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jmchiltonjmchilton
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Pull in upstream changes to existing files from bioc work.
These new abstractions allow the downstream work to get away with a lot less duplication relative to master. So this improves this code and should really simplify the diff when a new PR for the bioconductor stuff is opened.
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‎planemo/commands/cmd_tool_init.py‎

Lines changed: 24 additions & 210 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
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"""Module describing the planemo ``tool_init`` command."""
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import os
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import click
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@@ -8,226 +7,41 @@
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from planemo import tool_builder
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from planemo.cli import command_function
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REUSING_MACROS_MESSAGE = ("Macros file macros.xml already exists, assuming "
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" it has relevant planemo-generated definitions.")
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# --input_format
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# --output_format
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# --advanced_options
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@click.command("tool_init")
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@click.option(
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"-i",
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"--id",
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type=click.STRING,
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prompt=True,
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help="Short identifier for new tool (no whitespace)",
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)
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@options.tool_init_id_option()
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@options.force_option(what="tool")
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@click.option(
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"-t",
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"--tool",
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default=None,
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type=click.Path(exists=False,
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file_okay=True,
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dir_okay=False,
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writable=True,
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resolve_path=True),
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help="Output path for new tool (default is <id>.xml)",
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)
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@click.option(
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"-n",
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"--name",
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type=click.STRING,
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prompt=True,
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help="Name for new tool (user facing)",
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)
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@click.option(
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"--version",
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default="0.1.0",
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type=click.STRING,
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help="Tool XML version.",
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)
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@click.option(
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"-d",
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"--description",
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type=click.STRING,
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default=None,
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prompt=False,
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help="Short description for new tool (user facing)",
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)
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@click.option(
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"-c",
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"--command",
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type=click.STRING,
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default=None,
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prompt=False,
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help=("Command potentially including cheetah variables ()"
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"(e.g. 'seqtk seq -a $input > $output')"),
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)
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@click.option(
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"--example_command",
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type=click.STRING,
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default=None,
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prompt=False,
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help=("Example to command with paths to build Cheetah template from "
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"(e.g. 'seqtk seq -a 2.fastq > 2.fasta'). Option cannot be used "
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"with --command, should be used --example_input and "
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"--example_output."),
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)
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@click.option(
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"--example_input",
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type=click.STRING,
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default=None,
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prompt=False,
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multiple=True,
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help=("For use with --example_command, replace input file (e.g. 2.fastq "
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"with a data input parameter)."),
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)
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@click.option(
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"--example_output",
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type=click.STRING,
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default=None,
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prompt=False,
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multiple=True,
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help=("For use with --example_command, replace input file (e.g. 2.fastq "
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"with a tool output)."),
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)
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@click.option(
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"--version_command",
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type=click.STRING,
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default=None,
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prompt=False,
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help="Command to print version (e.g. 'seqtk --version')",
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)
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@click.option(
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"--input",
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type=click.STRING,
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default=None,
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prompt=False,
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multiple=True,
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help="An input description (e.g. input.fasta)",
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)
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@click.option(
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"--output",
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type=click.STRING,
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multiple=True,
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default=None,
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prompt=False,
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help=("An output location (e.g. output.bam), the Galaxy datatype is "
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"inferred from the extension."),
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)
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@click.option(
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"--named_output",
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type=click.STRING,
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multiple=True,
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default=None,
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prompt=False,
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help=("Create a named output for use with command block for example "
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"specify --named_output=output1.bam and then use '-o $output1' "
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"in your command block."),
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)
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@click.option(
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"--help_text",
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type=click.STRING,
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default=None,
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prompt=False,
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help="Help text (reStructuredText)",
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)
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@click.option(
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"--help_from_command",
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type=click.STRING,
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default=None,
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prompt=False,
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help="Auto populate help from supplied command.",
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)
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@click.option(
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"--requirement",
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type=click.STRING,
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default=None,
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multiple=True,
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prompt=False,
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help="Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68')."
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)
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@click.option(
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"--container",
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type=click.STRING,
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default=None,
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multiple=True,
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prompt=False,
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help="Add a Docker image identifier for this tool."
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)
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@click.option(
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"--doi",
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type=click.STRING,
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default=None,
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multiple=True,
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prompt=False,
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help=("Supply a DOI (http://www.doi.org/) easing citation of the tool "
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"for Galaxy users (e.g. 10.1101/014043).")
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)
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@click.option(
170-
"--cite_url",
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type=click.STRING,
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default=None,
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multiple=True,
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prompt=False,
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help=("Supply a URL for citation.")
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)
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@click.option(
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"--test_case",
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is_flag=True,
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default=None,
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prompt=False,
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help=("For use with --example_commmand, generate a tool test case from "
183-
"the supplied example."),
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)
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@click.option(
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"--macros",
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is_flag=True,
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default=None,
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prompt=False,
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help="Generate a macros.xml for reuse across many tools.",
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)
14+
@options.tool_init_tool_option()
15+
@options.tool_init_name_option()
16+
@options.tool_init_version_option()
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@options.tool_init_description_option()
18+
@options.tool_init_command_option()
19+
@options.tool_init_example_command_option()
20+
@options.tool_init_example_input_option()
21+
@options.tool_init_example_output_option()
22+
@options.tool_init_named_output_option()
23+
@options.tool_init_input_option()
24+
@options.tool_init_output_option()
25+
@options.tool_init_help_text_option()
26+
@options.tool_init_help_from_command_option()
27+
@options.tool_init_doi_option()
28+
@options.tool_init_cite_url_option()
29+
@options.tool_init_test_case_option()
30+
@options.tool_init_macros_option()
31+
@options.tool_init_version_command_option()
32+
@options.tool_init_requirement_option()
33+
@options.tool_init_container_option()
19234
@options.build_cwl_option()
19335
@command_function
19436
def cli(ctx, **kwds):
19537
"""Generate tool outline from given arguments."""
19638
invalid = _validate_kwds(kwds)
197-
tool_id = kwds.get("id")
19839
if invalid:
19940
ctx.exit(invalid)
200-
output = kwds.get("tool")
201-
if not output:
202-
extension = "cwl" if kwds.get("cwl") else "xml"
203-
output = "%s.%s" % (tool_id, extension)
204-
if not io.can_write_to_path(output, **kwds):
205-
ctx.exit(1)
20641
tool_description = tool_builder.build(**kwds)
207-
io.write_file(output, tool_description.contents)
208-
io.info("Tool written to %s" % output)
209-
test_contents = tool_description.test_contents
210-
if test_contents:
211-
sep = "-" if "-" in tool_id else "_"
212-
tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
213-
if not io.can_write_to_path(tests_path, **kwds):
214-
ctx.exit(1)
215-
io.write_file(tests_path, test_contents)
216-
io.info("Tool tests written to %s" % tests_path)
217-
218-
macros = kwds["macros"]
219-
macros_file = "macros.xml"
220-
if macros and not os.path.exists(macros_file):
221-
io.write_file(macros_file, tool_description.macro_contents)
222-
elif macros:
223-
io.info(REUSING_MACROS_MESSAGE)
224-
if tool_description.test_files:
225-
if not os.path.exists("test-data"):
226-
io.info("No test-data directory, creating one.")
227-
io.shell("mkdir -p 'test-data'")
228-
for test_file in tool_description.test_files:
229-
io.info("Copying test-file %s" % test_file)
230-
io.shell("cp '%s' 'test-data'" % test_file)
42+
tool_builder.write_tool_description(
43+
ctx, tool_description, **kwds
44+
)
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23246

23347
def _validate_kwds(kwds):

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