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tool_init.rst

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tool_init command

This section is auto-generated from the help text for the planemo command tool_init. This help message can be generated with planemo tool_init --help.

Usage:

planemo tool_init [OPTIONS]

Help

Generate tool outline from given arguments. Options:

-i, --id TEXT             Short identifier for new tool (no whitespace)
-f, --force               Overwrite existing tool if present.
-t, --tool PATH           Output path for new tool (default is <id>.xml)
-n, --name TEXT           Name for new tool (user facing)
--version TEXT            Tool XML version.
-d, --description TEXT    Short description for new tool (user facing)
-c, --command TEXT        Command potentially including cheetah variables
                          ()(e.g. 'seqtk seq -a $input > $output')
--example_command TEXT    Example to command with paths to build Cheetah
                          template from (e.g. 'seqtk seq -a 2.fastq >
                          2.fasta'). Option cannot be used with --command,
                          should be used --example_input and --example_output.
--example_input TEXT      For use with --example_command, replace input file
                          (e.g. 2.fastq with a data input parameter).
--example_output TEXT     For use with --example_command, replace input file
                          (e.g. 2.fastq with a tool output).
--named_output TEXT       Create a named output for use with command block for
                          example specify --named_output=output1.bam and then
                          use '-o $output1' in your command block.
--input TEXT              An input description (e.g. input.fasta)
--output TEXT             An output location (e.g. output.bam), the Galaxy
                          datatype is inferred from the extension.
--help_text TEXT          Help text (reStructuredText)
--help_from_command TEXT  Auto populate help from supplied command.
--doi TEXT                Supply a DOI (http://www.doi.org/) easing citation
                          of the tool for Galxy users (e.g. 10.1101/014043).
--cite_url TEXT           Supply a URL for citation.
--test_case               For use with --example_commmand, generate a tool
                          test case from the supplied example.
--macros                  Generate a macros.xml for reuse across many tools.
--version_command TEXT    Command to print version (e.g. 'seqtk --version')
--requirement TEXT        Add a tool requirement package (e.g. 'seqtk' or
                          '[email protected]').
--container TEXT          Add a Docker image identifier for this tool.
--cwl                     Build a CWL tool instead of a Galaxy tool.
--help                    Show this message and exit.