New linter - lint order of XML appearing in the XML file.

The best practice guidelines prescribe a fixed order - this verifies that order. It will also print a little info box if unknown top-level tags are encountered - this may become a warning in the future (certainly if the XSD validation works out).

Fix tool_builder.py to actually produce best practice tools.

planemo/commands/cmd_normalize.py

@@ -9,22 +9,7 @@
     load_tool,
     raw_tool_xml_tree,
 )
-
-
-TAG_ORDER = [
-    'description',
-    'macros',
-    'requirements',
-    'code',
-    'stdio',
-    'version_command',
-    'command',
-    'inputs',
-    'outputs',
-    'tests',
-    'help',
-    'citations',
-]
+from galaxy.tools.linters.xml_order import TAG_ORDER
 
 
 @click.command('normalize')

planemo/tool_builder.py

@@ -20,9 +20,6 @@
     <expand macro="version_command" />
 {% endif %}
 {%- else %}
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
     <requirements>
 {%- for requirement in requirements %}
         {{ requirement }}
@@ -31,6 +28,9 @@
         {{ container }}
 {%- endfor %}
     </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
 {%- if version_command %}
     <version_command>{{ version_command }}</version_command>
 {%- endif %}

planemo_ext/galaxy/tools/linters/xml_order.py

@@ -0,0 +1,32 @@
+TAG_ORDER = [
+    'description',
+    'macros',
+    'requirements',
+    'code',
+    'stdio',
+    'version_command',
+    'command',
+    'inputs',
+    'outputs',
+    'tests',
+    'help',
+    'citations',
+]
+
+
+# Ensure the XML blocks appear in the correct order prescribed
+# by the tool author best practices.
+def lint_xml_ordering(tool_xml, lint_ctx):
+    last_tag = None
+    last_key = None
+    for elem in list(tool_xml.getroot()):
+        tag = elem.tag
+        if tag in TAG_ORDER:
+            key = TAG_ORDER.index(tag)
+            if last_key:
+                if last_key > key:
+                    lint_ctx.warn("Best practice violation [%s] elements should come before [%s]" % (tag, last_tag))
+            last_tag = tag
+            last_key = key
+        else:
+            lint_ctx.info("Unknown tag [%s] encoutered, this may result in a warning in the future." % tag)