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.

Author: jmchilton

planemo/commands/cmd_tool_init.py

@@ -1,5 +1,4 @@
 """Module describing the planemo ``tool_init`` command."""
-import os
 
 import click
 
@@ -8,226 +7,41 @@
 from planemo import tool_builder
 from planemo.cli import command_function
 
-REUSING_MACROS_MESSAGE = ("Macros file macros.xml already exists, assuming "
-                          " it has relevant planemo-generated definitions.")
 
-
-# --input_format
-# --output_format
-# --advanced_options
 @click.command("tool_init")
-@click.option(
-    "-i",
-    "--id",
-    type=click.STRING,
-    prompt=True,
-    help="Short identifier for new tool (no whitespace)",
-)
+@options.tool_init_id_option()
 @options.force_option(what="tool")
-@click.option(
-    "-t",
-    "--tool",
-    default=None,
-    type=click.Path(exists=False,
-                    file_okay=True,
-                    dir_okay=False,
-                    writable=True,
-                    resolve_path=True),
-    help="Output path for new tool (default is <id>.xml)",
-)
-@click.option(
-    "-n",
-    "--name",
-    type=click.STRING,
-    prompt=True,
-    help="Name for new tool (user facing)",
-)
-@click.option(
-    "--version",
-    default="0.1.0",
-    type=click.STRING,
-    help="Tool XML version.",
-)
-@click.option(
-    "-d",
-    "--description",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help="Short description for new tool (user facing)",
-)
-@click.option(
-    "-c",
-    "--command",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help=("Command potentially including cheetah variables ()"
-          "(e.g. 'seqtk seq -a $input > $output')"),
-)
-@click.option(
-    "--example_command",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help=("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."),
-)
-@click.option(
-    "--example_input",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    multiple=True,
-    help=("For use with --example_command, replace input file (e.g. 2.fastq "
-          "with a data input parameter)."),
-)
-@click.option(
-    "--example_output",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    multiple=True,
-    help=("For use with --example_command, replace input file (e.g. 2.fastq "
-          "with a tool output)."),
-)
-@click.option(
-    "--version_command",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help="Command to print version (e.g. 'seqtk --version')",
-)
-@click.option(
-    "--input",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    multiple=True,
-    help="An input description (e.g. input.fasta)",
-)
-@click.option(
-    "--output",
-    type=click.STRING,
-    multiple=True,
-    default=None,
-    prompt=False,
-    help=("An output location (e.g. output.bam), the Galaxy datatype is "
-          "inferred from the extension."),
-)
-@click.option(
-    "--named_output",
-    type=click.STRING,
-    multiple=True,
-    default=None,
-    prompt=False,
-    help=("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."),
-)
-@click.option(
-    "--help_text",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help="Help text (reStructuredText)",
-)
-@click.option(
-    "--help_from_command",
-    type=click.STRING,
-    default=None,
-    prompt=False,
-    help="Auto populate help from supplied command.",
-)
-@click.option(
-    "--requirement",
-    type=click.STRING,
-    default=None,
-    multiple=True,
-    prompt=False,
-    help="Add a tool requirement package (e.g. 'seqtk' or 'seqtk@1.68')."
-)
-@click.option(
-    "--container",
-    type=click.STRING,
-    default=None,
-    multiple=True,
-    prompt=False,
-    help="Add a Docker image identifier for this tool."
-)
-@click.option(
-    "--doi",
-    type=click.STRING,
-    default=None,
-    multiple=True,
-    prompt=False,
-    help=("Supply a DOI (http://www.doi.org/) easing citation of the tool "
-          "for Galaxy users (e.g. 10.1101/014043).")
-)
-@click.option(
-    "--cite_url",
-    type=click.STRING,
-    default=None,
-    multiple=True,
-    prompt=False,
-    help=("Supply a URL for citation.")
-)
-@click.option(
-    "--test_case",
-    is_flag=True,
-    default=None,
-    prompt=False,
-    help=("For use with --example_commmand, generate a tool test case from "
-          "the supplied example."),
-)
-@click.option(
-    "--macros",
-    is_flag=True,
-    default=None,
-    prompt=False,
-    help="Generate a macros.xml for reuse across many tools.",
-)
+@options.tool_init_tool_option()
+@options.tool_init_name_option()
+@options.tool_init_version_option()
+@options.tool_init_description_option()
+@options.tool_init_command_option()
+@options.tool_init_example_command_option()
+@options.tool_init_example_input_option()
+@options.tool_init_example_output_option()
+@options.tool_init_named_output_option()
+@options.tool_init_input_option()
+@options.tool_init_output_option()
+@options.tool_init_help_text_option()
+@options.tool_init_help_from_command_option()
+@options.tool_init_doi_option()
+@options.tool_init_cite_url_option()
+@options.tool_init_test_case_option()
+@options.tool_init_macros_option()
+@options.tool_init_version_command_option()
+@options.tool_init_requirement_option()
+@options.tool_init_container_option()
 @options.build_cwl_option()
 @command_function
 def cli(ctx, **kwds):
     """Generate tool outline from given arguments."""
     invalid = _validate_kwds(kwds)
-    tool_id = kwds.get("id")
     if invalid:
         ctx.exit(invalid)
-    output = kwds.get("tool")
-    if not output:
-        extension = "cwl" if kwds.get("cwl") else "xml"
-        output = "%s.%s" % (tool_id, extension)
-    if not io.can_write_to_path(output, **kwds):
-        ctx.exit(1)
     tool_description = tool_builder.build(**kwds)
-    io.write_file(output, tool_description.contents)
-    io.info("Tool written to %s" % output)
-    test_contents = tool_description.test_contents
-    if test_contents:
-        sep = "-" if "-" in tool_id else "_"
-        tests_path = "%s%stests.yml" % (kwds.get("id"), sep)
-        if not io.can_write_to_path(tests_path, **kwds):
-            ctx.exit(1)
-        io.write_file(tests_path, test_contents)
-        io.info("Tool tests written to %s" % tests_path)
-
-    macros = kwds["macros"]
-    macros_file = "macros.xml"
-    if macros and not os.path.exists(macros_file):
-        io.write_file(macros_file, tool_description.macro_contents)
-    elif macros:
-        io.info(REUSING_MACROS_MESSAGE)
-    if tool_description.test_files:
-        if not os.path.exists("test-data"):
-            io.info("No test-data directory, creating one.")
-            io.shell("mkdir -p 'test-data'")
-        for test_file in tool_description.test_files:
-            io.info("Copying test-file %s" % test_file)
-            io.shell("cp '%s' 'test-data'" % test_file)
+    tool_builder.write_tool_description(
+        ctx, tool_description, **kwds
+    )
 
 
 def _validate_kwds(kwds):