_fixed_with_group_volcano.pdf"  compare="sim_size" delta="10000" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool fits analysis of variance (ANOVA) fixed effects model with multiple grouping variables, their interactions and numerical characteristics.
The analysis is performed row wise, independently for each feature.
The user can choose whether to include interactions between grouping variables in the model or to use a pure additive model.
Numerical characteristics of the samples can be included for both scenarios.

--------------------------------------------------------------------------------

**Input**

    - Two input datasets are required.


@WIDE@

**NOTE:** The sample IDs must match the sample IDs in the Design File
(below). Extra columns will automatically be ignored.

@METADATA@

@UNIQID@

**Group(s)/Treatment(s)**

        - Name of the column(s) (comma separated) in your Design File that you want to use for ANOVA.(ie. treatment1,treatment2,weight).

**Type of Group(s)/Treatment(s)**

        - Type of data in your treatment column(s): 'C' for Categorical and 'N' for numerical. Match the order the groups are used. (ie. C,C,N).

**Calculate ANOVA with interactions**

        - If 'Yes', the ANOVA program will output interactions.

--------------------------------------------------------------------------------

**Output**

The user will get four different outputs from the fixed effects ANOVA tool:

(1) a TSV file with the results table containing the fixed effects ANOVA results for each variable, the corresponding contrast and analysis of the means.
(2) a TSV file with the flags for significant p-values.  The flags in the TSV file are equal to 1 if the difference between the groups is statistically significant using the specified α level.
(3) a PDF file with QQ (quantile-quantile) plots displaying the expected quantiles of a normal distribution on x-axis versus the observed quantiles on y-axis.
(4) and a Volcano plot with the fold change displayed on the x-axis and the -log 10 of the p-value from the test of the null hypothesis is displayed on the y-axis.  The red dashed line corresponds to p=0.01.

    ]]></help>
    <expand macro="citations"/>
</tool>