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Update galaxy.xsd to allow version_command's to have an interpreter a…

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jmchilton committed Sep 22, 2016
1 parent 1ef05d2 commit 7cca2e4a102f45ec88db315303533b21381b178f
Showing with 48 additions and 19 deletions.
  1. +48 −19 planemo/xml/xsd/tool/galaxy.xsd
@@ -61,23 +61,7 @@ the tool menu immediately following the hyperlink for the tool (based on the
</xs:annotation>
</xs:element>
<xs:element name="parallelism" type="Parallelism" minOccurs="0"/>
<xs:element name="version_command" type="xs:string" minOccurs="0">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[Specifies the command to be run in
order to get the tool's version string. The resulting value will be found in the
"Info" field of the history dataset.
Unlike the [``command``](#tool|command) tag, this value is taken as a literal and so there is no
need to escape values like ``$`` and command inputs are not available for variable
substitution.
### Example
```xml
<version_command>tophat -version</version_command>
```
]]></xs:documentation>
</xs:annotation>
<xs:element name="version_command" type="VersionCommand" minOccurs="0">
</xs:element>
<xs:element name="action" type="ToolAction" minOccurs="0" maxOccurs="1" />
<xs:element name="environment_variables" type="EnvironmentVariables" minOccurs="0" maxOccurs="1"/>
@@ -1428,7 +1412,7 @@ many of the default assertion tags that come with Galaxy and examples of each
can be found below.
The implementation of these tags are simply Python functions defined in the
[``galaxy.tools.verify.asserts``](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/verify/asserts]
[``galaxy.tools.verify.asserts``](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tools/verify/asserts)
module.
]]>
</xs:documentation>
@@ -4134,7 +4118,6 @@ define.</xs:documentation>
</xs:simpleContent>
</xs:complexType>


<xs:complexType name="ConfigFiles">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[See
@@ -4270,6 +4253,52 @@ response to this directive.
</xs:simpleContent>
</xs:complexType>

<xs:complexType name="VersionCommand">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[Specifies the command to be run in
order to get the tool's version string. The resulting value will be found in the
"Info" field of the history dataset.
Unlike the [``command``](#tool|command) tag, with the exception of the string
``$__tool_directory__`` this value is taken as a literal and so there is no
need to escape values like ``$`` and command inputs are not available for variable
substitution.
### Examples
A simple example for a [TopHat](https://ccb.jhu.edu/software/tophat/index.shtml)
tool definition might just be:
```xml
<version_command>tophat -version</version_command>
```
An example that leverages a Python script (e.g. ``count_reads.py``) shipped with
the tool might be:
```xml
<version_command>python $__tool_directory__/count_reads.py</version_command>
```
Examples are included in the test tools directory including:
- [version_command_plain.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_command_plain.xml)
- [version_command_tool_dir.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_tool_dir.xml)
- [version_command_interpreter.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/version_command_interpreter.xml) (*deprecated*)
]]></xs:documentation>
</xs:annotation>
<xs:simpleContent>
<xs:extension base="xs:string">
<xs:attribute name="interpreter" type="xs:string">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[*Deprecated*: Prefix the version command with an interpreter and the tool directory in order to execute a script shipped with the tool. It is better to just use ``<interpreter> $__tool_directory__/<script_name>``.]]></xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:extension>
</xs:simpleContent>
</xs:complexType>

<xs:complexType name="RequestParameterTranslation">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[

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