# HG changeset patch
# User iuc
# Date 1555338686 14400
# Node ID 2bb2e07a7a210e435de91b56ca7782c045252ac9
# Parent ca2def38369cbf97bec05fca4850d5024ba984da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
diff -r ca2def38369c -r 2bb2e07a7a21 jbrowse.py
--- a/jbrowse.py Thu Apr 11 09:35:00 2019 -0400
+++ b/jbrowse.py Mon Apr 15 10:31:26 2019 -0400
@@ -80,8 +80,7 @@
var opacity = (score - ({min})) / (({max}) - ({min}));
""",
'logarithmic': """
- var opacity = (score - ({min})) / (({max}) - ({min}));
- opacity = Math.log10(opacity) + Math.log10({max});
+ var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
""",
'blast': """
var opacity = 0;
@@ -682,6 +681,36 @@
}
self._add_track_json(data)
+ def traverse_to_option_parent(self, splitKey, outputTrackConfig):
+ trackConfigSubDict = outputTrackConfig
+ for part in splitKey[:-1]:
+ if trackConfigSubDict.get(part) is None:
+ trackConfigSubDict[part] = dict()
+ trackConfigSubDict = trackConfigSubDict[part]
+ assert isinstance(trackConfigSubDict, dict), 'Config element {} is not a dict'.format(trackConfigSubDict)
+ return trackConfigSubDict
+
+ def get_formatted_option(self, valType2ValDict, mapped_chars):
+ assert isinstance(valType2ValDict, dict) and len(valType2ValDict.items()) == 1
+ for valType, value in valType2ValDict.items():
+ if valType == "text":
+ for char, mapped_char in mapped_chars.items():
+ value = value.replace(mapped_char, char)
+ elif valType == "integer":
+ value = int(value)
+ elif valType == "float":
+ value = float(value)
+ else: # boolean
+ value = {'true': True, 'false': False}[value]
+ return value
+
+ def set_custom_track_options(self, customTrackConfig, outputTrackConfig, mapped_chars):
+ for optKey, optType2ValDict in customTrackConfig.items():
+ splitKey = optKey.split('.')
+ trackConfigOptionParent = self.traverse_to_option_parent(splitKey, outputTrackConfig)
+ optVal = self.get_formatted_option(optType2ValDict, mapped_chars)
+ trackConfigOptionParent[splitKey[-1]] = optVal
+
def process_annotations(self, track):
category = track['category'].replace('__pd__date__pd__', TODAY)
outputTrackConfig = {
@@ -747,6 +776,10 @@
menus = self.cs.parse_menus(track['conf']['options'])
outputTrackConfig.update(menus)
+ customTrackConfig = track['conf']['options'].get('custom_config', {})
+ if customTrackConfig:
+ self.set_custom_track_options(customTrackConfig, outputTrackConfig, mapped_chars)
+
# import pprint; pprint.pprint(track)
# import sys; sys.exit()
if dataset_ext in ('gff', 'gff3', 'bed'):
diff -r ca2def38369c -r 2bb2e07a7a21 jbrowse.xml
--- a/jbrowse.xml Thu Apr 11 09:35:00 2019 -0400
+++ b/jbrowse.xml Mon Apr 15 10:31:26 2019 -0400
@@ -210,6 +210,15 @@
#end for
#end if
+ #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
+
+ #for $custom_option in $track.data_format.jb_custom_config.option:
+ <${custom_option.opt_key}>
+ <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}
+
+ #end for
+
+ #end if
#if str($track.data_format.data_format_select) == "wiggle":
@@ -318,7 +327,8 @@
BlastView="${plugins.BlastView}"
theme=""
/>
-]]>
+
+]]>
@@ -431,11 +441,13 @@
+
+
@@ -487,6 +499,7 @@
description="note,description"
height="10px"/>
+
@@ -503,6 +516,7 @@
type="integer"
help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message."
value="5000000" />
+
@@ -545,6 +559,7 @@
help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />
+
@@ -642,7 +657,7 @@
-
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@@ -650,7 +665,7 @@
-
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@@ -846,7 +861,7 @@
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@@ -909,7 +924,7 @@
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@@ -927,6 +942,7 @@
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@@ -946,7 +962,59 @@
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@@ -965,7 +1033,7 @@
-
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@@ -975,7 +1043,7 @@
-
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@@ -1022,7 +1090,7 @@
-
+
\$GALAXY_JBROWSE_SHARED_DIR
- galaxy2
+ galaxy3
+
+
+
+
+ ^[\w]+(\.\w+)*$
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diff -r ca2def38369c -r 2bb2e07a7a21 test-data/bam/test.xml
--- a/test-data/bam/test.xml Thu Apr 11 09:35:00 2019 -0400
+++ b/test-data/bam/test.xml Mon Apr 15 10:31:26 2019 -0400
@@ -54,15 +54,14 @@
display_name="test_history"/>
+
+
false
/tmp/tmpWtvfKr/files/_metadata_files/000/metadata_1.dat
+ 5000000
@@ -87,6 +89,7 @@
ComboTrackSelector=""
Bookmarks=""
GCContent=""
+ BlastView="True"
theme=""
/>
-
\ No newline at end of file
+
diff -r ca2def38369c -r 2bb2e07a7a21 test-data/custom_config/test.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_config/test.xml Mon Apr 15 10:31:26 2019 -0400
@@ -0,0 +1,119 @@
+
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+ 11
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+ 20
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+ true
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+ true
+ true
+ true
+ true
+ false
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+ http://localhost
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diff -r ca2def38369c -r 2bb2e07a7a21 test-data/gencode/test.xml
--- a/test-data/gencode/test.xml Thu Apr 11 09:35:00 2019 -0400
+++ b/test-data/gencode/test.xml Mon Apr 15 10:31:26 2019 -0400
@@ -45,6 +45,7 @@
ComboTrackSelector=""
Bookmarks=""
GCContent=""
+ BlastView="True"
theme=""
/>
diff -r ca2def38369c -r 2bb2e07a7a21 test-data/gff3/test.xml
--- a/test-data/gff3/test.xml Thu Apr 11 09:35:00 2019 -0400
+++ b/test-data/gff3/test.xml Mon Apr 15 10:31:26 2019 -0400
@@ -158,6 +158,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -212,6 +214,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -272,6 +276,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -332,6 +338,8 @@
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+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -394,6 +402,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -456,6 +466,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -510,6 +522,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
@@ -564,6 +578,8 @@
+
+
NeatHTMLFeatures/View/Track/NeatFeatures
diff -r ca2def38369c -r 2bb2e07a7a21 test-data/menus/test.xml
--- a/test-data/menus/test.xml Thu Apr 11 09:35:00 2019 -0400
+++ b/test-data/menus/test.xml Mon Apr 15 10:31:26 2019 -0400
@@ -57,7 +57,6 @@
data_lines="27"
comment_lines="19"
columns="9"
- column_names=""
delimiter="__tc__"
attributes="6"
/>
@@ -73,7 +72,7 @@