comparison toolfactory/rgToolFactory2.py @ 127:98c8a76b3638 draft

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126:def0f754ee1b

import sys
import tarfile
import tempfile
import time

from bioblend import ConnectionError
from bioblend import toolshed

import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp

import lxml

import yaml


myversion = "V2.2 February 2021"
verbose = True
debug = True

                num_dashes=ndash,
            )
            aninput.positional = self.is_positional
            if self.is_positional:
                if p["origCL"].upper() == "STDIN":
                    aparm.positional = 9999998
                    aparm.command_line_override = "> $%s" % newname
                else:
                    aparm.positional = int(p["origCL"])
                    aparm.command_line_override = "$%s" % newname
            self.tinputs.append(aninput)
            tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
            self.testparam.append(tparm)
        for p in self.addpar:
            newname = p["name"]

                    else:
                        newname = f"{entry.name}.txt"
                    dest = os.path.join(self.repdir, newname)
                    src = os.path.join(self.testdir, entry.name)
                    shutil.copyfile(src, dest)


    def planemo_test_once(self):
        """planemo is a requirement so is available for testing but needs a
        different call if in the biocontainer - see above
        and for generating test outputs if command or test overrides are

127:98c8a76b3638

import sys
import tarfile
import tempfile
import time


import galaxyxml.tool as gxt
import galaxyxml.tool.parameters as gxtp
import lxml
import yaml
from bioblend import ConnectionError
from bioblend import toolshed


myversion = "V2.2 February 2021"
verbose = True
debug = True

                num_dashes=ndash,
            )
            aninput.positional = self.is_positional
            if self.is_positional:
                if p["origCL"].upper() == "STDIN":
                    aninput.positional = 9999998
                    aninput.command_line_override = "> $%s" % newname
                else:
                    aninput.positional = int(p["origCL"])
                    aninput.command_line_override = "$%s" % newname
            self.tinputs.append(aninput)
            tparm = gxtp.TestParam(name=newname, value="%s_sample" % newname)
            self.testparam.append(tparm)
        for p in self.addpar:
            newname = p["name"]

                    else:
                        newname = f"{entry.name}.txt"
                    dest = os.path.join(self.repdir, newname)
                    src = os.path.join(self.testdir, entry.name)
                    shutil.copyfile(src, dest)

    def planemo_test_once(self):
        """planemo is a requirement so is available for testing but needs a
        different call if in the biocontainer - see above
        and for generating test outputs if command or test overrides are