comparison jbrowse2.py @ 120:af482048ca1a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 59fe39774d791bc684811b6ce03e13ef093d074e

119:2fff478aca4b

import logging
import os
import re
import shutil
import ssl
import struct
import subprocess
import tempfile
import urllib.request
import xml.etree.ElementTree as ET

    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version=JB2VER)
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()

    # This should be done ASAP
    GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
    # Sometimes this comes as `localhost` without a protocol
    if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
        # so we'll prepend `http://` and hope for the best. Requests *should*

    trackI = 0
    for ass in root.findall("assembly"):
        genomes = [
            {
                "path": x.attrib["path"],
                "label": x.attrib["label"].split(" ")[0].replace(",", ""),
                "useuri": x.attrib["useuri"],
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in ass.findall("metadata/genomes/genome")
        ]

                for x in trackfiles:
                    isBed = False
                    if x.attrib['ext'] == "bed":
                        isBed = True
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"),
                        trackI,
                    )
                    trackI += 1
                    track_conf["useuri"] = x.attrib["useuri"]
                    if is_multi_bigwig:
                        multi_bigwig_paths.append(
                            (
                                track_conf["label"],
                                track_conf["useuri"],
                                os.path.realpath(x.attrib["path"]),
                            )
                        )
                    else:

120:af482048ca1a

import logging
import os
import re
import shutil
import ssl
import string
import struct
import subprocess
import tempfile
import urllib.request
import xml.etree.ElementTree as ET

    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version=JB2VER)
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()
    removeMe = string.punctuation.replace('.','').replace('/','').replace('-','')
    nopunct = str.maketrans(dict.fromkeys(removeMe))
    # This should be done ASAP
    GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
    # Sometimes this comes as `localhost` without a protocol
    if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
        # so we'll prepend `http://` and hope for the best. Requests *should*

    trackI = 0
    for ass in root.findall("assembly"):
        genomes = [
            {
                "path": x.attrib["path"],
                "label": x.attrib["label"].split(" ")[0].translate(nopunct),
                "useuri": x.attrib["useuri"],
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in ass.findall("metadata/genomes/genome")
        ]

                for x in trackfiles:
                    isBed = False
                    if x.attrib['ext'] == "bed":
                        isBed = True
                    track_conf["label"] = "%s_%d" % (
                        x.attrib["label"].translate(nopunct),
                        trackI,
                    )
                    trackI += 1
                    track_conf["useuri"] = x.attrib["useuri"]
                    if is_multi_bigwig:
                        multi_bigwig_paths.append(
                            (
                                track_conf["label"].translate(nopunct),
                                track_conf["useuri"],
                                os.path.realpath(x.attrib["path"]),
                            )
                        )
                    else: