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The Basics

For fully featured Seqtk wrappers check out Eric Rasche's wrappers on GitHub.

Galaxy tool files are just XML files, so at this point one could open a text editor and start writing the tool. Planemo has a command tool_init to quickly generate some of the boilerplate XML, so let's start by doing that.

$ planemo tool_init --id 'seqtk_seq' --name 'Convert to FASTA (seqtk)'

The tool_init command can take various complex arguments - but the two most basic ones are shown above --id and --name. Every Galaxy tool needs an id (this is a short identifier used by Galaxy itself to identify the tool) and a name (this is displayed to the Galaxy user and should be a short description of the tool). A tool's name can have whitespace but its id must not.

The above command will generate the file seqtk_seq.xml - which looks like this.

.. literalinclude:: writing/seqtk_seq_v1.xml
   :language: xml

This tool file has the common sections required for a Galaxy tool but you will still need to open up the editor and fill out the command template, describe input parameters, tool outputs, write a help section, etc.

The tool_init command can do a little bit better than this as well. We can use the test command we tried above seqtk seq -a 2.fastq > 2.fasta as an example to generate a command block by specifing the inputs and the outputs as follows.

$ planemo tool_init --force \
                    --id 'seqtk_seq' \
                    --name 'Convert to FASTA (seqtk)' \
                    --requirement [email protected] \
                    --example_command 'seqtk seq -a 2.fastq > 2.fasta' \
                    --example_input 2.fastq \
                    --example_output 2.fasta

This will generate the following XML file - which now has correct definitions for the input and output as well as an actual command template.

.. literalinclude:: writing/seqtk_seq_v2.xml
   :language: xml
   :emphasize-lines: 5-13


$ planemo tool_init --force \
                    --id 'seqtk_seq' \
                    --name 'Convert to FASTA (seqtk)' \
                    --requirement [email protected] \
                    --example_command 'seqtk seq -a 2.fastq > 2.fasta' \
                    --example_input 2.fastq \
                    --example_output 2.fasta \
                    --test_case \
                    --cite_url 'https://github.com/lh3/seqtk' \
                    --help_from_command 'seqtk seq'

In addition to demonstrating --help_from_command, this demonstrates generating a test case from our example with --test_case and adding a citation for the underlying tool. The resulting tool XML file is:

.. literalinclude:: writing/seqtk_seq_v3.xml
   :language: xml
   :emphasize-lines: 14-55


$ planemo l
Linting tool /opt/galaxy/tools/seqtk_seq.xml
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 1 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Convert to FASTA (seqtk)].
.. CHECK: Tool defines an id [seqtk_seq].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.

By default lint will find all the tools in your current working directory, but we could have specified a particular tool with planemo lint seqtk_seq.xml.

Next we can run our tool's functional test with the test (or just t) command. This will print a lot of output (as it starts a Galaxy instance) but should ultimately reveal our one test passed.