annotate scatter_plot_2D.xml @ 2:caba07f41453 draft default tip

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

<tool id="secimtools_scatter_plot_2D" name="Scatter Plot 2D" version="@WRAPPER_VERSION@">
    <description>- A standalone tool.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
scatter_plot_2D.py
--input $input
--ID $uniqID

--X $x
--Y $y
--figure $figure

#if $design
    --design $design
#end if

#if $group
    --group $group
#end if

#if $color
    --color $color
#end if

#if $palette
    --palette $palette
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Long Dataset" help="Input dataset in tab-separated long format. Please see the description of the file format below. If the file is not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="SampleID" help="Name of the column in your long dataset that has the unique sample idenifiers (sampleID)."/>
        <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in your long format dataset for X values."/>
        <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in your long format dataset for Y values."/>
        <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="group" type="text" size="30" value="" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classification to be used for coloring."/>
        <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options are diverging, qualitative, sequential, cubehelix, tableau, and  wesanderson. Please see the descriptions for the palettes below."/>
        <param name="color" type="text" size="30" label="Color Scheme [Optional]" help="Select color scheme within the palette. Default color scheme for palette tableau = Tableau_20. User must specify a color scheme if the palette field has been filled. Please see the descriptions for the color schemes below."/>
    </inputs>
    <outputs>
        <data format="pdf" name="figure" label="${tool.name} on ${on_string}: scatter plots"/>
    </outputs>
    <tests>
        <test>
            <param name="input"   value="ST000006_principal_component_analysis_score_out.tsv"/>
            <param name="design"  value="ST000006_design_group_name_underscore.tsv"/>
            <param name="uniqID"  value="sampleID" />
            <param name="group"   value="White_wine_type_and_source" />
            <param name="x"       value="PC1" />
            <param name="y"       value="PC2" />
            <output name="figure" file="ST000006_scatter_plot_2D_default_figure.pdf" compare="sim_size" delta="10000"/>
        </test>
        <test>
            <param name="input"   value="ST000006_principal_component_analysis_score_out.tsv"/>
            <param name="design"  value="ST000006_design_group_name_underscore.tsv"/>
            <param name="uniqID"  value="sampleID" />
            <param name="group"   value="White_wine_type_and_source" />
            <param name="x"       value="PC1" />
            <param name="y"       value="PC2" />
            <param name="palette" value="sequential" />
            <param name="color"   value="Blues_3" />
            <output name="figure" file="ST000006_scatter_plot_2D_palette_color_figure.pdf" compare="sim_size" delta="10000"/>
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@



**Tool Description**

The tool provides a 2D scatter plot of values in a Long Format file. Please see the description of the Long Format below.
If coloring by group is desired, the column with the sample names in the Long Format dataset has to have the name "sampleID" to match the name in the Design File.
Scatter plot 2D allows the user to plot any pair of values from the Principal Component Analysis (PCA) output or plot other data.

NOTE: The user should ensure that the input datasets have no missing values.

The user has an option to specify the palette and the color scheme within the palette.
If the palette is specified by the user, the color scheme must to be specified.
The list of available palettes are:

diverging,
qualitative,
sequential,
cubehelix,
tableau (default), and
wesanderson.

The lists of corresponding color schemes for each palattes are available via the links below:


https://jiffyclub.github.io/palettable/tableau/

https://jiffyclub.github.io/palettable/colorbrewer/diverging/

https://jiffyclub.github.io/palettable/colorbrewer/qualitative/

https://jiffyclub.github.io/palettable/colorbrewer/sequential/

https://jiffyclub.github.io/palettable/cubehelix/

https://jiffyclub.github.io/palettable/wesanderson/


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

**Input**

    - Two input datasets are required.

@LONG@


**Sample ID**

    - Name of the column in your Long Dataset that has unique sample IDs. If coloring by group, the sampleIDs must match the sampleIDs in the Design File (below).


**X Group Title**

    - Name of the column in the Long Format dataset for X values.

**Y Group Title**

    - Name of the column in the Long Format dataset for Y values.

@DF@

**Group/Treatment [Optional]**

    - Name of the column in your Design File that contains group classification to be used for coloring.


**Palette [Optional]**

    - Choice of the palette. Default =  tableau. Other options include: diverging, qualitative, sequential, cubehelix, and wesanderson.

**Color Scheme [Optional]**

    - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. The user must specify the color scheme if the Palette field has been filled.

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

**Output**

The tool produces a PDF file with the 2D scatter plot.
Coloring of the features by group and the corresponding legend will be included in the plot if the user provides a Design file and Palette.

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