comparison runner.py @ 19:cefa7625d6cb draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 2840545abeeca2dc0a6e6df138633e561d379e52

18:a5769923297c

        for segment in self.segalign_segments:
            yield segment


class LastzCommand:
    lastz_command_regex = re.compile(r"lastz (.+?)?ref\.2bit\[nameparse=darkspace\]\[multiple\]\[subset=ref_block(\d+)\.name\] (.+?)?query\.2bit\[nameparse=darkspace\]\[subset=query_block(\d+)\.name] --format=(\S+) --ydrop=(\d+) --gappedthresh=(\d+) --strand=(minus|plus)(?: --ambiguous=(\S+))?(?: --(notrivial))?(?: --scoring=(\S+))? --segments=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.segments --output=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.(\S+) 2> tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.err")

    def __init__(self, line: str) -> None:
        self.line = line
        self.args: list[str] = []
        self.target_filename: str = ''

19:cefa7625d6cb

        for segment in self.segalign_segments:
            yield segment


class LastzCommand:
    lastz_command_regex = re.compile(r"lastz (.+?)?ref\.2bit\[nameparse=darkspace\]\[multiple\]\[subset=ref_block(\d+)\.name\] (.+?)?query\.2bit\[nameparse=darkspace\]\[subset=query_block(\d+)\.name] --format=(\S+) --ydrop=(\d+) --gappedthresh=(\d+) --strand=(minus|plus)(?: --ambiguous=(\S+))?(?: --(notrivial))?(?: --scores=(\S+))? --segments=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.segments --output=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.(\S+) 2> tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.err")

    def __init__(self, line: str) -> None:
        self.line = line
        self.args: list[str] = []
        self.target_filename: str = ''