diff seaborn_pairgrid.xml @ 0:4a46d83cb08f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn commit 24dc6373560bd5e409fca84154634f5a528001c3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seaborn_pairgrid.xml	Wed May 14 08:39:22 2025 +0000
@@ -0,0 +1,117 @@
+<tool id="seaborn_pairgrid" name="seaborn pair-wise scatterplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
+    <description>of all-vs-all column combinations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="edam"/>
+    <expand macro="requirements"/>
+    <expand macro="creator" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '${run_script}'
+    ]]></command>
+
+    <configfiles>
+        <configfile name="run_script"><![CDATA[
+index_col = $index_col
+
+@INIT@
+
+from scipy.stats import gaussian_kde
+
+def scatter_density(x, y, **kwargs):
+    kwargs.pop('color')
+    # Calculate the point density
+    xy = np.vstack([x, y])
+    z = gaussian_kde(xy)(xy)
+    plt.scatter(x, y, c=z, cmap="jet", **kwargs)
+
+
+g = sns.PairGrid(data)
+g.map_lower(sns.regplot, scatter_kws=dict(s=4))
+g.map_lower(sns.kdeplot, levels=4, color=".2")
+g.map_upper(scatter_density, s=6)
+g.map_diag(sns.histplot)
+
+plt.savefig(f"{output_file}", format=output_format, dpi=300)
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="inputs"/>
+        <param argument="index_col" type="boolean" truevalue="0" falsevalue="None" checked="false" label="Is the first column the index?" help="Specify whether the first column of the input data should be treated as the index. If selected, the first column will not be used as data for plotting." />
+        <expand macro="transformation"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="png" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- Test 1: Generate a pairgrid plot with default settings -->
+        <test>
+            <param name="input_data" value="mtcars.txt" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_image_channels channels="4"/>
+                    <has_image_height height="8250"/>
+                    <has_image_width width="8250" />
+                    <has_image_center_of_mass center_of_mass="4143.08, 4103.67" eps="0.1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool generates a scatterplot matrix (pair-wise scatterplots) of all column combinations in the input dataset using the Seaborn library. The scatterplot matrix provides a visual summary of the relationships between variables in the dataset, making it useful for exploratory data analysis.
+The tool uses Seaborn's `PairGrid` functionality to create the matrix, with the following features:
+
+- **Lower Triangle**: Regression plots and kernel density estimates (KDE).
+- **Upper Triangle**: Scatterplots with point density coloring.
+- **Diagonal**: Histograms of individual variables.
+
+**Usage**
+
+1. **Input**: Provide a tabular data file in one of the supported formats (TSV, CSV, TXT, or Parquet). Optionally, specify whether the first column should be treated as the index.
+2. **Advanced Options**: Apply transformations to the data (e.g., log10 or log2) before plotting.
+3. **Output**: The tool generates a PNG image of the scatterplot matrix, which can be downloaded or used in further analyses.
+
+**Input**
+
+- **Input Data Table**: Upload your data file in TSV, CSV, TXT, or Parquet format. The file should contain numerical data for plotting.
+- **Index Column**: Specify whether the first column of the input data should be treated as the index. If selected, the first column will not be used for plotting.
+- **Data Transformation**: Apply transformations such as log10 or log2 to numerical data before plotting.
+
+**Output**
+
+The tool generates a PNG file containing the scatterplot matrix. The file can be downloaded or used as input for other tools in Galaxy.
+
+**Example Input**
+
+Here is an example of a simple input dataset:
+
++------------+------------+------------+------------+
+| Category   | Value1     | Value2     | Value3     |
++============+============+============+============+
+| A          | 10         | 20         | 30         |
++------------+------------+------------+------------+
+| B          | 15         | 25         | 35         |
++------------+------------+------------+------------+
+| C          | 20         | 30         | 40         |
++------------+------------+------------+------------+
+
+**Example Output**
+
+The tool will generate a scatterplot matrix where:
+- The lower triangle contains regression plots and KDE plots.
+- The upper triangle contains scatterplots with point density coloring.
+- The diagonal contains histograms of individual variables.
+
+**Links**
+
+- For more information about Seaborn's `PairGrid`, visit the official documentation: https://seaborn.pydata.org/generated/seaborn.PairGrid.html
+- For detailed parameter descriptions, refer to the Galaxy tool documentation.
+    ]]></help>
+    <expand macro="citation"/>
+</tool>