diff maplot.xml @ 0:e9212adafd7a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d5065f0bdf2d38c2344d96d68537223c1096daab

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maplot.xml	Thu May 15 12:55:13 2025 +0000
@@ -0,0 +1,142 @@
+<tool id="maplot" name="MA plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description>Generate MA plots for visualizing data distributions.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_0092</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0337</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="6.0.0">plotly</requirement>
+        <requirement type="package" version="1.13.1">scipy</requirement>
+        <requirement type="package" version="2.2.3">pandas</requirement>
+        <requirement type="package" version="0.14.4">statsmodels</requirement>
+        <requirement type="package" version="3.9.4">matplotlib-base</requirement>
+        <requirement type="package" version="0.2.1">python-kaleido</requirement>
+    </requirements>
+    <creator>
+        <person
+            givenName="Helge"
+            familyName="Hecht"
+            url="https://github.com/hechth"
+            identifier="0000-0001-6744-996X" />
+        <organization
+            url="https://www.recetox.muni.cz/"
+            email="[e-mail]"
+            name="RECETOX MUNI" />
+    </creator>
+    <command detect_errors="exit_code"><![CDATA[
+    python3 '$__tool_directory__/maplot.py'
+        --file_path '$file_path'
+        --file_extension '$file_path.ext'
+        --frac $frac
+        --it $it
+        --num_bins $num_bins
+        --window_width $window_width
+        --size $size
+        --scale $scale
+        --y_scale_factor $y_scale_factor
+        --max_num_cols $max_num_cols
+        #if $backend_conditional.backend == "plotly"
+        --interactive
+        #end if
+        --output_format '$output_format'
+        --output_file '$output_file'
+    ]]></command>
+
+    <inputs>
+        <param argument="--file_path" type="data" label="Input File" format="csv,tsv,tabular,parquet" help="The input file containing the data to be visualized." />
+        <param argument="--frac" type="float" value="0.8" label="LOESS Smoothing Fraction" help="The fraction of data points used for LOESS smoothing. This controls the degree of smoothing applied to the data." />
+        <param argument="--it" type="integer" value="5" label="Number of Iterations" help="The number of iterations for LOESS smoothing. Increasing this value may improve accuracy but will also increase computation time." />
+        <param argument="--num_bins" type="integer" value="100" label="Number of Bins" help="The number of bins to use for the histogram. This determines the granularity of the histogram visualization." />
+        <param argument="--window_width" type="integer" value="5" label="Window Width" help="The width of the moving average window. This affects how the data is smoothed over a range of values." />
+        <param argument="--size" type="integer" value="500" label="Plot Size" help="The size of the plot in pixels. Larger values produce higher-resolution plots." />
+        <param argument="--scale" type="integer" value="3" label="Scale Factor" help="The scale factor for the plot. This controls the resolution of the output plot." />
+        <param argument="--y_scale_factor" type="float" value="1.1" label="Y-Axis Scale Factor" help="A factor to scale the Y-axis. This can be used to adjust the vertical range of the plot." />
+        <param argument="--max_num_cols" type="integer" value="100" label="Maximum Number of Columns" help="The maximum number of columns to display in the plot. This limits the number of subplots in the visualization." />
+
+        <conditional name="backend_conditional">
+            <param name="backend" type="select" label="Backend for Plotting" help="Choose the backend for generating the plot. Plotly supports interactive plots, while Matplotlib generates static plots.">
+                <option value="plotly" selected="true">Plotly</option>
+                <option value="matplotlib">Matplotlib</option>
+            </param>
+            <when value="plotly">
+                <param argument="--output_format" type="select" label="Output Format" help="The output format for the plot when using Plotly. Options include PDF, PNG, and HTML.">
+                    <option value="pdf" selected="true">PDF</option>
+                    <option value="png">PNG</option>
+                    <option value="html">HTML</option>
+                </param>
+            </when>
+            <when value="matplotlib">
+                <param argument="--output_format" type="select" label="Output Format" help="The output format for the plot when using Matplotlib. Options include PDF and PNG.">
+                    <option value="pdf" selected="true">PDF</option>
+                    <option value="png">PNG</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="pdf" label="MA plot with ${backend_conditional.backend} on ${on_string}">
+            <change_format>
+                <when input="output_format" value="png" format="png" />
+                <when input="output_format" value="html" format="html" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="file_path" value="ma_plot_testdata_4.csv" />
+            <conditional name="backend_conditional">
+                <param name="backend" value="plotly" />
+                <param name="output_format" value="pdf" />
+            </conditional>
+            <output name="output_file" file="output_plotly.pdf" />
+        </test>
+    
+        <!-- Test case for Matplotlib backend with default parameters -->
+        <test>
+            <param name="file_path" value="ma_plot_testdata_4.csv" />
+            <conditional name="backend_conditional">
+                <param name="backend" value="matplotlib" />
+                <param name="output_format" value="pdf" />
+            </conditional>
+            <output name="output_file" file="output_matplotlib.pdf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool generates MA plots for visualizing data distributions. It supports two backends for plotting: Plotly and Matplotlib. Users can customize various parameters such as smoothing, binning, and scaling to tailor the visualization to their needs.
+
+**Input**
+
+- **Input File**: A CSV, TSV, tabular, or Parquet file containing the data to be visualized.
+
+**Parameters**
+
+- **LOESS Smoothing Fraction**: Fraction of data points used for LOESS smoothing.
+- **Number of Iterations**: Number of iterations for LOESS smoothing.
+- **Number of Bins**: Number of bins for the histogram.
+- **Window Width**: Width of the moving average window.
+- **Plot Size**: Size of the plot in pixels.
+- **Scale Factor**: Scale factor for the plot resolution.
+- **Y-Axis Scale Factor**: Factor to scale the Y-axis.
+- **Maximum Number of Columns**: Maximum number of columns to display in the plot.
+- **Backend for Plotting**: Choose between Plotly and Matplotlib.
+- **Output Format**: Format of the output plot (PDF, PNG, or HTML).
+
+**Output**
+
+The tool generates a plot in the specified format (PDF, PNG, or HTML).
+    ]]></help>
+    <citations>
+        <citation type="doi">10.2307/2987937</citation>
+        <citation type="doi">10.1016/S0140-6736(86)90837-8</citation>
+    </citations>
+</tool>
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