Improved output and test linters.

Mostly enhanced to recognize output collections but there are some other smaller enhancements there as well.

Author: jmchilton

planemo_ext/galaxy/tools/linters/outputs.py

@@ -1,25 +1,31 @@
 
 
 def lint_output(tool_xml, lint_ctx):
-    outputs = tool_xml.findall("./outputs/data")
-    if not outputs:
-        lint_ctx.warn("Tool contains no outputs, most tools should produce outputs.")
-        return
+    outputs = tool_xml.findall("./outputs")
+    if len(outputs) == 0:
+        lint_ctx.warn("Tool contains no outputs section, most tools should produce outputs.")
+    if len(outputs) > 1:
+        lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
 
     num_outputs = 0
-    for output in outputs:
+    for output in list(outputs[0]):
+        if output.tag not in ["data", "collection"]:
+            lint_ctx.warn("Unknown element found in outputs [%s]" % output.tag)
+            continue
         num_outputs += 1
         output_attrib = output.attrib
-        format_set = False
-        if "format" in output_attrib:
-            format_set = True
-            format = output_attrib["format"]
-            if format == "input":
-                lint_ctx.warn("Using format='input' on output data, format_source attribute is less ambiguous and should be used instead.")
-        elif "format_source" in output_attrib:
-            format_set = True
-
-        if not format_set:
-            lint_ctx.warn("Tool data output doesn't define an output format.")
-
-    lint_ctx.info("%d output datasets found.", num_outputs)
+        if output.tag == "data":
+            format_set = False
+            if "format" in output_attrib:
+                format_set = True
+                format = output_attrib["format"]
+                if format == "input":
+                    lint_ctx.warn("Using format='input' on output data, format_source attribute is less ambiguous and should be used instead.")
+            elif "format_source" in output_attrib:
+                format_set = True
+            if not format_set:
+                lint_ctx.warn("Tool data output doesn't define an output format.")
+        elif output.tag == "collection":
+            if "type" not in output_attrib:
+                lint_ctx.warn("Collection output with undefined 'type' found.")
+    lint_ctx.info("%d outputs found.", num_outputs)

planemo_ext/galaxy/tools/linters/tests.py

@@ -16,7 +16,7 @@ def lint_tsts(tool_xml, lint_ctx):
         if len(test.findall("assert_stdout")) > 0:
             has_test = True
 
-        outputs = test.findall("output")
+        outputs = test.findall("output") + test.findall("output_collection")
         if len(outputs) > 0:
             has_test = True
         if not has_test:

tests/data/tools/ok_test_output_collections.xml

@@ -0,0 +1,36 @@
+<tool id="collection_split_on_column" name="collection_split_on_column" version="1.0.0">
+    <command>
+      mkdir outputs; cd outputs; awk '{ print \$2 > \$1 ".tabular" }' $input1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Input Table" help="Table to split on first column" format="tabular" />
+    </inputs>
+    <outputs>
+        <collection name="split_output" type="list" label="Table split on first column">
+            <discover_datasets pattern="__name_and_ext__" directory="outputs" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="tinywga.fam" />
+            <output_collection name="split_output" type="list">
+                <element name="101">
+                    <assert_contents>
+                        <has_text_matching expression="^1\n2\n3\n$" />
+                    </assert_contents>
+                </element>
+                <element name="1334">
+                    <assert_contents>
+                        <has_text_matching expression="^1\n10\n11\n12\n13\n2\n$" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+        Some Awesome Help!
+    </help>
+    <citations>
+        <citation type="doi">10.1101/014043</citation>
+    </citations>
+</tool>