Update linting for newer detect_errors attribute.

Fixes #233.

planemo_ext/galaxy/tools/linters/command.py

@@ -11,7 +11,7 @@ def lint_command(tool_xml, lint_ctx):
         lint_ctx.error("No command tag found, must specify a command template to execute.")
         return
 
-    command = commands[0]
+    command = get_command(tool_xml)
     if "TODO" in command:
         lint_ctx.warn("Command template contains TODO text.")
 
@@ -20,10 +20,23 @@ def lint_command(tool_xml, lint_ctx):
     for key, value in command_attrib.items():
         if key == "interpreter":
             interpreter_type = value
+        elif key == "detect_errors":
+            detect_errors = value
+            if detect_errors not in ["default", "exit_code", "aggressive"]:
+                lint_ctx.warn("Unknown detect_errors attribute [%s]" % detect_errors)
         else:
             lint_ctx.warn("Unknown attribute [%s] encountered on command tag." % key)
 
     interpreter_info = ""
     if interpreter_type:
         interpreter_info = " with interpreter of type [%s]" % interpreter_type
     lint_ctx.info("Tool contains a command%s." % interpreter_info)
+
+
+def get_command(tool_xml):
+    root = tool_xml.getroot()
+    commands = root.findall("command")
+    command = None
+    if len(commands) == 1:
+        command = commands[0]
+    return command

planemo_ext/galaxy/tools/linters/stdio.py

@@ -1,9 +1,12 @@
+from .command import get_command
 
 
 def lint_stdio(tool_xml, lint_ctx):
     stdios = tool_xml.findall("./stdio")
     if not stdios:
-        lint_ctx.info("No stdio definition found, tool will determine an error from stderr.")
+        command = get_command(tool_xml)
+        if command is None or not command.get("detect_errors"):
+            lint_ctx.info("No stdio definition found, tool will determine an error from stderr.")
         return
 
     if len(stdios) > 1: