jbrowse2: jbrowse2.py annotate

annotate jbrowse2.py @ 0:61add3f58f26 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532

author	iuc
date	Thu, 02 Oct 2025 10:19:44 +0000
parents
children

rev	line source
0 61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1 #!/usr/bin/env python
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	2 import argparse
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	3 import csv
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	4 import datetime
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	5 import hashlib
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	6 import json
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	7 import logging
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	8 import os
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	9 import re
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	10 import shutil
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	11 import subprocess
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	12 import xml.etree.ElementTree as ET
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	13 from collections import defaultdict
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	14
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	15 import requests
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	16
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	17
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	18 logging.basicConfig(level=logging.DEBUG)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	19 log = logging.getLogger("jbrowse")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	21 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	22 GALAXY_INFRASTRUCTURE_URL = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	23 mapped_chars = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	24 ">": "__gt__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	25 "<": "__lt__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	26 "'": "__sq__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	27 '"': "__dq__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	28 "[": "__ob__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	29 "]": "__cb__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	30 "{": "__oc__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	31 "}": "__cc__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	32 "@": "__at__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	33 "#": "__pd__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	34 "": "__cn__",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	35 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	36
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	37
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	38 def etree_to_dict(t):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	39 if t is None:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	40 return {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	41
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	42 d = {t.tag: {} if t.attrib else None}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	43 children = list(t)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	44 if children:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	45 dd = defaultdict(list)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	46 for dc in map(etree_to_dict, children):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	47 for k, v in dc.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	48 dd[k].append(v)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	49 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	50 if t.attrib:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	51 d[t.tag].update(("@" + k, v) for k, v in t.attrib.items())
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	52 if t.text:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	53 text = t.text.strip()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	54 if children or t.attrib:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	55 if text:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	56 d[t.tag]["#text"] = text
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	57 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	58 d[t.tag] = text
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	59 return d
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	60
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	61
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	62 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	63
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	64
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	65 def metadata_from_node(node):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	66 metadata = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	67
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	68 if len(node.findall("dataset")) == 1:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	69
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	70 for key, value in node.findall("dataset")[0].attrib.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	71 metadata[f"dataset_{key}"] = value
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	72
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	73 for key, value in node.findall("history")[0].attrib.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	74 metadata[f"history_{key}"] = value
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	75
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	76 for key, value in node.findall("metadata")[0].attrib.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	77 metadata[f"metadata_{key}"] = value
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	78
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	79 for key, value in node.findall("tool")[0].attrib.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	80 metadata[f"tool_{key}"] = value
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	81
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	82 # Additional Mappings applied:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	83 metadata[
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	84 "dataset_edam_format"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	85 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	86 metadata["dataset_edam_format"], metadata["dataset_file_ext"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	87 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	88 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	89 metadata["history_user_email"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	90 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	91 metadata[
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	92 "history_display_name"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	93 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	94 galaxy=GALAXY_INFRASTRUCTURE_URL,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	95 encoded_hist_id=metadata["history_id"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	96 hist_name=metadata["history_display_name"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	97 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	98 metadata[
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	99 "tool_tool"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	100 ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	101 galaxy=GALAXY_INFRASTRUCTURE_URL,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	102 encoded_id=metadata["dataset_id"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	103 tool_id=metadata["tool_tool_id"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	104 # tool_version=metadata['tool_tool_version'],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	105 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	106
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	107 # Load additional metadata from a TSV file if any given by user
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	108 bonus = node.findall("bonus")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	109 if bonus and "src" in bonus[0].attrib and bonus[0].attrib["src"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	110 with open(bonus[0].attrib["src"], "r") as bonus_tsv:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	111 bonus_content = csv.reader(bonus_tsv, delimiter="\t", quotechar='"')
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	112 for row in bonus_content:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	113 if len(row) == 2:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	114 if row[0] in metadata:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	115 log.warning(f"Overwriting existing metadata {row[0]} with value from bonus file {row[1]}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	116 metadata[row[0]] = row[1]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	117 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	118 log.warning(f"Skipping invalid bonus metadata line: {row}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	119
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	120 return metadata
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	121
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	122
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	123 class JbrowseConnector(object):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	124 def __init__(self, jbrowse, outdir, update):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	125 self.jbrowse = jbrowse
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	126 self.outdir = outdir
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	127 self.update = update
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	128
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	129 self.tracksToIndex = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	130
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	131 # This is the id of the current assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	132 self.assembly_ids = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	133
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	134 self.default_views = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	135
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	136 self.plugins = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	137
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	138 self.use_synteny_viewer = False
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	139
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	140 self.synteny_tracks = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	141
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	142 self.clone_jbrowse(self.jbrowse, self.outdir)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	143
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	144 # If upgrading, look at the existing data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	145 self.check_existing(self.outdir)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	146
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	147 def get_cwd(self, cwd):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	148 if cwd:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	149 return self.outdir
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	150 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	151 return subprocess.check_output(['pwd']).decode('utf-8').strip()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	152 # return None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	153
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	154 def subprocess_check_call(self, command, output=None, cwd=True):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	155 if output:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	156 log.debug(f"cd {self.get_cwd(cwd)} && {' '.join(command)} > {output.name}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	157 subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	158 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	159 log.debug(f"cd {self.get_cwd(cwd)} && {' '.join(command)}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	160 subprocess.check_call(command, cwd=self.get_cwd(cwd))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	161
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	162 def subprocess_popen(self, command, cwd=True):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	163 log.debug(f"cd {self.get_cwd(cwd)} && {command}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	164 p = subprocess.Popen(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	165 command,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	166 cwd=self.get_cwd(cwd),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	167 shell=True,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	168 stdin=subprocess.PIPE,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	169 stdout=subprocess.PIPE,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	170 stderr=subprocess.PIPE,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	171 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	172 output, err = p.communicate()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	173 retcode = p.returncode
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	174 if retcode != 0:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	175 log.error(f"cd {self.get_cwd(cwd)} && {command}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	176 log.error(output)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	177 log.error(err)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	178 raise RuntimeError(f"Command failed with exit code {retcode}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	179
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	180 def subprocess_check_output(self, command, cwd=True):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	181 log.debug(f"cd {self.get_cwd(cwd)} && {' '.join(command)}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	182 return subprocess.check_output(command, cwd=self.get_cwd(cwd))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	183
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	184 def symlink_or_copy(self, src, dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	185 # Use to support symlinking in jbrowse1, in jbrowse2 prefer to use remote uri
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	186 cmd = ["cp", src, dest]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	187
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	188 return self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	189
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	190 def _prepare_track_style(self, xml_conf):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	191 style_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	192 "type": "LinearBasicDisplay", # No ideal default, but should be overwritten anyway
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	193 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	194
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	195 if "display" in xml_conf["style"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	196 style_data["type"] = xml_conf["style"]["display"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	197
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	198 style_data["displayId"] = f"{xml_conf['label']}_{style_data['type']}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	199
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	200 style_data.update(self._prepare_renderer_config(style_data["type"], xml_conf["style"]))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	201
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	202 return {"displays": [style_data]}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	203
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	204 def _prepare_renderer_config(self, display_type, xml_conf):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	205
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	206 style_data = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	207
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	208 # if display_type in ("LinearBasicDisplay", "LinearVariantDisplay"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	209 # TODO LinearVariantDisplay does not understand these options when written in config.json
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	210 if display_type in ("LinearBasicDisplay"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	211
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	212 # Doc: https://jbrowse.org/jb2/docs/config/svgfeaturerenderer/
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	213 style_data["renderer"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	214 "type": "SvgFeatureRenderer",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	215 "showLabels": xml_conf.get("show_labels", True),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	216 "showDescriptions": xml_conf.get("show_descriptions", True),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	217 "labels": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	218 "name": xml_conf.get("labels_name", "jexl:get(feature,'name') \|\| get(feature,'id')"),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	219 "description": xml_conf.get("descriptions_name", "jexl:get(feature,'note') \|\| get(feature,'description')")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	220 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	221 "displayMode": xml_conf.get("display_mode", "normal"),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	222 "maxHeight": xml_conf.get("max_height", 1200),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	223 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	224
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	225 elif display_type == "LinearArcDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	226
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	227 # Doc: https://jbrowse.org/jb2/docs/config/arcrenderer/
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	228 style_data["renderer"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	229 "type": "ArcRenderer",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	230 "label": xml_conf.get("labels_name", "jexl:get(feature,'score')"),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	231 "displayMode": xml_conf.get("display_mode", "arcs"),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	232 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	233
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	234 elif display_type == "LinearWiggleDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	235
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	236 wig_renderer = xml_conf.get("renderer", "xyplot")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	237 style_data["defaultRendering"] = wig_renderer
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	238
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	239 elif display_type == "MultiLinearWiggleDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	240
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	241 wig_renderer = xml_conf.get("renderer", "multirowxy")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	242 style_data["defaultRendering"] = wig_renderer
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	243
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	244 elif display_type == "LinearSNPCoverageDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	245
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	246 # Does not work
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	247 # style_data["renderer"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	248 # "type": "SNPCoverageRenderer",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	249 # "displayCrossHatches": xml_conf.get("display_cross_hatches", True),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	250 # }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	251
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	252 style_data["scaleType"] = xml_conf.get("scale_type", "linear")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	253 if "min_score" in xml_conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	254 style_data["minScore"] = xml_conf["min_score"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	255
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	256 if "max_score" in xml_conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	257 style_data["maxScore"] = xml_conf["max_score"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	258
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	259 # Doc: https://jbrowse.org/jb2/docs/config/snpcoveragerenderer/
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	260
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	261 return style_data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	262
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	263 def _prepare_format_details(self, xml_conf):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	264 formatDetails = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	265 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	266
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	267 if "feature" in xml_conf["formatdetails"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	268 feat_jexl = xml_conf["formatdetails"]["feature"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	269 for key, value in mapped_chars.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	270 feat_jexl = feat_jexl.replace(value, key)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	271 formatDetails["feature"] = feat_jexl
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	272
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	273 if "subfeature" in xml_conf["formatdetails"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	274 sfeat_jexl = xml_conf["formatdetails"]["subfeature"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	275 for key, value in mapped_chars.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	276 sfeat_jexl = sfeat_jexl.replace(value, key)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	277 formatDetails["subfeatures"] = sfeat_jexl
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	278
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	279 if "depth" in xml_conf["formatdetails"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	280 formatDetails["depth"] = int(xml_conf["formatdetails"]["depth"])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	281
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	282 return {"formatDetails": formatDetails}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	283
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	284 def _prepare_track_metadata(self, xml_conf):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	285 metadata = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	286 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	287
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	288 metadata = xml_conf["metadata"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	289
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	290 return {"metadata": metadata}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	291
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	292 def check_existing(self, destination):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	293 existing = os.path.join(destination, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	294 if os.path.exists(existing):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	295 with open(existing, "r") as existing_conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	296 conf = json.load(existing_conf)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	297 if "assemblies" in conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	298 for assembly in conf["assemblies"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	299 if "name" in assembly:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	300
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	301 # Look for a default scaffold
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	302 default_seq = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	303 if 'defaultSession' in conf and 'views' in conf['defaultSession']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	304 for view in conf['defaultSession']['views']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	305 if 'init' in view and 'assembly' in view['init'] and 'loc' in view['init']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	306 if view['init']['assembly'] == assembly["name"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	307 default_seq = view['init']['loc'].split(":")[0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	308 if "views" in view:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	309 subviews = view["views"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	310 for subview in subviews:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	311 if 'init' in subview and 'assembly' in subview['init'] and 'loc' in subview['init']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	312 if subview['init']['assembly'] == assembly["name"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	313 default_seq = subview['init']['loc'].split(":")[0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	314
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	315 self.assembly_ids[assembly["name"]] = default_seq
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	316
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	317 def _load_old_genome_views(self):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	318
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	319 views = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	320
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	321 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	322 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	323 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	324
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	325 # Find default synteny views existing from a previous jbrowse dataset
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	326 if 'defaultSession' in config_json and 'views' in config_json['defaultSession']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	327 for view in config_json['defaultSession']['views']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	328 if view['type'] != "LinearSyntenyView":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	329 if 'init' in view and 'assembly' in view['init']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	330 views[view['init']['assembly']] = view
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	331
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	332 return views
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	333
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	334 def _load_old_synteny_views(self):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	335
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	336 views = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	337
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	338 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	339 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	340 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	341
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	342 # Find default synteny views existing from a previous jbrowse dataset
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	343 if 'defaultSession' in config_json and 'views' in config_json['defaultSession']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	344 for view in config_json['defaultSession']['views']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	345 if view['type'] == "LinearSyntenyView":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	346 views.append(view)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	347
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	348 return views
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	349
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	350 def add_assembly(self, path, label, is_remote=False, cytobands=None, ref_name_aliases=None):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	351
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	352 if not is_remote:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	353 # Find a non-existing filename for the new genome
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	354 # (to avoid colision when upgrading an existing instance)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	355 rel_seq_path = os.path.join("data", label)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	356 seq_path = os.path.join(self.outdir, rel_seq_path)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	357 fn_try = 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	358 while (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	359 os.path.exists(seq_path + ".fasta")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	360 or os.path.exists(seq_path + ".fasta.gz")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	361 or os.path.exists(seq_path + ".fasta.gz.fai")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	362 or os.path.exists(seq_path + ".fasta.gz.gzi")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	363 ):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	364 rel_seq_path = os.path.join("data", f"{label}{fn_try}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	365 seq_path = os.path.join(self.outdir, rel_seq_path)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	366 fn_try += 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	367
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	368 # Check if the assembly already exists from a previous run (--update mode)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	369 if self.update:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	370
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	371 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	372 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	373 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	374
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	375 for asby in config_json['assemblies']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	376 if asby['name'] == label:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	377
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	378 # Find default views existing for this assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	379 if 'defaultSession' in config_json and 'views' in config_json['defaultSession']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	380 for view in config_json['defaultSession']['views']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	381 if 'init' in view and 'assembly' in view['init']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	382 if view['init']['assembly'] == label:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	383
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	384 log.info("Found existing assembly from existing JBrowse2 instance, preserving it")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	385
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	386 self.default_views[view['init']['assembly']] = view
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	387
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	388 return label
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	389
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	390 # Copy ref alias file if any
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	391 if ref_name_aliases:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	392 copied_ref_name_aliases = seq_path + ".aliases"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	393 shutil.copy(ref_name_aliases, copied_ref_name_aliases)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	394 copied_ref_name_aliases = rel_seq_path + ".aliases"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	395
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	396 # Copy cytobands file if any
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	397 if cytobands:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	398 copied_cytobands = seq_path + ".cytobands"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	399 shutil.copy(cytobands, copied_cytobands)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	400 copied_cytobands = rel_seq_path + ".cytobands"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	401
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	402 # Find a non-existing label for the new genome
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	403 # (to avoid colision when upgrading an existing instance)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	404 lab_try = 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	405 uniq_label = label
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	406 while uniq_label in self.assembly_ids:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	407 uniq_label = label + str(lab_try)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	408 lab_try += 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	409
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	410 if is_remote:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	411
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	412 # Find a default scaffold to display
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	413 with requests.get(path + ".fai", stream=True) as response:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	414 response.raise_for_status()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	415 first_seq = next(response.iter_lines())
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	416 first_seq = first_seq.decode("utf-8").split('\t')[0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	417
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	418 self.assembly_ids[uniq_label] = first_seq
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	419
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	420 # We assume we just need to suffix url with .fai and .gzi for indexes.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	421 cmd_jb = [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	422 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	423 "add-assembly",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	424 "--name",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	425 uniq_label,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	426 "--type",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	427 "bgzipFasta",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	428 "--out",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	429 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	430 "--skipCheck",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	431 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	432
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	433 if ref_name_aliases:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	434 cmd_jb.extend([
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	435 "--refNameAliases",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	436 copied_ref_name_aliases,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	437 ])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	438
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	439 cmd_jb.append(path) # Path is an url in remote mode
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	440
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	441 self.subprocess_check_call(cmd_jb)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	442 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	443 # Find a default scaffold to display
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	444 with open(path, "r") as fa_handle:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	445 fa_header = fa_handle.readline()[1:].strip().split(" ")[0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	446
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	447 self.assembly_ids[uniq_label] = fa_header
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	448
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	449 copied_genome = seq_path + ".fasta"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	450 shutil.copy(path, copied_genome)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	451
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	452 # Compress with bgzip
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	453 cmd = ["bgzip", copied_genome]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	454 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	455
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	456 # FAI Index
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	457 cmd = ["samtools", "faidx", copied_genome + ".gz"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	458 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	459
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	460 cmd_jb = [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	461 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	462 "add-assembly",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	463 "--load",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	464 "inPlace",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	465 "--name",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	466 uniq_label,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	467 "--type",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	468 "bgzipFasta",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	469 "--out",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	470 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	471 "--skipCheck",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	472 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	473
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	474 if ref_name_aliases:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	475 cmd_jb.extend([
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	476 "--refNameAliases",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	477 copied_ref_name_aliases,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	478 ])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	479
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	480 cmd_jb.append(rel_seq_path + ".fasta.gz")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	481
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	482 self.subprocess_check_call(cmd_jb)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	483
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	484 if cytobands:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	485 self.add_cytobands(uniq_label, copied_cytobands)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	486
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	487 return uniq_label
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	488
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	489 def add_cytobands(self, assembly_name, cytobands_path):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	490
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	491 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	492 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	493 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	494
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	495 config_data = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	496
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	497 config_data["cytobands"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	498 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	499 "type": "CytobandAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	500 "cytobandLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	501 "uri": cytobands_path
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	502 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	503 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	504 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	505
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	506 filled_assemblies = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	507 for assembly in config_json["assemblies"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	508 if assembly["name"] == assembly_name:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	509 assembly.update(config_data)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	510 filled_assemblies.append(assembly)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	511 config_json["assemblies"] = filled_assemblies
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	512
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	513 with open(config_path, "w") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	514 json.dump(config_json, config_file, indent=2)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	515
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	516 def text_index(self):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	517
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	518 for ass in self.tracksToIndex:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	519 tracks = self.tracksToIndex[ass]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	520 args = [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	521 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	522 "text-index",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	523 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	524 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	525 "--assemblies",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	526 ass,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	527 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	528
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	529 tracks = ",".join(tracks)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	530 if tracks:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	531 args += ["--tracks", tracks]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	532
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	533 log.info(f"-----> Running text-index on assembly {ass} and tracks {tracks}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	534
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	535 # Only run index if we want to index at least one
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	536 # If --tracks is not specified, it will index everything
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	537 self.subprocess_check_call(args)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	538
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	539 def add_gc_content(self, parent, trackData, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	540
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	541 adapter = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	542 existing = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	543 if os.path.exists(existing):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	544 with open(existing, "r") as existing_conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	545 conf = json.load(existing_conf)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	546 if "assemblies" in conf:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	547 for assembly in conf["assemblies"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	548 if assembly.get('name', "") == parent['uniq_id']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	549 adapter = assembly.get('sequence', {}).get('adapter', {})
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	550
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	551 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	552 "type": "GCContentTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	553 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	554 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	555 "adapter": adapter,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	556 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	557 "assemblyNames": [parent['uniq_id']],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	558 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	559
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	560 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	561
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	562 json_track_data.update(style_json)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	563
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	564 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	565 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	566 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	567 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	568 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	569 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	570 json.dumps(json_track_data),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	571 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	572 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	573
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	574 def add_bigwig(self, parent, data, trackData, wiggleOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	575
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	576 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	577 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	578 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	579 rel_dest = os.path.join("data", trackData["label"] + ".bw")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	580 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	581 self.symlink_or_copy(os.path.realpath(data), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	582
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	583 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	584
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	585 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	586
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	587 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	588
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	589 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	590 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	591 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	592 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	593 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	594 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	595 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	596 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	597 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	598
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	599 def add_bigwig_multi(self, parent, data_files, trackData, wiggleOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	600
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	601 subadapters = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	602
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	603 sub_num = 0
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	604 for data in data_files:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	605 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	606 rel_dest = data[1]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	607 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	608 rel_dest = os.path.join("data", f"{trackData['label']}_sub{sub_num}.bw")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	609 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	610 self.symlink_or_copy(os.path.realpath(data[1]), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	611
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	612 subadapters.append({
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	613 "type": "BigWigAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	614 "name": data[0],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	615 "bigWigLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	616 "uri": rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	617 "locationType": "UriLocation"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	618 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	619 })
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	620 sub_num += 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	621
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	622 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	623 "type": "MultiQuantitativeTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	624 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	625 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	626 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	627 "type": "MultiWiggleAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	628 "subadapters": subadapters
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	629 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	630 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	631 "assemblyNames": [parent['uniq_id']],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	632 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	633
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	634 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	635
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	636 json_track_data.update(style_json)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	637
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	638 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	639
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	640 json_track_data.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	641
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	642 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	643 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	644 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	645 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	646 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	647 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	648 json.dumps(json_track_data),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	649 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	650 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	651
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	652 # Anything ending in "am" (Bam or Cram)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	653 def add_xam(self, parent, data, trackData, xamOpts, index=None, ext="bam", **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	654 index_ext = "bai"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	655 if ext == "cram":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	656 index_ext = "crai"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	657
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	658 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	659 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	660 # Index will be set automatically as xam url + xai .suffix by add-track cmd
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	661 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	662 rel_dest = os.path.join("data", trackData["label"] + f".{ext}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	663 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	664 self.symlink_or_copy(os.path.realpath(data), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	665
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	666 if index is not None and os.path.exists(os.path.realpath(index)):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	667 # xai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	668 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	669 ["cp", os.path.realpath(index), dest + f".{index_ext}"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	670 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	671 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	672 # Can happen in exotic condition
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	673 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	674 # => no index generated by galaxy, but there might be one next to the symlink target
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	675 # this trick allows to skip the bam sorting made by galaxy if already done outside
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	676 if os.path.exists(os.path.realpath(data) + f".{index_ext}"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	677 self.symlink_or_copy(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	678 os.path.realpath(data) + f".{index_ext}", dest + f".{index_ext}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	679 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	680 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	681 log.warn(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	682 f"Could not find a bam index (.{index_ext} file) for {data}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	683 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	684
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	685 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	686
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	687 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	688
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	689 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	690
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	691 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	692 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	693 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	694 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	695 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	696 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	697 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	698 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	699 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	700
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	701 def add_vcf(self, parent, data, trackData, vcfOpts={}, zipped=False, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	702 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	703 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	704 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	705 if zipped:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	706 rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	707 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	708 shutil.copy(os.path.realpath(data), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	709 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	710 rel_dest = os.path.join("data", trackData["label"] + ".vcf")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	711 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	712 shutil.copy(os.path.realpath(data), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	713
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	714 cmd = ["bgzip", dest]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	715 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	716 cmd = ["tabix", dest + ".gz"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	717 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	718
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	719 rel_dest = os.path.join("data", trackData["label"] + ".vcf.gz")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	720
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	721 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	722
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	723 formatdetails = self._prepare_format_details(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	724
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	725 style_json.update(formatdetails)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	726
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	727 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	728
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	729 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	730
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	731 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	732 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	733 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	734 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	735 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	736 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	737 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	738 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	739 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	740
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	741 def add_gff(self, parent, data, format, trackData, gffOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	742 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	743 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	744 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	745 rel_dest = os.path.join("data", trackData["label"] + ".gff")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	746 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	747 rel_dest = rel_dest + ".gz"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	748
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	749 self._sort_gff(data, dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	750
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	751 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	752
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	753 formatdetails = self._prepare_format_details(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	754
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	755 style_json.update(formatdetails)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	756
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	757 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	758
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	759 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	760
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	761 if gffOpts.get('index', 'false') in ("yes", "true", "True"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	762 if parent['uniq_id'] not in self.tracksToIndex:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	763 self.tracksToIndex[parent['uniq_id']] = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	764 self.tracksToIndex[parent['uniq_id']].append(trackData["label"])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	765
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	766 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	767 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	768 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	769 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	770 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	771 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	772 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	773 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	774 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	775
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	776 def add_bed(self, parent, data, format, trackData, gffOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	777 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	778 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	779 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	780 rel_dest = os.path.join("data", trackData["label"] + ".bed")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	781 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	782 rel_dest = rel_dest + ".gz"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	783
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	784 self._sort_bed(data, dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	785
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	786 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	787
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	788 formatdetails = self._prepare_format_details(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	789
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	790 style_json.update(formatdetails)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	791
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	792 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	793
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	794 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	795
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	796 if gffOpts.get('index', 'false') in ("yes", "true", "True"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	797 if parent['uniq_id'] not in self.tracksToIndex:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	798 self.tracksToIndex[parent['uniq_id']] = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	799 self.tracksToIndex[parent['uniq_id']].append(trackData["label"])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	800
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	801 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	802 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	803 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	804 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	805 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	806 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	807 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	808 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	809 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	810
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	811 def add_paf(self, parent, data, trackData, pafOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	812
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	813 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	814 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	815
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	816 if rel_dest.endswith('pif') or rel_dest.endswith('pif.gz'):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	817 adapter = "pif"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	818 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	819 adapter = "paf"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	820 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	821 rel_dest = os.path.join("data", trackData["label"] + ".pif.gz")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	822 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	823
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	824 cmd = ["jbrowse", "make-pif", "--out", dest, os.path.realpath(data)]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	825 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	826
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	827 adapter = "pif"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	828
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	829 if trackData["style"]["display"] == "LinearBasicDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	830 # Normal style track
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	831
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	832 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	833 "type": "SyntenyTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	834 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	835 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	836 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	837 "type": "PairwiseIndexedPAFAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	838 "pifGzLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	839 "uri": rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	840 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	841 "index": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	842 "location": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	843 "uri": rel_dest + ".tbi",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	844 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	845 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	846 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	847 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	848 "assemblyNames": [parent['uniq_id']],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	849 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	850 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	851 # Synteny viewer
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	852
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	853 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	854 "type": "SyntenyTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	855 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	856 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	857 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	858 "assemblyNames": [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	859 parent['uniq_id'],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	860 "", # Placeholder until we know the next genome id
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	861 ],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	862 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	863 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	864 "assemblyNames": [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	865 parent['uniq_id'],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	866 "", # Placeholder until we know the next genome id
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	867 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	868 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	869
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	870 if adapter == "pif":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	871 json_track_data["adapter"].update({
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	872 "type": "PairwiseIndexedPAFAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	873 "pifGzLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	874 "uri": rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	875 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	876 "index": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	877 "location": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	878 "uri": rel_dest + ".tbi",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	879 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	880 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	881 })
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	882 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	883 json_track_data["adapter"].update({
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	884 "type": "PAFAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	885 "pafLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	886 "uri": rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	887 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	888 })
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	889
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	890 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	891
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	892 json_track_data.update(style_json)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	893
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	894 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	895
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	896 json_track_data.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	897
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	898 if trackData["style"]["display"] == "LinearBasicDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	899 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	900 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	901 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	902 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	903 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	904 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	905 json.dumps(json_track_data),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	906 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	907 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	908 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	909 self.synteny_tracks.append(json_track_data)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	910
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	911 def add_hic(self, parent, data, trackData, hicOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	912 if trackData['remote']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	913 rel_dest = data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	914 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	915 rel_dest = os.path.join("data", trackData["label"] + ".hic")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	916 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	917 self.symlink_or_copy(os.path.realpath(data), dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	918
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	919 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	920
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	921 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	922
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	923 style_json.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	924
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	925 self._add_track(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	926 trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	927 trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	928 trackData["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	929 rel_dest,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	930 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	931 config=style_json,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	932 remote=trackData['remote']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	933 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	934
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	935 def add_maf(self, parent, data, trackData, mafOpts, **kwargs):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	936
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	937 # Add needed plugin
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	938 plugin_def = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	939 "name": "MafViewer",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	940 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	941 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	942 self.plugins.append(plugin_def)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	943
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	944 rel_dest = os.path.join("data", trackData["label"] + ".maf")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	945 dest = os.path.join(self.outdir, rel_dest)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	946
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	947 assembly_name = mafOpts.get("assembly_name", "")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	948 if not assembly_name:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	949 # Guess from assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	950 assembly_name = parent['uniq_id']
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	951
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	952 self._convert_maf(data, dest, assembly_name)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	953
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	954 # Extract samples list
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	955 mafs = open(data, "r").readlines()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	956 mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	957 samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	958 sampu = list(dict.fromkeys(samp))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	959 samples = [x.split(".")[0] for x in sampu]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	960 samples.sort()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	961
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	962 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	963 "type": "MafTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	964 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	965 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	966 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	967 "type": "MafTabixAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	968 "samples": samples,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	969 "bedGzLocation": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	970 "uri": rel_dest + ".gz",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	971 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	972 "index": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	973 "location": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	974 "uri": rel_dest + ".gz.tbi",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	975 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	976 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	977 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	978 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	979 "assemblyNames": [parent['uniq_id']],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	980 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	981
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	982 style_json = self._prepare_track_style(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	983
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	984 json_track_data.update(style_json)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	985
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	986 track_metadata = self._prepare_track_metadata(trackData)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	987
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	988 json_track_data.update(track_metadata)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	989
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	990 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	991 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	992 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	993 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	994 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	995 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	996 json.dumps(json_track_data),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	997 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	998 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	999
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1000 def add_sparql(self, parent, url, query, query_refnames, trackData):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1001 json_track_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1002 "type": "FeatureTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1003 "trackId": trackData["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1004 "name": trackData["key"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1005 "adapter": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1006 "type": "SPARQLAdapter",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1007 "endpoint": {"uri": url, "locationType": "UriLocation"},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1008 "queryTemplate": query,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1009 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1010 "category": [trackData["category"]],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1011 "assemblyNames": [parent['uniq_id']],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1012 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1013
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1014 if query_refnames:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1015 json_track_data["adapter"]["refNamesQueryTemplate"]: query_refnames
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1016
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1017 # TODO handle metadata somehow for sparql too
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1018
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1019 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1020 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1021 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1022 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1023 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1024 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1025 json.dumps(json_track_data),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1026 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1027 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1028
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1029 def _add_track(self, track_id, label, category, path, assembly, config=None, trackType=None, load_action="inPlace", assemblies=None, remote=False):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1030 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1031 Adds a track to config.json using Jbrowse add-track cli
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1032
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1033 By default, using `--load inPlace`: the file is supposed to be already placed at the `path` relative to
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1034 the outdir, `jbrowse add-track` will not touch it and trust us that the file is there and ready to use.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1035
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1036 With `load_action` parameter, you can ask `jbrowse add-track` to copy/move/symlink the file for you.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1037 Not done by default because we often need more control on file copying/symlink for specific cases (indexes, symlinks of symlinks, ...)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1038 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1039
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1040 cmd = [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1041 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1042 "add-track",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1043 "--name",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1044 label,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1045 "--category",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1046 category,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1047 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1048 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1049 "--trackId",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1050 track_id,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1051 "--assemblyNames",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1052 assemblies if assemblies else assembly['uniq_id'],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1053 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1054
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1055 if not remote:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1056 cmd.append("--load")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1057 cmd.append(load_action)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1058
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1059 if config:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1060 cmd.append("--config")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1061 cmd.append(json.dumps(config))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1062
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1063 if trackType:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1064 cmd.append("--trackType")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1065 cmd.append(trackType)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1066
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1067 cmd.append(path)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1068
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1069 self.subprocess_check_call(cmd)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1070
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1071 def _sort_gff(self, data, dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1072 # Only index if not already done
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1073 if not os.path.exists(dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1074 # Not using jbrowse sort-gff because it uses sort and has the problem exposed on https://github.com/tao-bioinfo/gff3sort
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1075 cmd = f"gff3sort.pl --precise '{data}' \| grep -v \"^$\" > '{dest}'"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1076 self.subprocess_popen(cmd, cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1077
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1078 self.subprocess_check_call(["bgzip", "-f", dest], cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1079 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest + ".gz"], cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1080
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1081 def _sort_bed(self, data, dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1082 # Only index if not already done
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1083 if not os.path.exists(dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1084 cmd = ["sort", "-k1,1", "-k2,2n", data]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1085 with open(dest, "w") as handle:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1086 self.subprocess_check_call(cmd, output=handle)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1087
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1088 self.subprocess_check_call(["bgzip", "-f", dest])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1089 self.subprocess_check_call(["tabix", "-f", "-p", "bed", dest + ".gz"])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1090
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1091 def _convert_maf(self, data, dest, assembly_name):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1092 # Only convert if not already done
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1093 if not os.path.exists(dest):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1094
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1095 dest_bed = dest + ".bed"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1096 cmd = ["python", os.path.join(SELF_LOCATION, "maf2bed.py"), assembly_name, data, dest_bed]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1097 self.subprocess_check_call(cmd, cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1098
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1099 cmd = ["sort", "-k1,1", "-k2,2n", dest_bed]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1100 with open(dest, "w") as handle:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1101 self.subprocess_check_call(cmd, output=handle)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1102
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1103 self.subprocess_check_call(["bgzip", "-f", dest], cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1104 self.subprocess_check_call(["tabix", "-f", "-p", "bed", dest + ".gz"], cwd=False)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1105
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1106 def process_annotations(self, track, parent):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1107 category = track["category"].replace("__pd__date__pd__", TODAY)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1108
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1109 track_labels = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1110
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1111 for i, (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1112 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1113 dataset_ext,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1114 track_human_label,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1115 extra_metadata,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1116 ) in enumerate(track["trackfiles"]):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1117 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1118 for key, value in mapped_chars.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1119 track_human_label = track_human_label.replace(value, key)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1120
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1121 is_multi = type(dataset_path) is list
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1122
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1123 log.info(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1124 f"-----> Processing track {category} / {track_human_label} ({dataset_ext}, {len(dataset_path) if is_multi else 1} files)"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1125 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1126
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1127 outputTrackConfig = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1128 "category": category,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1129 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1130
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1131 outputTrackConfig["key"] = track_human_label
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1132 # We add extra data to hash for the case of non-file tracks
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1133 if (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1134 "conf" in track
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1135 and "options" in track["conf"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1136 and "url" in track["conf"]["options"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1137 ):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1138 non_file_info = track["conf"]["options"]["url"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1139 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1140 non_file_info = ""
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1141
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1142 # I chose to use track['category'] instead of 'category' here. This
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1143 # is intentional. This way re-running the tool on a different date
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1144 # will not generate different hashes and make comparison of outputs
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1145 # much simpler.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1146 hashData = [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1147 str(dataset_path),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1148 track_human_label,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1149 track["category"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1150 non_file_info,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1151 parent["uniq_id"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1152 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1153 hashData = "\|".join(hashData).encode("utf-8")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1154 outputTrackConfig["label"] = hashlib.md5(hashData).hexdigest() + f"_{track['track_num']}_{i}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1155 outputTrackConfig["metadata"] = extra_metadata
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1156
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1157 outputTrackConfig["style"] = track["style"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1158
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1159 outputTrackConfig["formatdetails"] = track["formatdetails"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1160
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1161 outputTrackConfig["remote"] = track["remote"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1162
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1163 # Guess extension for remote data
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1164 if dataset_ext == "gff,gff3,bed":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1165 if dataset_path.endswith(".bed") or dataset_path.endswith(".bed.gz"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1166 dataset_ext = "bed"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1167 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1168 dataset_ext = "gff"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1169 elif dataset_ext == "vcf,vcf_bgzip":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1170 if dataset_path.endswith(".vcf.gz"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1171 dataset_ext = "vcf_bgzip"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1172 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1173 dataset_ext = "vcf"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1174
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1175 if dataset_ext in ("gff", "gff3"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1176 self.add_gff(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1177 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1178 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1179 dataset_ext,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1180 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1181 track["conf"]["options"]["gff"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1182 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1183 elif dataset_ext == "bed":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1184 self.add_bed(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1185 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1186 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1187 dataset_ext,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1188 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1189 track["conf"]["options"]["gff"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1190 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1191 elif dataset_ext == "bigwig":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1192 if is_multi:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1193 self.add_bigwig_multi(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1194 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1195 dataset_path, outputTrackConfig, track["conf"]["options"]["wiggle"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1196 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1197 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1198 self.add_bigwig(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1199 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1200 dataset_path, outputTrackConfig, track["conf"]["options"]["wiggle"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1201 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1202 elif dataset_ext == "maf":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1203 self.add_maf(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1204 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1205 dataset_path, outputTrackConfig, track["conf"]["options"]["maf"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1206 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1207 elif dataset_ext == "bam":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1208
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1209 if track["remote"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1210 bam_index = dataset_path + '.bai'
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1211 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1212 real_indexes = track["conf"]["options"]["pileup"]["bam_indices"][
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1213 "bam_index"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1214 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1215 if not isinstance(real_indexes, list):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1216 # <bam_indices>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1217 # <bam_index>/path/to/a.bam.bai</bam_index>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1218 # </bam_indices>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1219 #
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1220 # The above will result in the 'bam_index' key containing a
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1221 # string. If there are two or more indices, the container
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1222 # becomes a list. Fun!
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1223 real_indexes = [real_indexes]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1224
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1225 bam_index = real_indexes[i]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1226
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1227 self.add_xam(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1228 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1229 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1230 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1231 track["conf"]["options"]["pileup"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1232 index=bam_index,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1233 ext="bam",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1234 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1235 elif dataset_ext == "cram":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1236
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1237 if track["remote"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1238 cram_index = dataset_path + '.crai'
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1239 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1240 real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1241 "cram_index"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1242 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1243 if not isinstance(real_indexes, list):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1244 # <bam_indices>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1245 # <bam_index>/path/to/a.bam.bai</bam_index>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1246 # </bam_indices>
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1247 #
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1248 # The above will result in the 'bam_index' key containing a
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1249 # string. If there are two or more indices, the container
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1250 # becomes a list. Fun!
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1251 real_indexes = [real_indexes]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1252
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1253 cram_index = real_indexes[i]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1254
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1255 self.add_xam(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1256 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1257 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1258 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1259 track["conf"]["options"]["cram"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1260 index=cram_index,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1261 ext="cram",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1262 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1263 elif dataset_ext == "vcf":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1264 self.add_vcf(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1265 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1266 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1267 outputTrackConfig
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1268 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1269 elif dataset_ext == "vcf_bgzip":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1270 self.add_vcf(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1271 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1272 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1273 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1274 zipped=True
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1275 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1276 elif dataset_ext == "paf": # https://fr.wikipedia.org/wiki/Paf_le_chien
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1277 self.add_paf(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1278 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1279 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1280 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1281 track["conf"]["options"]["synteny"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1282 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1283 elif dataset_ext in ("hic"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1284 self.add_hic(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1285 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1286 dataset_path,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1287 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1288 track["conf"]["options"]["hic"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1289 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1290 elif dataset_ext == "sparql":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1291 sparql_query = track["conf"]["options"]["sparql"]["query"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1292 for key, value in mapped_chars.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1293 sparql_query = sparql_query.replace(value, key)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1294 sparql_query_refnames = track["conf"]["options"]["sparql"].get("query_refnames", "")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1295 if sparql_query_refnames:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1296 for key, value in mapped_chars.items():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1297 sparql_query_refnames = sparql_query_refnames.replace(value, key)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1298 self.add_sparql(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1299 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1300 track["conf"]["options"]["sparql"]["url"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1301 sparql_query,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1302 sparql_query_refnames,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1303 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1304 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1305 elif dataset_ext == "gc":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1306 self.add_gc_content(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1307 parent,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1308 outputTrackConfig,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1309 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1310 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1311 log.error(f"Do not know how to handle {dataset_ext}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1312
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1313 track_labels.append(outputTrackConfig["label"])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1314
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1315 # Return non-human label for use in other fields
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1316 return track_labels
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1317
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1318 def add_default_view_genome(self, genome, default_loc, tracks_on):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1319
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1320 refName = ""
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1321 start = end = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1322 if default_loc:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1323 loc_match = re.search(r"^(\w+):(\d+)\.+(\d+)$", default_loc)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1324 if loc_match:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1325 refName = loc_match.group(1)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1326 start = int(loc_match.group(2))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1327 end = int(loc_match.group(3))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1328
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1329 if not refName and self.assembly_ids[genome['uniq_id']]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1330 refName = self.assembly_ids[genome['uniq_id']]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1331
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1332 if start and end:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1333 loc_str = f"{refName}:{start}-{end}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1334 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1335 loc_str = refName
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1336
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1337 # Updating an existing jbrowse instance, merge with pre-existing view
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1338 view_specs = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1339 if self.update:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1340 for existing in self.default_views.values():
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1341 if len(existing) and existing["type"] == "LinearGenomeView":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1342 if existing['init']['assembly'] == genome['uniq_id']:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1343 view_specs = existing
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1344 if loc_str:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1345 view_specs['init']['loc'] = loc_str
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1346 view_specs['init']['tracks'].extend(tracks_on)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1347
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1348 if view_specs is None: # Not updating, or updating from synteny
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1349 view_specs = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1350 "type": "LinearGenomeView",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1351 "init": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1352 "assembly": genome['uniq_id'],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1353 "loc": loc_str,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1354 "tracks": tracks_on
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1355 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1356 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1357
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1358 return view_specs
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1359
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1360 def add_default_view_synteny(self, genome_views, synteny_tracks):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1361
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1362 # Add json for cached synteny tracks
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1363 # We cache them because we need to know the target genome uniq_id
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1364 for strack in synteny_tracks:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1365
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1366 # Target assembly is the next genome, find its uniq_id
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1367 query_assembly = strack["assemblyNames"][0]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1368 ass_uniq_ids = list(self.assembly_ids.keys())
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1369 query_index = ass_uniq_ids.index(query_assembly)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1370 target_assembly = ass_uniq_ids[query_index + 1]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1371
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1372 strack["assemblyNames"][1] = target_assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1373 strack["adapter"]["assemblyNames"][1] = target_assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1374
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1375 self.subprocess_check_call(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1376 [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1377 "jbrowse",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1378 "add-track-json",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1379 "--target",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1380 self.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1381 json.dumps(strack),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1382 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1383 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1384
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1385 # Configure the synteny view
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1386 levels = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1387
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1388 for strack in synteny_tracks:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1389 lev = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1390 "type": "LinearSyntenyViewHelper",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1391 "tracks": [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1392 {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1393 "type": "SyntenyTrack",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1394 "configuration": strack["trackId"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1395 "displays": [
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1396 {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1397 "type": "LinearSyntenyDisplay",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1398 "configuration": strack["trackId"] + "_LinearSyntenyDisplay"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1399 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1400 ]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1401 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1402 ],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1403 "height": 100,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1404 "level": len(levels)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1405 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1406 levels.append(lev)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1407
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1408 view_specs = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1409 "type": "LinearSyntenyView",
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1410 "views": genome_views,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1411 "levels": levels
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1412 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1413
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1414 return view_specs
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1415
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1416 def add_default_session(self, default_views):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1417 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1418 Add some default session settings: set some assemblies/tracks on/off
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1419
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1420 This allows to select a default view:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1421 - jb type (Linear, Circular, etc)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1422 - default location on an assembly
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1423 - default tracks
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1424 - ...
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1425
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1426 Now using this method:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1427 https://github.com/GMOD/jbrowse-components/pull/4907
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1428
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1429 Different methods that were tested/discussed earlier:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1430 - using a defaultSession item in config.json before PR 4970: this proved to be difficult:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1431 forced to write a full session block, including hard-coded/hard-to-guess items,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1432 no good way to let Jbrowse2 display a scaffold without knowing its size
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1433 - using JBrowse2 as an embedded React component in a tool-generated html file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1434 it works but it requires generating js code to actually do what we want = chosing default view, assembly, tracks, ...
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1435 - writing a session-spec inside the config.json file: this is not yet supported as of 2.10.2 (see PR 4148 below)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1436 a session-spec is a kind of simplified defaultSession where you don't need to specify every aspect of the session
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1437 - passing a session-spec through URL params by embedding the JBrowse2 index.html inside an iframe
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1438
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1439 Xrefs to understand the choices:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1440 https://github.com/GMOD/jbrowse-components/issues/2708
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1441 https://github.com/GMOD/jbrowse-components/discussions/3568
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1442 https://github.com/GMOD/jbrowse-components/pull/4148
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1443 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1444
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1445 if self.use_synteny_viewer:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1446 session_name = "Synteny"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1447 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1448 session_name = ', '.join(x['init']['assembly'] for x in default_views)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1449
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1450 session_spec = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1451 "name": session_name,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1452 "views": default_views
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1453 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1454
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1455 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1456 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1457 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1458
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1459 config_json["defaultSession"].update(session_spec)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1460
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1461 with open(config_path, "w") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1462 json.dump(config_json, config_file, indent=2)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1463
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1464 def add_general_configuration(self, data):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1465 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1466 Add some general configuration to the config.json file
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1467 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1468
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1469 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1470 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1471 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1472
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1473 config_data = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1474
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1475 config_data["disableAnalytics"] = data.get("analytics", "false") == "true"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1476
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1477 config_data["theme"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1478 "palette": {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1479 "primary": {"main": data.get("primary_color", "#0D233F")},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1480 "secondary": {"main": data.get("secondary_color", "#721E63")},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1481 "tertiary": {"main": data.get("tertiary_color", "#135560")},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1482 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1483 },
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1484 "typography": {"fontSize": int(data.get("font_size", 10))},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1485 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1486
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1487 config_json["configuration"].update(config_data)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1488
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1489 with open(config_path, "w") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1490 json.dump(config_json, config_file, indent=2)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1491
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1492 def add_plugins(self, data):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1493 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1494 Add plugins to the config.json file
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1495 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1496
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1497 config_path = os.path.join(self.outdir, "config.json")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1498 with open(config_path, "r") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1499 config_json = json.load(config_file)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1500
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1501 if "plugins" not in config_json:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1502 config_json["plugins"] = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1503
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1504 config_json["plugins"].extend(data)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1505
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1506 with open(config_path, "w") as config_file:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1507 json.dump(config_json, config_file, indent=2)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1508
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1509 def clone_jbrowse(self, jbrowse_dir, destination):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1510 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1511 Clone a JBrowse directory into a destination directory.
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1512
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1513 Not using `jbrowse create` command to allow running on internet-less compute + to make sure code is frozen
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1514 """
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1515
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1516 copytree(jbrowse_dir, destination)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1517 try:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1518 shutil.rmtree(os.path.join(destination, "test_data"))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1519 except OSError as e:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1520 log.error(f"Error: {e.filename} - {e.strerror}.")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1521
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1522 if not os.path.exists(os.path.join(destination, "data")):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1523 # It can already exist if upgrading an instance
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1524 os.makedirs(os.path.join(destination, "data"))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1525 log.info(f"makedir {os.path.join(destination, 'data')}")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1526
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1527 os.symlink("./data/config.json", os.path.join(destination, "config.json"))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1528
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1529
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1530 def copytree(src, dst, symlinks=False, ignore=None):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1531 for item in os.listdir(src):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1532 s = os.path.join(src, item)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1533 d = os.path.join(dst, item)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1534 if os.path.isdir(s):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1535 shutil.copytree(s, d, symlinks, ignore)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1536 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1537 shutil.copy2(s, d)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1538
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1539
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1540 def parse_style_conf(item):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1541 if "type" in item.attrib and item.attrib["type"] in ["boolean", "integer"]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1542 if item.attrib["type"] == "boolean":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1543 return item.text in ("yes", "true", "True")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1544 elif item.attrib["type"] == "integer":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1545 return int(item.text)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1546 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1547 return item.text
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1548
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1549
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1550 def validate_synteny(real_root):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1551
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1552 if len(real_root.findall('assembly/tracks/track[@format="synteny"]')) == 0:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1553 # No synteny data, all good
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1554 return False
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1555
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1556 assemblies = real_root.findall("assembly")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1557
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1558 if len(assemblies[-1].findall('tracks/track[@format="synteny"]')) > 0 and \
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1559 assemblies[-1].find('tracks/track[@format="synteny"]/options/style/display').text == "LinearSyntenyDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1560 raise RuntimeError("You should not set a synteny track on the last genome.")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1561
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1562 for assembly in assemblies[1:0]:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1563 if len(assembly.findall('tracks/track[@format="synteny"]')) != 1 and \
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1564 assembly.find('tracks/track[@format="synteny"]/options/style/display').text == "LinearSyntenyDisplay":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1565 raise RuntimeError("To use the synteny viewer, you should add a synteny track to each assembly, except the last one.")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1566
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1567 return True
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1568
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1569
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1570 if __name__ == "__main__":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1571 parser = argparse.ArgumentParser(description="", epilog="")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1572 parser.add_argument("xml", type=argparse.FileType("r"), help="Track Configuration")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1573
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1574 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1575 parser.add_argument("--update", help="Update an existing JBrowse2 instance", action="store_true")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1576 parser.add_argument("--outdir", help="Output directory", default="out")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1577 args = parser.parse_args()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1578
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1579 tree = ET.parse(args.xml.name)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1580 real_root = tree.getroot()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1581
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1582 # This should be done ASAP
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1583 # Sometimes this comes as `localhost` without a protocol
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1584 GALAXY_INFRASTRUCTURE_URL = real_root.find("metadata/galaxyUrl").text
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1585 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1586 # so we'll prepend `http://` and hope for the best. Requests should
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1587 # be GET and not POST so it should redirect OK
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1588 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1589
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1590 jc = JbrowseConnector(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1591 jbrowse=args.jbrowse,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1592 outdir=args.outdir,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1593 update=args.update,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1594 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1595
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1596 # Synteny options are special, check them first
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1597 jc.use_synteny_viewer = validate_synteny(real_root)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1598
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1599 for assembly in real_root.findall("assembly"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1600 genome_el = assembly.find('genome')
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1601
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1602 is_remote = genome_el.attrib.get("remote", "false") == "true"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1603
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1604 genome = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1605 "path": genome_el.attrib["path"] if is_remote else os.path.realpath(genome_el.attrib["path"]),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1606 "meta": metadata_from_node(genome_el.find("metadata")),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1607 "label": genome_el.attrib["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1608 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1609
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1610 cytobands = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1611 cytobands_el = genome_el.find("cytobands")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1612 if cytobands_el is not None and "path" in cytobands_el.attrib:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1613 cytobands = cytobands_el.attrib["path"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1614
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1615 ref_name_aliases = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1616 ref_name_aliases_el = genome_el.find("ref_name_aliases")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1617 if ref_name_aliases_el is not None and "path" in ref_name_aliases_el.attrib:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1618 ref_name_aliases = ref_name_aliases_el.attrib["path"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1619
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1620 log.debug("Processing genome", genome)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1621 genome["uniq_id"] = jc.add_assembly(genome["path"], genome["label"], is_remote, cytobands, ref_name_aliases)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1622
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1623 default_tracks_on = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1624
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1625 track_num = 0
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1626 for track in assembly.findall("tracks/track"):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1627 track_conf = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1628 track_conf["trackfiles"] = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1629 track_conf["track_num"] = track_num
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1630
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1631 trackfiles = track.findall("files/trackFile") or []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1632
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1633 is_multi = False
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1634 multi_paths = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1635 multi_type = None
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1636 multi_metadata = {}
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1637 try:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1638 multi_in_xml = track.find("options/multitrack")
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1639 if multi_in_xml is not None and parse_style_conf(multi_in_xml):
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1640 is_multi = True
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1641 multi_paths = []
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1642 multi_type = trackfiles[0].attrib["ext"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1643 except KeyError:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1644 pass
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1645
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1646 is_remote = False
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1647 if trackfiles:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1648 for x in trackfiles:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1649 if is_multi:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1650 is_remote = x.attrib.get("remote", "false") == "true"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1651 multi_paths.append(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1652 (x.attrib["label"], x.attrib["path"] if is_remote else os.path.realpath(x.attrib["path"]))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1653 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1654 multi_metadata.update(metadata_from_node(x.find("metadata")))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1655 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1656 metadata = metadata_from_node(x.find("metadata"))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1657 is_remote = x.attrib.get("remote", "false") == "true"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1658 track_conf["trackfiles"].append(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1659 (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1660 x.attrib["path"] if is_remote else os.path.realpath(x.attrib["path"]),
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1661 x.attrib["ext"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1662 x.attrib["label"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1663 metadata,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1664 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1665 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1666 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1667 # For tracks without files (sparql, gc)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1668 track_conf["trackfiles"].append(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1669 (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1670 "", # N/A, no path for sparql or gc
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1671 track.attrib["format"],
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1672 track.find("options/label").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1673 {},
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1674 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1675 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1676
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1677 if is_multi:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1678 etal_tracks_nb = len(multi_paths[1:])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1679 multi_label = f"{multi_paths[0][0]} + {etal_tracks_nb} other track{'s' if etal_tracks_nb > 1 else ''}"
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1680
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1681 track_conf["trackfiles"].append(
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1682 (
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1683 multi_paths, # Passing an array of paths to represent as one track
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1684 multi_type, # First file type
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1685 multi_label, # First file label
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1686 multi_metadata, # Mix of all metadata for multiple bigwig => only last file metadata coming from galaxy + custom oness
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1687 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1688 )
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1689 track_conf["category"] = track.attrib["cat"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1690 track_conf["format"] = track.attrib["format"]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1691 track_conf["style"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1692 item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1693 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1694
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1695 track_conf["style"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1696 item.tag: parse_style_conf(item) for item in (track.find("options/style") or [])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1697 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1698
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1699 track_conf["style_labels"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1700 item.tag: parse_style_conf(item)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1701 for item in (track.find("options/style_labels") or [])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1702 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1703 track_conf["formatdetails"] = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1704 item.tag: parse_style_conf(item) for item in (track.find("options/formatdetails") or [])
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1705 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1706
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1707 track_conf["conf"] = etree_to_dict(track.find("options"))
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1708
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1709 track_conf["remote"] = is_remote
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1710
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1711 track_labels = jc.process_annotations(track_conf, genome)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1712
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1713 if track.attrib["visibility"] == "default_on":
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1714 for tlabel in track_labels:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1715 default_tracks_on.append(tlabel)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1716
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1717 track_num += 1
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1718
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1719 default_loc = assembly.find("defaultLocation").text
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1720
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1721 jc.default_views[genome['uniq_id']] = jc.add_default_view_genome(genome, default_loc, default_tracks_on)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1722
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1723 if jc.use_synteny_viewer:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1724 synteny_view = jc.add_default_view_synteny(list(jc.default_views.values()), jc.synteny_tracks)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1725
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1726 views_for_session = jc._load_old_synteny_views()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1727
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1728 views_for_session.append(synteny_view)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1729 else:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1730 old_views = jc._load_old_genome_views()
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1731
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1732 for old_view in old_views:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1733 if old_view not in jc.default_views:
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1734 jc.default_views[old_view] = old_views[old_view]
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1735
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1736 views_for_session = list(jc.default_views.values())
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1737
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1738 general_data = {
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1739 "analytics": real_root.find("metadata/general/analytics").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1740 "primary_color": real_root.find("metadata/general/primary_color").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1741 "secondary_color": real_root.find("metadata/general/secondary_color").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1742 "tertiary_color": real_root.find("metadata/general/tertiary_color").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1743 "quaternary_color": real_root.find("metadata/general/quaternary_color").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1744 "font_size": real_root.find("metadata/general/font_size").text,
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1745 }
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1746
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1747 jc.add_default_session(views_for_session)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1748 jc.add_general_configuration(general_data)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1749 jc.add_plugins(jc.plugins)
61add3f58f26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532 iuc parents: diff changeset	1750 jc.text_index()

Mercurial > repos > iuc > jbrowse2

annotate jbrowse2.py @ 0:61add3f58f26 draft default tip