add script to split Galaxy tool by subparsers

scripts/supparser_split.py

@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+
+# script that tries to split a Galaxy tool that covers multiple subparsers
+# into separate tools
+
+import sys
+import re
+
+import lxml.etree as ET
+
+
+def parse_conditional(xml_file):
+    # Parse the XML file
+    tree = ET.parse(xml_file)
+    root = tree.getroot()
+    inputs = root.find("./inputs")
+    # Find all conditional elements under the tool
+    conditional = inputs.find("./conditional")
+    assert (
+        conditional.tag == "conditional"
+    ), "First child of inputs needs to be a conditional"
+    conditional_name = conditional.attrib["name"]
+
+    select = conditional.find("*")
+    assert select.tag == "param", "First child of the conditional needs to be a param"
+    select_name = select.attrib["name"]
+
+    # List to store values of param-options
+    option_values = []
+    for param_option in select.findall("./option"):
+        option_values.append(param_option.attrib["value"])
+
+    return conditional_name, select_name, option_values
+
+
+def split(xml_file, cond_name, select_name, options):
+
+    for option in options:
+        tree = ET.parse(xml_file)
+        root = tree.getroot()
+
+        # replace conditional with the children of the corresponding when block
+        inputs = root.find("./inputs")
+        conditional = inputs.find(f'./conditional[@name="{cond_name}"]')
+        index = list(inputs).index(conditional)
+        when = inputs.find(
+            f'./conditional[@name="{cond_name}"]/when[@value="{option}"]'
+        )
+
+        inputs.remove(conditional)
+        for child in reversed(list(when)):
+            inputs.insert(index, child)
+
+        # command
+        command = root.find("./command")
+        new_command = []
+        if_name = None
+        for line in command.text.split("\n"):
+
+            if_match = re.match(
+                f"^( *)#if (?:str\()?\${cond_name}.{select_name}(?:\))? == [\"'](.*)[\"'].*",
+                line,
+            )
+            if if_match:
+                indent = len(if_match.group(1))
+                if_name = if_match.group(2)
+                continue
+            if if_name is None:
+                new_command.append(line)
+                continue
+            elif_match = re.match(
+                f"^( {{{indent}}})#elif (?:str\()?\${cond_name}.{select_name}(?:\))? == [\"'](.*)[\"'].*",
+                line,
+            )
+            if elif_match:
+                if_name = elif_match.group(2)
+                continue
+            if re.match(f"^( {{{indent}}})#end if", line):
+                if_name = None
+                continue
+
+            if if_name == option:
+                new_command.append(line[indent:].replace(f"${cond_name}.", "$"))
+
+            command.text = ET.CDATA("\n".join(new_command))
+        # outputs
+        outputs = root.find("./outputs")
+        for output in outputs.getchildren():
+            filter = output.find("./filter")
+            if filter is not None:
+                if not eval(
+                    filter.text.replace(f'{cond_name}["{select_name}"]', f'"{option}"')
+                ):
+                    outputs.remove(output)
+                else:
+                    output.remove(filter)
+        # test
+
+        tests = root.find("./tests")
+        for test in tests.getchildren():
+            if test.find(f'.//param[@name="{select_name}"][@value="{option}"]') is None:
+                tests.remove(test)
+            else:
+                conditional = test.find(f'./conditional[@name="{cond_name}"]')
+                if conditional is not None:
+                    conditional_index = list(test).index(conditional)
+                    test.remove(conditional)
+                    for child in conditional:
+                        test.insert(conditional_index, child)
+                param = test.find(f'./param[@name="{select_name}"]')
+                if param is not None:
+                    test.remove(param)
+
+        # id, name
+        root.attrib["id"] = f"{root.attrib['id']}_{option.replace('-', '_')}"
+        root.attrib["name"] = f"{root.attrib['name']}: {option}"
+
+        ET.indent(tree.getroot(), space="    ")
+        tree.write(f"{option}.xml")
+
+
+xml_file = sys.argv[1]
+cond_name, select_name, options = parse_conditional(xml_file)
+split(xml_file, cond_name, select_name, options)