merge Release dev to main

galaxy_tools/README.md

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+# SPAC Galaxy Tools
+
+   ## Requirements
+   - Galaxy instance with Docker enabled
+   - Docker image: nciccbr/spac:v1
+
+   ## Installation
+   1. Pull Docker image: `docker pull nciccbr/spac:v1`
+   2. Copy tool directory to Galaxy's tools folder
+   3. Add to tool_conf.xml:
+```xml
+      <tool file="spac_boxplot/spac_boxplot.xml"/>

galaxy_tools/refactor_tools/run_spac_template.sh

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+#!/usr/bin/env bash
+# run_spac_template.sh - Universal wrapper for SPAC Galaxy tools
+set -eu
+
+PARAMS_JSON="${1:?Missing params.json path}"
+TEMPLATE_NAME="${2:?Missing template name}"
+
+# Get the directory where this script is located (the tool directory)
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+# Look for spac_galaxy_runner.py in multiple locations
+if [ -f "$SCRIPT_DIR/spac_galaxy_runner.py" ]; then
+    # If it's in the same directory as this script
+    RUNNER_PATH="$SCRIPT_DIR/spac_galaxy_runner.py"
+elif [ -f "$__tool_directory__/spac_galaxy_runner.py" ]; then
+    # If Galaxy provides tool directory
+    RUNNER_PATH="$__tool_directory__/spac_galaxy_runner.py"
+else
+    # Fallback to trying the module approach
+    echo "Warning: spac_galaxy_runner.py not found locally, trying as module" >&2
+    python3 -m spac_galaxy_runner "$PARAMS_JSON" "$TEMPLATE_NAME"
+    exit $?
+fi
+
+# Run the runner script directly
+echo "Running: python3 $RUNNER_PATH $PARAMS_JSON $TEMPLATE_NAME" >&2
+python3 "$RUNNER_PATH" "$PARAMS_JSON" "$TEMPLATE_NAME"

galaxy_tools/refactor_tools/spac_arcsinh_normalization.xml

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+<tool id="spac_arcsinh_normalization" name="Arcsinh Normalization [SPAC] [DMAP]" version="1.0.0" profile="24.2">
+    <description>Normalize features either by a user-defined co-factor or a determined percentile, allowing for ef...</description>
+
+    <requirements>
+        <container type="docker">nciccbr/spac:v1</container>
+    </requirements>
+
+    <environment_variables>
+        <variable name="SPAC_PYTHON">python3</variable>
+    </environment_variables>
+
+        <command detect_errors="exit_code"><![CDATA[
+            set -eu &&
+            export GALAXY_OUTPUTS_SPEC='{"analysis": "transform_output.pickle"}' &&
+
+            ## Debug: Show params.json
+            echo "=== params.json ===" >&2 &&
+            cat "$params_json" >&2 &&
+            echo "==================" >&2 &&
+
+            ## Save snapshot
+            cp "$params_json" params_snapshot.json &&
+
+            ## Run wrapper
+            bash $__tool_directory__/run_spac_template.sh "$params_json" "arcsinh_normalization"
+        ]]></command>
+
+    <configfiles>
+        <inputs name="params_json" filename="params.json" data_style="paths"/>
+    </configfiles>
+
+    <inputs>
+        <param name="Upstream_Analysis" type="data" format="h5ad,binary" label="Upstream Analysis" help="Link to prior processed dataset in the analysis."/>
+        <param name="Table_to_Process" type="text" value="Original"  label="Table to Process" help="Source table to perform the computation. Original refers to the raw dataset."/>
+        <param name="Co_Factor" type="text" value="5.0"  label="Co-Factor" help="A fixed positive number to use as a co-factor for the transformation. If provided, it takes precedence over the percentile argument. If &quot;None&quot;, the Percentile method will be used. Default is &quot;5.0&quot;."/>
+        <param name="Percentile" type="text" value="None"  label="Percentile" help="The percentile to determine the co-factor if the co-factor is not provided. The percentile is computed for each feature (column) individually. Default is &quot;None&quot;."/>
+        <param name="Output_Table_Name" type="text" value="arcsinh"  label="Output Table Name" help="Name of the table to be added to the analysis."/>
+        <param name="Per_Batch" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Per Batch" help="Whether to apply the transformation per batch. If &quot;True&quot;, the transformation is applied per batch."/>
+        <param name="Annotation" type="text" value="None"  label="Annotation" help="The name of the annotation to define batches. Required if Per Batch is &quot;True&quot;."/>
+    </inputs>
+
+    <outputs>
+        <data name="analysis" format="binary" from_work_dir="transform_output.pickle" label="${tool.name} on ${on_string}: Analysis"/>
+        <data name="params_snapshot" format="json" from_work_dir="params_snapshot.json" label="${tool.name} on ${on_string}: Params Snapshot"/>
+        <data name="config_used" format="json" from_work_dir="config_used.json" label="${tool.name} on ${on_string}: Config Used"/>
+        <data name="execution_log" format="txt" from_work_dir="tool_stdout.txt" label="${tool.name} on ${on_string}: Execution Log"/>
+    </outputs>
+
+    <help><![CDATA[
+        **Arcsinh Normalization [SPAC] [DMAP]**
+
+Normalize features either by a user-defined co-factor or a determined percentile, allowing for effective normalization of high-range values in single-cell datasets. This transformation can also be applied per batch if specified.
+[GitHub Documentation](https://fnlcr-dmap.github.io/SCSAWorkflow/spac.html#spac.transformations.arcsinh_transformation) for further information.
+
+This tool is part of the SPAC (SPAtial single-Cell analysis) toolkit.
+
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">
+@misc{spac_toolkit,
+    author = {FNLCR DMAP Team},
+    title = {SPAC: SPAtial single-Cell analysis},
+    year = {2024},
+    url = {https://github.com/FNLCR-DMAP/SCSAWorkflow}
+}
+        </citation>
+    </citations>
+</tool>

galaxy_tools/refactor_tools/spac_boxplot.xml

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+<tool id="spac_boxplot" name="Boxplot [SPAC] [DMAP]" version="1.0.0" profile="24.2">
+    <description>Create a boxplot visualization of the features in the analysis dataset.</description>
+
+    <requirements>
+        <container type="docker">nciccbr/spac:v1</container>
+    </requirements>
+
+    <environment_variables>
+        <variable name="SPAC_PYTHON">python3</variable>
+    </environment_variables>
+
+        <command detect_errors="exit_code"><![CDATA[
+            set -eu &&
+            export GALAXY_OUTPUTS_SPEC='{"DataFrames": "dataframe_folder", "figures": "figure_folder"}' &&
+
+            ## Debug: Show params.json
+            echo "=== params.json ===" >&2 &&
+            cat "$params_json" >&2 &&
+            echo "==================" >&2 &&
+
+            ## Save snapshot
+            cp "$params_json" params_snapshot.json &&
+
+            ## Run wrapper
+            bash $__tool_directory__/run_spac_template.sh "$params_json" "boxplot"
+        ]]></command>
+
+    <configfiles>
+        <inputs name="params_json" filename="params.json" data_style="paths"/>
+    </configfiles>
+
+    <inputs>
+        <param name="Upstream_Analysis" type="data" format="h5ad,binary" label="Upstream Analysis" help="Link to prior processed dataset in the analysis."/>
+        <param name="Table_to_Visualize" type="text" value="Original"  label="Table to Visualize" help="Source table to perform the visualization. Default is Original, referring to the raw dataset."/>
+        <param name="Feature_s_to_Plot" type="text" area="true" value="All"  label="Feature(s) to Plot" help="The feature(s) to plot in the box plot. Default &quot;All&quot; will plot all features. (Enter as comma-separated list or one per line)"/>
+        <param name="Primary_Annotation" type="text" value="None"  label="Primary Annotation" help="The annotation to group the visualizations. Use &quot;None&quot; to disable."/>
+        <param name="Secondary_Annotation" type="text" value="None"  label="Secondary Annotation" help="Secondary annotation to create subdivisions within each category defined by the primary annotation, offering a deeper level of analysis, such as comparing time points within each treatment condition. Default is &quot;None&quot;."/>
+        <param name="Value_Axis_Log_Scale" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Value Axis Log Scale" help="Make the Y-axis (or X-axis if the plot is horizontal) in log scale. Negative values in the data disable the log scale."/>
+        <param name="Figure_Title" type="text" value="BoxPlot"  label="Figure Title" help="Title of the figure"/>
+        <param name="Horizontal_Plot" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Horizontal Plot" help="To plot the boxplot in horizontal orientation. Default is vertical."/>
+        <param name="Figure_Width" type="float" value="12"  label="Figure Width" help="Width of the figure, inch."/>
+        <param name="Figure_Height" type="float" value="8"  label="Figure Height" help="Height of the figure, inch."/>
+        <param name="Figure_DPI" type="float" value="300"  label="Figure DPI" help="Higher the DPI, clearer the image."/>
+        <param name="Font_Size" type="float" value="10"  label="Font Size" help="Figure font size."/>
+        <param name="Keep_Outliers" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep Outliers" help="True to keep the outliers for every feature, False to remove them"/>
+    </inputs>
+
+    <outputs>
+        <collection name="dataframes" type="list" label="${tool.name} on ${on_string}: DataFrames">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv" directory="dataframe_folder" format="csv"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv" directory="dataframe_folder" format="tabular"/>
+        </collection>
+        <collection name="figures" type="list" label="${tool.name} on ${on_string}: Figures">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" directory="figure_folder" format="png"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" directory="figure_folder" format="pdf"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.svg" directory="figure_folder" format="svg"/>
+        </collection>
+        <data name="params_snapshot" format="json" from_work_dir="params_snapshot.json" label="${tool.name} on ${on_string}: Params Snapshot"/>
+        <data name="config_used" format="json" from_work_dir="config_used.json" label="${tool.name} on ${on_string}: Config Used"/>
+        <data name="execution_log" format="txt" from_work_dir="tool_stdout.txt" label="${tool.name} on ${on_string}: Execution Log"/>
+    </outputs>
+
+    <help><![CDATA[
+        **Boxplot [SPAC] [DMAP]**
+
+Create a boxplot visualization of the features in the analysis dataset.
+Please refer to , [GitHub Documentation](https://fnlcr-dmap.github.io/SCSAWorkflow/spac.html#spac.visualization.boxplot)
+
+This tool is part of the SPAC (SPAtial single-Cell analysis) toolkit.
+
+**List Parameters:** Use comma-separated values or one per line.
+**Special Values:** Enter "All" to select all items.
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">
+@misc{spac_toolkit,
+    author = {FNLCR DMAP Team},
+    title = {SPAC: SPAtial single-Cell analysis},
+    year = {2024},
+    url = {https://github.com/FNLCR-DMAP/SCSAWorkflow}
+}
+        </citation>
+    </citations>
+</tool>