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Update tool XSD for (hopefully deprecated) change_format syntax.

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Fixes #3552.
This commit is contained in:
John Chilton
2017-02-08 14:52:22 -05:00
parent 3b3bfad8e0
commit 7e98cde0a9
3 changed files with 46 additions and 4 deletions
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lib/galaxy/tools/xsd/galaxy.xsd
+15 -4
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@@ -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">
test/functional/tools/output_format_deprecated_when.xml
+30
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@@ -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>
test/functional/tools/samples_tool_conf.xml
+1
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@@ -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" />