Galaxy tool_conf.xml Editor

The ToolConfigEditor (tce) is a Groovy DSL used to modify Galaxy's tool_conf.xml files. When building custom LAPP/Galaxy appliances we need to update the tool_conf.xml file to include just the tools that are present in that appliance. While installing tools from Galaxy's tool shed will update the tool_conf.xml file there are several drawbacks to relying on the tool shed:

1. Not all tools we want to install are available on the tool shed
2. We may want to add a tool to more than once section of the tool_conf.xml

We could use XSL stylesheets to modify the tool_conf.xml file, but XSL is rather syntax heavy for our users. The ToolConfEditor DSL provides a much simpler syntax for expressing how the tool_conf.xml file should be modified.

NOTE Currenly only additive changes may be made. That is, it is not possible to delete tools from a tool_conf.xml file.

Usage

java -jar ToolConfEditor-x.y.z.jar [-m] -c <template> -o <output file> [-i <include dir>] module [module ...]

The examples assume that a script named tce is available on the path that call the jar file. See the install.sh script for an example of how to generate such a script. By default the install.sh script generates a startup script in $HOME/bin/tce.

Options

-m
--minimize
Removes empty section elements from the output.

-c <template>
--conf <template>
The tool_conf.xml file to me modified

-o <output file>
--output <output file>[optional]
Where the output will be written. If this is omitted the output will be written to stdout (System.out)

-i <include dir>
--include <include dir> [optional]
A directory to be searched for files included with the include directive.

module [module...]
A list of DSL files that will be processed in order. See the DSL Syntax section below for the syntax of the module files.

DSL Syntax

The ToolConfEditor DSL is a Groovy DSL so any valid Groovy syntax, and by extension most valid Java syntax, is supported. However, the ToolConfEditor adds support for the statements

id { tool_list }
id 'name', { tool_list }

where id is the value of the id attribute of the <section> element, name (if present) is the value of the name attribute, and tool_list is list of paths to the tool xml files. The tool_list can contain multiple tool definitions or defines multiple tools at once with the tools statement. For example:

foo {
  tool "foo/tool1.xml"
  tool "foo.tool2.xml"
}
bar 'This is a bar', {
  tools "bar/tool1.xml", "bar/tool2.xml"
}

This will result in the following tool_conf.xml:

<toolbox>
  <section id="foo" name="Unknown">
    <tool file="foo/tool1.xml"/>
    <tool file="foo/tool2.xml"/>
  </section>
  <section id="bar" name="This is a bar">
    <tool file="bar/tool1.xml"/>
    <tool file="bar/tool2.xml"/>
  </section>
</toolbox>