Adds PySCENIC AUCell Binarize (#329)

* Binarize passing tests

* Missing test data

* Better naming, description and docs

tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.py

@@ -0,0 +1,50 @@
+import argparse
+
+import pandas as pd
+from pyscenic.binarization import binarize
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Binarize AUC matrix")
+    parser.add_argument("input_file", help="Input TSV or CSV file")
+    parser.add_argument(
+        "--threshold-overrides",
+        type=str,
+        help="Threshold overrides in JSON format",
+    )
+    parser.add_argument("--seed", type=int, default=None, help="Random seed")
+    parser.add_argument(
+        "--num-workers", type=int, default=1, help="Number of workers"
+    )
+    parser.add_argument(
+        "--output-prefix", type=str, default="output", help="Output prefix"
+    )
+
+    args = parser.parse_args()
+
+    # Read input file
+    if args.input_file.endswith(".tsv"):
+        auc_mtx = pd.read_csv(args.input_file, sep="\t", index_col=0)
+    elif args.input_file.endswith(".csv"):
+        auc_mtx = pd.read_csv(args.input_file, index_col=0)
+    else:
+        raise ValueError("Input file must be a TSV or CSV file")
+
+    auc_mtx.apply(pd.to_numeric)
+    # Parse threshold overrides
+    threshold_overrides = None
+    if args.threshold_overrides:
+        import json
+
+        threshold_overrides = json.loads(args.threshold_overrides)
+
+    # Call binarize function
+    binarized_mtx, thresholds = binarize(
+        auc_mtx, threshold_overrides, args.seed, args.num_workers
+    )
+
+    # set column name for thresholds
+    thresholds.rename("threshold", inplace=True)
+
+    # Save output files
+    binarized_mtx.to_csv(f"{args.output_prefix}/binarized_mtx.tsv", sep="\t")
+    thresholds.to_csv(f"{args.output_prefix}/thresholds.tsv", sep="\t")

tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml

@@ -0,0 +1,81 @@
+<tool id="pyscenic_binarize" name="PySCENIC Binarize AUCell" profile="21.09" version="@TOOL_VERSION@+galaxy0">
+    <description>defines AUCell thresholds and tags cells as passing it or not</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        ln -s $input_file aucell.tsv &&
+        python '$__tool_directory__/pyscenic_binarize_aucell.py'
+        #if $threshold_overrides
+            --threshold-overrides '$threshold_overrides'
+        #end if
+        #if $seed
+            --seed '$seed'
+        #end if
+        --num-workers \${GALAXY_SLOTS:-1}
+        --output-prefix ./
+        aucell.tsv
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="tabular,txt" label="Input AUC matrix"/>
+        <param name="threshold_overrides" type="text" optional="true" label="Threshold overrides in JSON format" help="Override default threshold values for binarization"/>
+        <param name="seed" type="integer" optional="true" label="Random seed"/>
+    </inputs>
+    <outputs>
+        <data name="binarized_mtx" format="tsv" label="${tool.name} on ${on_string}: Binarized AUC matrix" from_work_dir="binarized_mtx.tsv"/>
+        <data name="thresholds" format="tsv" label="${tool.name} on ${on_string}: Binarization thresholds" from_work_dir="thresholds.tsv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="aucell_test_smaller.tsv"/>
+            <param name="seed" value="10"/>
+            <output name="binarized_mtx">
+                <assert_contents>
+                    <has_text_matching expression="D124DE\t0\t1"/>
+                    <has_n_lines n="5001"/>
+                </assert_contents>
+            </output>
+            <output name="thresholds">
+                <assert_contents>
+                    <has_text text="AUCell_1"/>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+        **What it does**
+
+        This tool binarizes an AUC matrix using the `binarize` function from the `pySCENIC` package. 
+        It produces a classification of the cell per given AUCell into passing or not passing an
+        automatically defined threshold, through binarization (when possible) of the AUCell distribution.
+        See the SCENIC paper or the PySCENIC notebooks for more details.
+
+        **Input**
+
+        - Input AUC matrix (TSV): The AUC matrix to be binarized (first column expected to be cell identifiers).
+        - Threshold overrides in JSON format (optional): Override default threshold values for binarization.
+        - Random seed (optional): Seed for random number generation.
+
+        **Output**
+
+        - Binarized AUC matrix: The binarized AUC matrix.
+        - Binarization thresholds: The threshold values used for binarization.
+
+        **Example**
+
+        Input AUC matrix (tsv file, as generated by the PySCENIC AUCell or Decoupler AUCell tools):
+        ```
+                 AUCellA  AUCellB  AUCellC
+        cell1    0.024    0.045    0.001
+        cell2    0.136    0.024    0.045
+        cellN    0.001    0.347    0.136
+        ```
+        ]]>
+    </help>
+    <expand macro="citations"/>
+</tool>