From 7e98cde0a9cf62f60b907ed14ee407f6183dee72 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 8 Feb 2017 08:58:37 -0500
Subject: [PATCH] Update tool XSD for (hopefully deprecated) change_format
 syntax.

Fixes #3552.
---
 lib/galaxy/tools/xsd/galaxy.xsd               | 19 +++++++++---
 .../tools/output_format_deprecated_when.xml   | 30 +++++++++++++++++++
 test/functional/tools/samples_tool_conf.xml   |  1 +
 3 files changed, 46 insertions(+), 4 deletions(-)
 create mode 100644 test/functional/tools/output_format_deprecated_when.xml

diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index 3ced93719fd..96f9f9289a2 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -4888,16 +4888,17 @@ for more examples.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:sequence/>
-    <xs:attribute name="input" type="xs:string" use="required">
+    <xs:attribute name="input" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">This value must be the attribute name of
+        <xs:documentation xml:lang="en">This attribute should be the name of
 the desired input parameter (e.g. ``input="out_format"`` above).</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="value" type="xs:string" use="required">
       <xs:annotation>
-        <xs:documentation xml:lang="en">This value must also be an attribute
-name of an input parameter (e.g. ``value="interval"`` above).</xs:documentation>
+        <xs:documentation xml:lang="en">This must be a possible value of the ``input``
+parameter (e.g. ``value="interval"`` above), or of the deprecated ``input_dataset``'s
+``attribute.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="format" type="xs:string" use="required">
@@ -4908,6 +4909,16 @@ name of an input parameter (e.g. ``value="interval"`` above).</xs:documentation>
 for a list of supported formats.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
+    <xs:attribute name="input_dataset" type="xs:string" gxdocs:deprecated="true">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Deprecated.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+    <xs:attribute name="attribute" type="xs:string" gxdocs:deprecated="true">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Deprecated.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
   </xs:complexType>
 
   <xs:complexType name="Citations">
diff --git a/test/functional/tools/output_format_deprecated_when.xml b/test/functional/tools/output_format_deprecated_when.xml
new file mode 100644
index 00000000000..63cf1b406e1
--- /dev/null
+++ b/test/functional/tools/output_format_deprecated_when.xml
@@ -0,0 +1,30 @@
+<tool id="output_format_deprecated_when" name="output_format_deprecated_when" version="1.0.0">
+  <command>
+    echo "test" > 5;
+  </command>
+  <inputs>
+    <param name="input_data_1" type="data" format="data" label="input_data_1" />
+  </inputs>
+  <outputs>
+    <data format="txt" from_work_dir="5" name="change_format_deprecated">
+      <change_format>
+        <when input_dataset="input_data_1" attribute="extension" value="fastq" format="fastq" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_data_1" value="1.fastqsanger" ftype="fastq" />
+      <output name="change_format_deprecated" ftype="fastq">
+        <assert_contents><has_line line="test" /></assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="input_data_1" value="1.fastqsanger" ftype="fastqsanger" />
+      <output name="change_format_deprecated" ftype="txt">
+        <!-- Fails to check subclasses, use format_soure if possible -->
+        <assert_contents><has_line line="test" /></assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 9ea7ee03ac7..40fa9c1f17b 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -48,6 +48,7 @@
   <tool file="gzipped_inputs.xml" />
   <tool file="output_order.xml" />
   <tool file="output_format.xml" />
+  <tool file="output_format_deprecated_when.xml" />
   <tool file="output_format_collection.xml" />
   <tool file="output_filter.xml" />
   <tool file="output_filter_exception_1.xml" />