# HG changeset patch
# User iuc
# Date 1740082985 0
# Node ID b0ea90bddf6684f51f08e620059a9bf32d7eb948

planemo upload for repository https://github.com/Teichlab/drug2cell commit 9c3372b3af7b42d66e740f07ab16fed3035783cc

diff -r 000000000000 -r b0ea90bddf66 drug2cell.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/drug2cell.xml	Thu Feb 20 20:23:05 2025 +0000
@@ -0,0 +1,70 @@
+<tool id="drug2cell" name="drug2cell" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+     <description>Collection of utility functions for gene group activity evaluation in scanpy</description>
+     <macros>
+        <token name="@TOOL_VERSION@">0.1.2</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="0.1.2">drug2cell</requirement>
+        <requirement type="package" version="1.10.4">scanpy</requirement>
+    </requirements>
+
+ <command>
+    <![CDATA[
+    python3 '$script' --adata '${adata}' --output '${d2c_output}'
+    ]]>
+ </command>
+ <configfiles>
+    <configfile name="script">
+<![CDATA[
+import drug2cell as d2c
+import scanpy as sc
+        
+# Load AnnData object
+adata = sc.read_h5ad("${adata}")
+
+# Run drug2cell
+d2c.score(adata)
+
+# Get the drug2cell results
+d2cell = adata.uns["drug2cell"]
+
+# Save the drug2cell results to a new .h5ad file
+d2cell.write("${d2c_output}")
+]]>
+    </configfile>
+ </configfiles>
+
+ <inputs>
+     <param name="adata" type="data" format="h5ad" label="AnnData Object" help="Select the processed AnnData object file containing your single-cell RNA-seq data"/>
+ </inputs>
+
+ <outputs>
+    <data name="d2c_output" format="h5ad" label="drug2cell Results" />
+ </outputs>
+
+<tests>
+    <test>
+        <param name="adata" value="tiny_adata.h5ad"/>
+        <output name="d2c_output" file="d2c_output.h5ad">
+            <assert_contents>
+                <has_h5_keys keys="obs,var"/>
+            </assert_contents>
+        </output>
+    </test>
+</tests>
+
+<help>
+    <![CDATA[
+    This tool uses the drug2cell package to score gene groups based on drug-target data from the ChEMBL database.
+    It performs differential expression analysis to identify gene groups up-regulated in particular clusters.
+    ]]>
+</help>
+
+
+<citations>
+    <citation type="doi">10.1038/s41586-023-06311-1</citation>
+ </citations>
+</tool>
+
+
diff -r 000000000000 -r b0ea90bddf66 test-data/d2c_output.h5ad
Binary file test-data/d2c_output.h5ad has changed
diff -r 000000000000 -r b0ea90bddf66 test-data/tiny_adata.h5ad
Binary file test-data/tiny_adata.h5ad has changed