--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatter_plot_3D.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,182 @@
+<tool id="secimtools_scatter_plot_3D" name="Scatter Plot 3D" 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_3D.py
+--input $input
+--ID $uniqID
+
+--X $x
+--Y $y
+--Z $z
+--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
+
+#if $rotation
+    --rotation $rotation
+#end if
+
+#if $elevation
+    --elevation $elevation
+#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 with unique sample identifiers (sampleID). If coloring by group, sampleIDs must match sampleIDs in the Design File."/>
+        <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in long format dataset for X values."/>
+        <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in long format dataset for Y values."/>
+        <param name="z" type="text" size="30" value="" label="Z Group Title" help="Name of the column in long format dataset for Z values."/>
+        <param name="rotation" type="text" size="30" value="" label="Azimuth (Rotation) Angle for Viewing [Optional]" help="The azimuth (rotation) angle for viewing in degrees. Default = 45 degrees. The ideal azimuth (rotation) angle may be a process of trial and error."/>
+        <param name="elevation" type="text" size="30" value="" label="Elevation Angle for Viewing [Optional]" help="The elevation angle for viewing in degrees. Default = 45 degrees. The ideal elevation angle may be a process of trial and error."/>
+        <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="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 that will be used for coloring."/>
+        <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options include diverging, qualitative, sequential, cubehelix, 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. The default color scheme for palette tableau = Tableau_20. User must specify 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" />
+            <param name="z"       value="PC3" />
+            <output name="figure" file="ST000006_scatter_plot_3D_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="z"         value="PC3" />
+            <param name="rotation"  value="30" />
+            <param name="elevation" value="23" />
+            <param name="palette"   value="sequential" />
+            <param name="color"     value="Blues_3" />
+            <output name="figure"   file="ST000006_scatter_plot_3D_palette_color_figure.pdf" compare="sim_size" delta="10000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+
+**Tool Description**
+
+The tool provides a 3D 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/
+
+
+**NOTE:** The user should ensure that the Long Format and Design File datasets have no missing values.
+
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+@LONG@
+
+
+**Sample ID**
+
+    - Name of the column in your Long Dataset that has the unique sample IDs. If coloring by group is desired based on the Design File sample IDs have to be saved in a column with the name sampleID to match the name in the Design File
+
+
+**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.
+
+**Z Group Title**
+
+    - Name of the column in the Long Format dataset for Z values.
+
+**Azimuth (Rotation) Angle for Viewing [Optional]:**
+
+    - The azimuth (rotation) angle for viewing in degrees. The default value = 45 degrees. The ideal azimuth (rotation) angle for viewing may involve trial and error.
+
+**Elevation Angle for Viewing [Optional]:**
+
+    - The elevation angle for viewing in degrees. The default value = 45 degrees. The ideal elevation angle for viewing may involve trial and error.
+
+@DF@
+
+**Group/Treatment [Optional]**
+
+    - Name of the column in your Design File that contains group classification for coloring.
+
+**Palette [Optional]**
+
+    - Choice of the palette. Default = tableau. The other options include:  diverging, qualitative, sequential, cubehelix, tableau, and wesanderson.
+
+**Color Scheme [Optional]**
+
+    - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. User has to specify Color Scheme if the Palette field has been filled.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool produces a PDF file containing a 3D scatter plot.
+The coloring of the features by group and the corresponding legend will be included in the plot if the user provides the Design File and Palette.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>