--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyscenic_binarize_aucell.xml	Sun Sep 15 10:13:34 2024 +0000
@@ -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>