diff set_path.py @ 1:90d60c9da21e draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/set_path.py	Fri Nov 10 14:20:45 2023 +0000
@@ -0,0 +1,31 @@
+import argparse
+import re
+import sys
+from xml.etree import ElementTree
+
+parser = argparse.ArgumentParser(
+    prog="set_path.py", description="update paths in mzmine batch XML"
+)
+parser.add_argument("--input", help="input XML")
+parser.add_argument("--output", help="output XML")
+parser.add_argument("--localdb", required=False, help="Local CVS DB for Search")
+args = parser.parse_args()
+
+PATHSEP = re.compile(r"[/\\]")
+tree = ElementTree.parse(args.input)
+
+for batchstep in tree.findall(".//batchstep"):
+    method = batchstep.attrib.get("method")
+    for current_file in batchstep.findall(".//current_file"):
+        if (
+            method
+            == "io.github.mzmine.modules.dataprocessing.id_localcsvsearch.LocalCSVDatabaseSearchModule"
+        ):
+            if args.localdb:
+                current_file.text = args.localdb
+            else:
+                sys.exit("Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given")
+        else:
+            current_file.text = f"./output/{PATHSEP.split(current_file.text)[-1]}"
+
+tree.write(args.output)