jbrowse: jbrowse.py annotate

annotate jbrowse.py @ 28:d0743cb18ed8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d

author	iuc
date	Fri, 22 Feb 2019 03:20:59 -0500
parents	61ce21e36cb5
children	2bb2e07a7a21

rev	line source
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1 #!/usr/bin/env python
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	2 import argparse
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	3 import binascii
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	4 import copy
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	5 import datetime
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	6 import hashlib
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	7 import json
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	8 import logging
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	9 import os
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	10 import shutil
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	11 import struct
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	12 import subprocess
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	13 import tempfile
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	14 import xml.etree.ElementTree as ET
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	15 from collections import defaultdict
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	16
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	17 from Bio.Data import CodonTable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18 logging.basicConfig(level=logging.INFO)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	19 log = logging.getLogger('jbrowse')
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	21 GALAXY_INFRASTRUCTURE_URL = None
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	22
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	23
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	24 class ColorScaling(object):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	26 COLOR_FUNCTION_TEMPLATE = """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	27 function(feature, variableName, glyphObject, track) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	28 var score = {score};
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	29 {opacity}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	33
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	34 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	35 function(feature, variableName, glyphObject, track) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36 var search_up = function self(sf, attr){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37 if(sf.get(attr) !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38 return sf.get(attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	40 if(sf.parent() === undefined) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	41 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	42 }}else{{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	43 return self(sf.parent(), attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	44 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 }};
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	46
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 var search_down = function self(sf, attr){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	48 if(sf.get(attr) !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	49 return sf.get(attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 if(sf.children() === undefined) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 }}else{{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 var kids = sf.children();
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 for(var child_idx in kids){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 var x = self(kids[child_idx], attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 if(x !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 return x;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	59 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	60 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	62 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 }};
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	64
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 var color = ({user_spec_color} \|\| search_up(feature, 'color') \|\| search_down(feature, 'color') \|\| {auto_gen_color});
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	66 var score = (search_up(feature, 'score') \|\| search_down(feature, 'score'));
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 {opacity}
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	68 if(score === undefined){{ opacity = 1; }}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	70 var red = parseInt(result[1], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	71 var green = parseInt(result[2], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	72 var blue = parseInt(result[3], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	73 if(isNaN(opacity) \|\| opacity < 0){{ opacity = 0; }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	75 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	76 """
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	77
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	78 OPACITY_MATH = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	79 'linear': """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	80 var opacity = (score - ({min})) / (({max}) - ({min}));
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	81 """,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	82 'logarithmic': """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	83 var opacity = (score - ({min})) / (({max}) - ({min}));
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	84 opacity = Math.log10(opacity) + Math.log10({max});
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	85 """,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	86 'blast': """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	87 var opacity = 0;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	88 if(score == 0.0) {{
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	89 opacity = 1;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	90 }} else {{
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	91 opacity = (20 - Math.log10(score)) / 180;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	92 }}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	93 """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	94 }
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	95
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	96 BREWER_COLOUR_IDX = 0
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	97 BREWER_COLOUR_SCHEMES = [
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	98 (166, 206, 227),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	99 (31, 120, 180),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	100 (178, 223, 138),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	101 (51, 160, 44),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	102 (251, 154, 153),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	103 (227, 26, 28),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	104 (253, 191, 111),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	105 (255, 127, 0),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	106 (202, 178, 214),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	107 (106, 61, 154),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	108 (255, 255, 153),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	109 (177, 89, 40),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	110 (228, 26, 28),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	111 (55, 126, 184),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	112 (77, 175, 74),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	113 (152, 78, 163),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	114 (255, 127, 0),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	115 ]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	116
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	117 BREWER_DIVERGING_PALLETES = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	118 'BrBg': ("#543005", "#003c30"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	119 'PiYg': ("#8e0152", "#276419"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 'PRGn': ("#40004b", "#00441b"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 'PuOr': ("#7f3b08", "#2d004b"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	122 'RdBu': ("#67001f", "#053061"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	123 'RdGy': ("#67001f", "#1a1a1a"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	124 'RdYlBu': ("#a50026", "#313695"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	125 'RdYlGn': ("#a50026", "#006837"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	126 'Spectral': ("#9e0142", "#5e4fa2"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	127 }
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	128
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	129 def __init__(self):
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	130 self.brewer_colour_idx = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	131
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	132 def rgb_from_hex(self, hexstr):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	133 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	134 return struct.unpack('BBB', binascii.unhexlify(hexstr))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	135
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	136 def min_max_gff(self, gff_file):
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	137 min_val = None
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	138 max_val = None
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	139 with open(gff_file, 'r') as handle:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	140 for line in handle:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	141 try:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	142 value = float(line.split('\t')[5])
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	143 min_val = min(value, (min_val or value))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	144 max_val = max(value, (max_val or value))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	145
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	146 if value < min_val:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	147 min_val = value
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	148
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	149 if value > max_val:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	150 max_val = value
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	151 except Exception:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	152 pass
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	153 return min_val, max_val
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	154
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	155 def hex_from_rgb(self, r, g, b):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	156 return '#%02x%02x%02x' % (r, g, b)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	157
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	158 def _get_colours(self):
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	159 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	160 self.brewer_colour_idx += 1
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	161 return r, g, b
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	162
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	163 def parse_menus(self, track):
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	164 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	165
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	166 if 'menu' in track['menus']:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	167 menu_list = [track['menus']['menu']]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	168 if isinstance(track['menus']['menu'], list):
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	169 menu_list = track['menus']['menu']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	170
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	171 for m in menu_list:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	172 tpl = {
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	173 'action': m['action'],
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	174 'label': m.get('label', '{name}'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	175 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	176 }
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	177 if 'url' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	178 tpl['url'] = m['url']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	179 if 'content' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	180 tpl['content'] = m['content']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	181 if 'title' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	182 tpl['title'] = m['title']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	183
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	184 trackConfig['menuTemplate'].append(tpl)
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	185
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	186 return trackConfig
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	187
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 def parse_colours(self, track, trackFormat, gff3=None):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 # Wiggle tracks have a bicolor pallete
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 trackConfig = {'style': {}}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191 if trackFormat == 'wiggle':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	196 if trackConfig['style']['pos_color'] == '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	197 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	198 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	199
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	200 # Wiggle tracks can change colour at a specified place
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	201 bc_pivot = track['wiggle']['bicolor_pivot']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	202 if bc_pivot not in ('mean', 'zero'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	203 # The values are either one of those two strings
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	204 # or a number
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	205 bc_pivot = float(bc_pivot)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	206 trackConfig['bicolor_pivot'] = bc_pivot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	207 elif 'scaling' in track:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	208 if track['scaling']['method'] == 'ignore':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	209 if track['scaling']['scheme']['color'] != '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	210 trackConfig['style']['color'] = track['scaling']['scheme']['color']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	211 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	212 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	213 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	214 # Scored method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	215 algo = track['scaling']['algo']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	216 # linear, logarithmic, blast
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	217 scales = track['scaling']['scales']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	218 # type __auto__, manual (min, max)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	219 scheme = track['scaling']['scheme']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	220 # scheme -> (type (opacity), color)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	221 # ==================================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 # GENE CALLS OR BLAST
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	223 # ==================================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 if trackFormat == 'blast':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	225 red, green, blue = self._get_colours()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	226 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	227 'score': "feature._parent.get('score')",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	228 'opacity': self.OPACITY_MATH['blast'],
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	229 'red': red,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	230 'green': green,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	231 'blue': blue,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 trackConfig['style']['color'] = color_function.replace('\n', '')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	234 elif trackFormat == 'gene_calls':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235 # Default values, based on GFF3 spec
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236 min_val = 0
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 max_val = 1000
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	238 # Get min/max and build a scoring function since JBrowse doesn't
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	239 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 min_val, max_val = self.min_max_gff(gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	241 else:
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	242 min_val = scales.get('min', 0)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	243 max_val = scales.get('max', 1000)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	245 if scheme['color'] == '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246 user_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 elif scheme['color'].startswith('#'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	249 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250 auto_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 user_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	255 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	256 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 'user_spec_color': user_color,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 'auto_gen_color': auto_color,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 trackConfig['style']['color'] = color_function.replace('\n', '')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262 return trackConfig
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	264
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	265 def etree_to_dict(t):
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	266 if t is None:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	267 return {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	268
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	269 d = {t.tag: {} if t.attrib else None}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	270 children = list(t)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271 if children:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	272 dd = defaultdict(list)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	273 for dc in map(etree_to_dict, children):
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	274 for k, v in dc.items():
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	275 dd[k].append(v)
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	276 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	277 if t.attrib:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	278 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	279 if t.text:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	280 text = t.text.strip()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	281 if children or t.attrib:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	282 if text:
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	283 d[t.tag]['#text'] = text
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	284 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	285 d[t.tag] = text
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	286 return d
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	287
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	288
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	289 # score comes from feature._parent.get('score') or feature.get('score')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	290
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	291 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	292
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	293
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	294 def metadata_from_node(node):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	295 metadata = {}
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	296 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	297 if len(node.findall('dataset')) != 1:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	298 # exit early
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	299 return metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	300 except Exception:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	301 return {}
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	302
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	303 for (key, value) in node.findall('dataset')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	304 metadata['dataset_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	305
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	306 for (key, value) in node.findall('history')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	307 metadata['history_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	308
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	309 for (key, value) in node.findall('metadata')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	310 metadata['metadata_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	311
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	312 for (key, value) in node.findall('tool')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	313 metadata['tool_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	314
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	315 # Additional Mappings applied:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	316 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	317 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	318 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	319 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	320 encoded_hist_id=metadata['history_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	321 hist_name=metadata['history_display_name']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	322 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	323 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	324 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	325 encoded_id=metadata['dataset_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	326 tool_id=metadata['tool_tool_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	327 tool_version=metadata['tool_tool_version'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	328 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	329 return metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	330
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	331
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	332 class JbrowseConnector(object):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	333
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	334 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	335 self.TN_TABLE = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	336 'gff3': '--gff',
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	337 'gff': '--gff',
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	338 'bed': '--bed',
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	339 'genbank': '--gbk',
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	340 }
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	341
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	342 self.cs = ColorScaling()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	343 self.jbrowse = jbrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	344 self.outdir = outdir
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	345 self.genome_paths = genomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	346 self.standalone = standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	347 self.gencode = gencode
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	348 self.tracksToIndex = []
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	349
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	350 if standalone:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	351 self.clone_jbrowse(self.jbrowse, self.outdir)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	352 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	353 try:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	354 os.makedirs(self.outdir)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	355 except OSError:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	356 # Ignore if the folder exists
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	357 pass
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	358
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	359 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	360 os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	361 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	362 # Ignore if the folder exists
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	363 pass
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	364
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	365 self.process_genomes()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 self.update_gencode()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368 def update_gencode(self):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	369 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	370 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	371 with open(trackList, 'r') as handle:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	372 trackListData = json.load(handle)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	373
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	374 trackListData['tracks'][0].update({
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	375 'codonStarts': table.start_codons,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	376 'codonStops': table.stop_codons,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	377 'codonTable': table.forward_table,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	378 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	379
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	380 with open(trackList, 'w') as handle:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	381 json.dump(trackListData, handle, indent=2)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	382
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	383 def subprocess_check_call(self, command):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	384 log.debug('cd %s && %s', self.outdir, ' '.join(command))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	385 subprocess.check_call(command, cwd=self.outdir)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	386
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	387 def subprocess_popen(self, command):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	388 log.debug('cd %s && %s', self.outdir, command)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	389 p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	390 output, err = p.communicate()
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	391 retcode = p.returncode
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	392 if retcode != 0:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	393 log.error('cd %s && %s', self.outdir, command)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	394 log.error(output)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	395 log.error(err)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	396 raise RuntimeError("Command failed with exit code %s" % (retcode))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	397
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	398 def _jbrowse_bin(self, command):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	399 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	400
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	401 def process_genomes(self):
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	402 for genome_node in self.genome_paths:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	403 # We only expect one input genome per run. This for loop is just
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	404 # easier to write than the alternative / catches any possible
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	405 # issues.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	406
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	407 # Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse's data dir
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	408 local_genome = os.path.realpath('./genome.fasta')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	409 shutil.copy(genome_node['path'], local_genome)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	410
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	411 cmd = ['samtools', 'faidx', local_genome]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	412 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	413
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	414 self.subprocess_check_call([
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	415 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	416 '--trackConfig', json.dumps({'metadata': genome_node['meta']}),
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	417 '--indexed_fasta', os.path.realpath(local_genome)])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	418
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	419 os.unlink(local_genome)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	420 os.unlink(local_genome + '.fai')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	421
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	422 def generate_names(self):
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	423 # Generate names
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	424 args = [
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	425 'perl', self._jbrowse_bin('generate-names.pl'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	426 '--hashBits', '16'
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	427 ]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	428
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	429 tracks = ','.join(self.tracksToIndex)
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	430 if tracks:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	431 args += ['--tracks', tracks]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	432 else:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	433 # No tracks to index, index only the refseq
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	434 args += ['--tracks', 'DNA']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	435
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	436 self.subprocess_check_call(args)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	437
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	438 def _add_json(self, json_data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	439 cmd = [
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	440 'perl', self._jbrowse_bin('add-json.pl'),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	441 json.dumps(json_data),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	442 os.path.join('data', 'trackList.json')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	443 ]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 self.subprocess_check_call(cmd)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	445
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 def _add_track_json(self, json_data):
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	447 if len(json_data) == 0:
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448 return
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	449
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 tmp = tempfile.NamedTemporaryFile(delete=False)
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	451 json.dump(json_data, tmp)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 tmp.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	454 os.path.join('data', 'trackList.json')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	455 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 os.unlink(tmp.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	457
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	458 def _blastxml_to_gff3(self, xml, min_gap=10):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	459 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	460 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	461 '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	462 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	463 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	464 gff3_unrebased.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	465 return gff3_unrebased.name
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	466
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	467 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	468 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	469
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	470 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	471 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	472 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	473 if blastOpts.get('protein', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	474 cmd.append('--protein2dna')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	475 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	476 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	477 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	478 gff3_rebased.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	479
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	480 # Replace original gff3 file
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	481 shutil.copy(gff3_rebased.name, gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	482 os.unlink(gff3_rebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	483
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	484 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	485
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	486 self._sort_gff(gff3, dest)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	487
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	488 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	489 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	490 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	491 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	492 })
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	493
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	494 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	495
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	496 trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	497 trackData['type'] = 'BlastView/View/Track/CanvasFeatures'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	498
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	499 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	500
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	501 os.unlink(gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	502
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	503 if blastOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	504 self.tracksToIndex.append("%s" % trackData['label'])
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	505
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	506 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	507 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	508 cmd = ['ln', '-s', data, dest]
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	509 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	510
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	511 url = os.path.join('raw', trackData['label'] + '.bw')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	512 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	513 "urlTemplate": url,
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	514 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	515 "type": "JBrowse/View/Track/Wiggle/Density",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	516 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	517
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	518 trackData['type'] = wiggleOpts['type']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	519 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 if 'min' in wiggleOpts and 'max' in wiggleOpts:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522 trackData['min_score'] = wiggleOpts['min']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	523 trackData['max_score'] = wiggleOpts['max']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	524 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	525 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	526
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	527 trackData['scale'] = wiggleOpts['scale']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	528
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	529 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	530
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	531 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	532
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	533 urls = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	534 for idx, bw in enumerate(data):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	535 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	536 cmd = ['ln', '-s', bw[1], dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	537 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	538
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	539 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	540
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	541 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	542 "urlTemplates": urls,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	543 "showTooltips": "true",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	544 "storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	545 "type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	546 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	547 if 'XYPlot' in wiggleOpts['type']:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	548 trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	549
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	550 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	551
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	552 if 'min' in wiggleOpts and 'max' in wiggleOpts:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	553 trackData['min_score'] = wiggleOpts['min']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	554 trackData['max_score'] = wiggleOpts['max']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	555 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	556 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	557
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	558 trackData['scale'] = wiggleOpts['scale']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	559
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	560 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	561
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	562 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	563 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	564 cmd = ['ln', '-s', os.path.realpath(data), dest]
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	565 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	566
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	567 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	568 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	569
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	570 url = os.path.join('raw', trackData['label'] + '.bam')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	571 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	572 "urlTemplate": url,
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	573 "type": "JBrowse/View/Track/Alignments2",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	574 "storeClass": "JBrowse/Store/SeqFeature/BAM",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	575 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	576 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	577
14 18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	578 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	579 # So remove the default 'feature' value for these bam tracks
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	580 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	581 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	582
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	583 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	584
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	585 if bamOpts.get('auto_snp', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	586 trackData2 = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	587 trackData2.update({
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	588 "type": "JBrowse/View/Track/SNPCoverage",
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	589 "key": trackData['key'] + " - SNPs/Coverage",
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	590 "label": trackData['label'] + "_autosnp",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	591 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	592 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	593 self._add_track_json(trackData2)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	594
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	595 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	596 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	597 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	598 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	599 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	600 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	601 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	602 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	603 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	604
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	605 url = os.path.join('raw', trackData['label'] + '.vcf.gz')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	606 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	607 "urlTemplate": url,
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	608 "type": "JBrowse/View/Track/HTMLVariants",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	609 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	610 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	611 self._add_track_json(trackData)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	612
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	613 def _sort_gff(self, data, dest):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	614
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	615 if not os.path.exists(dest):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	616 # Only index if not already done
28 d0743cb18ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d iuc parents: 27 diff changeset	617 cmd = "gff3sort.pl --precise '%s' \| grep -v \"^$\" > '%s'" % (data, dest)
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	618 self.subprocess_popen(cmd)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	619
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	620 cmd = ['bgzip', '-f', dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	621 self.subprocess_popen(' '.join(cmd))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	622 cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	623 self.subprocess_popen(' '.join(cmd))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	624
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	625 def add_features(self, data, format, trackData, gffOpts, **kwargs):
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	626
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	627 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	628
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	629 self._sort_gff(data, dest)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	630
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	631 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	632 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	633 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	634 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	635 })
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	636
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	637 if 'match' in gffOpts:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	638 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	639
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	640 trackType = 'JBrowse/View/Track/CanvasFeatures'
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	641 if 'trackType' in gffOpts:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	642 trackType = gffOpts['trackType']
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	643 trackData['type'] = trackType
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	644 trackData['trackType'] = trackType # Probably only used by old jbrowse versions
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	645
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	646 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	647 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	648 trackData['transcriptType'] = gffOpts['transcriptType']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	649 if 'subParts' in gffOpts and gffOpts['subParts']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	650 trackData['subParts'] = gffOpts['subParts']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	651 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	652 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	653 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	654 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	655 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	656
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	657 self._add_track_json(trackData)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	658
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	659 if gffOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	660 self.tracksToIndex.append("%s" % trackData['label'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	661
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	662 def add_rest(self, url, trackData):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	663 data = {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	664 "label": trackData['label'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	665 "key": trackData['key'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	666 "category": trackData['category'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	667 "type": "JBrowse/View/Track/HTMLFeatures",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	668 "storeClass": "JBrowse/Store/SeqFeature/REST",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	669 "baseUrl": url
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	670 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	671 self._add_track_json(data)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	672
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	673 def add_sparql(self, url, query, trackData):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	674 data = {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	675 "label": trackData['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	676 "key": trackData['key'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	677 "category": trackData['category'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	678 "type": "JBrowse/View/Track/CanvasFeatures",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	679 "storeClass": "JBrowse/Store/SeqFeature/SPARQL",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	680 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	681 "queryTemplate": query
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	682 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	683 self._add_track_json(data)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	684
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	685 def process_annotations(self, track):
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	686 category = track['category'].replace('__pd__date__pd__', TODAY)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	687 outputTrackConfig = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	688 'style': {
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	689 'label': track['style'].get('label', 'description'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	690 'className': track['style'].get('className', 'feature'),
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	691 'description': track['style'].get('description', ''),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	692 },
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	693 'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	694 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	695 'maxHeight': track['style'].get('maxHeight', '600'),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	696 'category': category,
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	697 }
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	698
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	699 mapped_chars = {
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	700 '>': '__gt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	701 '<': '__lt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	702 "'": '__sq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	703 '"': '__dq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	704 '[': '__ob__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	705 ']': '__cb__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	706 '{': '__oc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	707 '}': '__cc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	708 '@': '__at__',
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	709 '#': '__pd__',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	710 "": '__cn__'
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	711 }
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	712
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	713 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	714 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	715 for key, value in mapped_chars.items():
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	716 track_human_label = track_human_label.replace(value, key)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	717
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	718 log.info('Processing %s / %s', category, track_human_label)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	719 outputTrackConfig['key'] = track_human_label
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	720 # We add extra data to hash for the case of REST + SPARQL.
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	721 if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	722 rest_url = track['conf']['options']['url']
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	723 else:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	724 rest_url = ''
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	725
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	726 # I chose to use track['category'] instead of 'category' here. This
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	727 # is intentional. This way re-running the tool on a different date
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	728 # will not generate different hashes and make comparison of outputs
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	729 # much simpler.
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	730 hashData = [str(dataset_path), track_human_label, track['category'], rest_url]
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	731 hashData = '\|'.join(hashData).encode('utf-8')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	732 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	733 outputTrackConfig['metadata'] = extra_metadata
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	734
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	735 # Colour parsing is complex due to different track types having
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	736 # different colour options.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	737 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	738 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	739 for key in colourOptions:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	740 if key == 'style':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	741 for subkey in colourOptions['style']:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	742 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	743 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	744 outputTrackConfig[key] = colourOptions[key]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	745
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	746 if 'menus' in track['conf']['options']:
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	747 menus = self.cs.parse_menus(track['conf']['options'])
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	748 outputTrackConfig.update(menus)
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	749
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	750 # import pprint; pprint.pprint(track)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	751 # import sys; sys.exit()
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	752 if dataset_ext in ('gff', 'gff3', 'bed'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	753 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	754 track['conf']['options']['gff'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	755 elif dataset_ext == 'bigwig':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	756 self.add_bigwig(dataset_path, outputTrackConfig,
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	757 track['conf']['options']['wiggle'])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	758 elif dataset_ext == 'bigwig_multiple':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	759 self.add_bigwig_multiple(dataset_path, outputTrackConfig,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	760 track['conf']['options']['wiggle'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	761 elif dataset_ext == 'bam':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	762 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	763 if not isinstance(real_indexes, list):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	764 # <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	765 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	766 # </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	767 #
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	768 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	769 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	770 # becomes a list. Fun!
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	771 real_indexes = [real_indexes]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	772
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	773 self.add_bam(dataset_path, outputTrackConfig,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	774 track['conf']['options']['pileup'],
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	775 bam_index=real_indexes[i])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	776 elif dataset_ext == 'blastxml':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	777 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	778 elif dataset_ext == 'vcf':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	779 self.add_vcf(dataset_path, outputTrackConfig)
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	780 elif dataset_ext == 'rest':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	781 self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	782 elif dataset_ext == 'sparql':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	783 sparql_query = track['conf']['options']['sparql']['query']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	784 for key, value in mapped_chars.items():
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	785 sparql_query = sparql_query.replace(value, key)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	786 self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	787 else:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	788 log.warn('Do not know how to handle %s', dataset_ext)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	789
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	790 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	791 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	792
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	793 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	794 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	795 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	796 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	797
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	798 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	799 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	800
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	801 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	802 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	803
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	804 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	805 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	806 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	807
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	808 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	809 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	810 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	811 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	812 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	813 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	814 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	815 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	816 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	817 generalData['plugins'] = data['plugins']
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	818
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	819 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	820 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	821
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	822 if 'GCContent' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	823 self._add_track_json({
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	824 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	825 "type": "GCContent/View/Track/GCContentXY",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	826 "label": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	827 "key": "GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	828 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	829 "bicolor_pivot": 0.5,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	830 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	831 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	832 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	833 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	834 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	835 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	836 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	837 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	838 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	839 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	840 # TODO: Expose params for everyone.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	841 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	842 self._add_track_json({
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	843 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	844 "type": "GCContent/View/Track/GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	845 "label": "GC skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	846 "key": "GCSkew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	847 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	848 "gcMode": "skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	849 "min_score": -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	850 "bicolor_pivot": 0,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	851 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	852 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	853 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	854 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	855 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	856 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	857 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	858 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	859 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	860 }
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	861 # TODO: Expose params for everyone.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	862 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	863
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	864 if 'ComboTrackSelector' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	865 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	866 trackListJson = json.load(handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	867 trackListJson.update({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	868 "trackSelector": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	869 "renameFacets": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	870 "tool_tool": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	871 "tool_tool_id": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	872 "tool_tool_version": "Tool Version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	873 "dataset_edam_format": "EDAM",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	874 "dataset_size": "Size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	875 "history_display_name": "History Name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	876 "history_user_email": "Owner",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	877 "metadata_dbkey": "Dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	878 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	879 "displayColumns": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	880 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	881 "tool_tool",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	882 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	883 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	884 "dataset_size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	885 "history_display_name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	886 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	887 "metadata_dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	888 ],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	889 "type": "Faceted",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	890 "title": ["Galaxy Metadata"],
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	891 "icon": "https://galaxyproject.org/images/logos/galaxy-icon-square.png",
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	892 "escapeHTMLInData": False
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	893 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	894 "trackMetadata": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	895 "indexFacets": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	896 "category",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	897 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	898 "tool_tool_id",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	899 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	900 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	901 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	902 "history_display_name"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	903 ]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	904 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	905 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	906 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	907 json.dump(trackListJson, handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	908
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	909 def clone_jbrowse(self, jbrowse_dir, destination):
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	910 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	911 """
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	912 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	913 # unlike copytree
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	914 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	915 log.debug(' '.join(cmd))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	916 subprocess.check_call(cmd)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	917 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	918 log.debug(' '.join(cmd))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	919 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	920
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	921 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	922 # JBrowse releases come with some broken symlinks
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	923 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	924 log.debug(' '.join(cmd))
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	925 symlinks = subprocess.check_output(cmd)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	926 for i in symlinks:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	927 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	928 os.unlink(i)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	929 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	930 pass
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	931
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	932
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	933 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	934 parser = argparse.ArgumentParser(description="", epilog="")
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	935 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	936
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	937 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	938 parser.add_argument('--outdir', help='Output directory', default='out')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	939 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	940 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0")
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	941 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	942
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	943 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	944 root = tree.getroot()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	945
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	946 # This should be done ASAP
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	947 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	948 # Sometimes this comes as `localhost` without a protocol
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	949 if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	950 # so we'll prepend `http://` and hope for the best. Requests should
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	951 # be GET and not POST so it should redirect OK
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	952 GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	953
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	954 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	955 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	956 outdir=args.outdir,
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	957 genomes=[
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	958 {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	959 'path': os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	960 'meta': metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	961 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	962 for x in root.findall('metadata/genomes/genome')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	963 ],
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	964 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	965 gencode=root.find('metadata/gencode').text
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	966 )
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	967
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	968 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	969 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	970 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	971 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	972 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	973 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	974 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	975 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	976 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	977 'trackPadding': int(root.find('metadata/general/trackPadding').text),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	978 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	979 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	980 'show_tracklist': root.find('metadata/general/show_tracklist').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	981 'show_nav': root.find('metadata/general/show_nav').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	982 'show_overview': root.find('metadata/general/show_overview').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	983 'show_menu': root.find('metadata/general/show_menu').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	984 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	985 },
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	986 'plugins': [],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	987 'plugins_python': [],
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	988 }
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	989
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	990 plugins = root.find('plugins').attrib
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	991 if plugins['GCContent'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	992 extra_data['plugins_python'].append('GCContent')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	993 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	994 'location': 'https://cdn.jsdelivr.net/gh/elsiklab/gccontent@5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	995 'name': 'GCContent'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	996 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	997
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	998 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	999 # if plugins['Bookmarks'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1000 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1001 # 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1002 # 'name': 'Bookmarks'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1003 # })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1004
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1005 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1006 if plugins['ComboTrackSelector'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1007 extra_data['plugins_python'].append('ComboTrackSelector')
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1008 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1009 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1010 # 'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1011 # 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1012 # 'name': 'ComboTrackSelector'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1013 # })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1014
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1015 if plugins['theme'] == 'Minimalist':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1016 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	1017 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-minimalist-theme@d698718442da306cf87f033c72ddb745f3077775/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1018 'name': 'MinimalistTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1019 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1020 elif plugins['theme'] == 'Dark':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1021 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	1022 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-dark-theme@689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1023 'name': 'DarkTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1024 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1025
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1026 if plugins['BlastView'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1027 extra_data['plugins_python'].append('BlastView')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1028 extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1029 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1030 'name': 'BlastView'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1031 })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1032
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1033 for track in root.findall('tracks/track'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1034 track_conf = {}
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1035 track_conf['trackfiles'] = []
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1036
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1037 is_multi_bigwig = False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1038 try:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1039 if track.find('options/wiggle/multibigwig') and (track.find('options/wiggle/multibigwig').text == 'True'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1040 is_multi_bigwig = True
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1041 multi_bigwig_paths = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1042 except KeyError:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1043 pass
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1044
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1045 trackfiles = track.findall('files/trackFile')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1046 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1047 for x in track.findall('files/trackFile'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1048 if is_multi_bigwig:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1049 multi_bigwig_paths.append((x.attrib['label'], os.path.realpath(x.attrib['path'])))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1050 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1051 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1052 metadata = metadata_from_node(x.find('metadata'))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1053
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1054 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1055 os.path.realpath(x.attrib['path']),
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1056 x.attrib['ext'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1057 x.attrib['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1058 metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1059 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1060 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1061 # For tracks without files (rest, sparql)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1062 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1063 '', # N/A, no path for rest or sparql
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1064 track.attrib['format'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1065 track.find('options/label').text,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1066 {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1067 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1068
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1069 if is_multi_bigwig:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1070 metadata = metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1071
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1072 track_conf['trackfiles'].append((
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1073 multi_bigwig_paths, # Passing an array of paths to represent as one track
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1074 'bigwig_multiple',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1075 'MultiBigWig', # Giving an hardcoded name for now
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1076 {} # No metadata for multiple bigwig
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1077 ))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1078
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1079 track_conf['category'] = track.attrib['cat']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1080 track_conf['format'] = track.attrib['format']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1081 try:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1082 # Only pertains to gff3 + blastxml. TODO?
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1083 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1084 except TypeError:
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1085 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1086 pass
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1087 track_conf['conf'] = etree_to_dict(track.find('options'))
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1088 keys = jc.process_annotations(track_conf)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1089
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1090 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1091 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1092
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1093 jc.add_final_data(extra_data)
20 558d652cd681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02 iuc parents: 17 diff changeset	1094 jc.generate_names()

Mercurial > repos > iuc > jbrowse

annotate jbrowse.py @ 28:d0743cb18ed8 draft