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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty |
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modified:
jbrowse2.py macros.xml |
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added:
abjbrowse2.py abjbrowse2.xml |
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| diff -r 247e17ce504b -r 1d86925dbb4c abjbrowse2.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abjbrowse2.py Mon Jan 22 11:52:19 2024 +0000 |
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| b'@@ -0,0 +1,1097 @@\n+#!/usr/bin/env python\n+import argparse\n+import binascii\n+import datetime\n+import hashlib\n+import json\n+import logging\n+import os\n+import re\n+import shutil\n+import struct\n+import subprocess\n+import tempfile\n+import xml.etree.ElementTree as ET\n+from collections import defaultdict\n+\n+logging.basicConfig(level=logging.INFO)\n+log = logging.getLogger(\'jbrowse\')\n+TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n+GALAXY_INFRASTRUCTURE_URL = None\n+\n+\n+class ColorScaling(object):\n+\n+ COLOR_FUNCTION_TEMPLATE = """\n+ function(feature, variableName, glyphObject, track) {{\n+ var score = {score};\n+ {opacity}\n+ return \'rgba({red}, {green}, {blue}, \' + opacity + \')\';\n+ }}\n+ """\n+\n+ COLOR_FUNCTION_TEMPLATE_QUAL = r"""\n+ function(feature, variableName, glyphObject, track) {{\n+ var search_up = function self(sf, attr){{\n+ if(sf.get(attr) !== undefined){{\n+ return sf.get(attr);\n+ }}\n+ if(sf.parent() === undefined) {{\n+ return;\n+ }}else{{\n+ return self(sf.parent(), attr);\n+ }}\n+ }};\n+\n+ var search_down = function self(sf, attr){{\n+ if(sf.get(attr) !== undefined){{\n+ return sf.get(attr);\n+ }}\n+ if(sf.children() === undefined) {{\n+ return;\n+ }}else{{\n+ var kids = sf.children();\n+ for(var child_idx in kids){{\n+ var x = self(kids[child_idx], attr);\n+ if(x !== undefined){{\n+ return x;\n+ }}\n+ }}\n+ return;\n+ }}\n+ }};\n+\n+ var color = ({user_spec_color} || search_up(feature, \'color\') || search_down(feature, \'color\') || {auto_gen_color});\n+ var score = (search_up(feature, \'score\') || search_down(feature, \'score\'));\n+ {opacity}\n+ if(score === undefined){{ opacity = 1; }}\n+ var result = /^#?([a-f\\d]{{2}})([a-f\\d]{{2}})([a-f\\d]{{2}})$/i.exec(color);\n+ var red = parseInt(result[1], 16);\n+ var green = parseInt(result[2], 16);\n+ var blue = parseInt(result[3], 16);\n+ if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}\n+ return \'rgba(\' + red + \',\' + green + \',\' + blue + \',\' + opacity + \')\';\n+ }}\n+ """\n+\n+ OPACITY_MATH = {\n+ \'linear\': """\n+ var opacity = (score - ({min})) / (({max}) - ({min}));\n+ """,\n+ \'logarithmic\': """\n+ var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));\n+ """,\n+ \'blast\': """\n+ var opacity = 0;\n+ if(score == 0.0) {{\n+ opacity = 1;\n+ }} else {{\n+ opacity = (20 - Math.log10(score)) / 180;\n+ }}\n+ """\n+ }\n+\n+ BREWER_COLOUR_IDX = 0\n+ BREWER_COLOUR_SCHEMES = [\n+ (166, 206, 227),\n+ (31, 120, 180),\n+ (178, 223, 138),\n+ (51, 160, 44),\n+ (251, 154, 153),\n+ (227, 26, 28),\n+ (253, 191, 111),\n+ (255, 127, 0),\n+ (202, 178, 214),\n+ (106, 61, 154),\n+ (255, 255, 153),\n+ (177, 89, 40),\n+ (228, 26, 28),\n+ (55, 126, 184),\n+ (77, 175, 74),\n+ (152, 78, 163),\n+ (255, 127, 0),\n+ ]\n+\n+ BREWER_DIVERGING_PALLETES = {\n+ \'BrBg\': ("#543005", "#003c30"),\n+ \'PiYg\': ("#8e0152", "#276419"),\n+ \'PRGn\': ("#40004b", "#00441b"),\n+ \'PuOr\': ("#7f3b08", "#2d004b"),\n+ \'RdBu\': ("#67001f", "#053061"),\n+ \'RdGy\': ("#67001f", "#1a1a1a"),\n+ \'RdYlBu\': ("#a50026", "#313695"),\n+ \'RdYlGn\': ("#a50026", "#006837"),\n+ \'Spectral\': ("#9e0142", "#5e4fa2"),\n+ }\n+\n+ def __init__(self):\n+ self.brewer_colour_idx = 0\n+\n+ def rgb_from_hex(self, hexstr):\n+ # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-b'..b'ation\')\n+\n+ parser.add_argument(\'--jbrowse\', help=\'Folder containing a jbrowse release\')\n+ parser.add_argument(\'--outdir\', help=\'Output directory\', default=\'out\')\n+ parser.add_argument(\'--version\', \'-V\', action=\'version\', version="%(prog)s 0.8.0")\n+ args = parser.parse_args()\n+\n+ tree = ET.parse(args.xml.name)\n+ root = tree.getroot()\n+\n+ # This should be done ASAP\n+ GALAXY_INFRASTRUCTURE_URL = root.find(\'metadata/galaxyUrl\').text\n+ # Sometimes this comes as `localhost` without a protocol\n+ if not GALAXY_INFRASTRUCTURE_URL.startswith(\'http\'):\n+ # so we\'ll prepend `http://` and hope for the best. Requests *should*\n+ # be GET and not POST so it should redirect OK\n+ GALAXY_INFRASTRUCTURE_URL = \'http://\' + GALAXY_INFRASTRUCTURE_URL\n+\n+ jc = JbrowseConnector(\n+ jbrowse=args.jbrowse,\n+ outdir=args.outdir,\n+ genomes=[\n+ {\n+ \'path\': os.path.realpath(x.attrib[\'path\']),\n+ \'meta\': metadata_from_node(x.find(\'metadata\')),\n+ \'label\': x.attrib[\'label\']\n+ }\n+ for x in root.findall(\'metadata/genomes/genome\')\n+ ]\n+ )\n+\n+ default_session_data = {\n+ \'visibility\': {\n+ \'default_on\': [],\n+ \'default_off\': [],\n+ },\n+ \'style\': {},\n+ \'style_labels\': {}\n+ }\n+\n+ # TODO add metadata to tracks\n+ for track in root.findall(\'tracks/track\'):\n+ track_conf = {}\n+ track_conf[\'trackfiles\'] = []\n+\n+ trackfiles = track.findall(\'files/trackFile\')\n+ if trackfiles:\n+ for x in track.findall(\'files/trackFile\'):\n+ if trackfiles:\n+ metadata = metadata_from_node(x.find(\'metadata\'))\n+\n+ track_conf[\'trackfiles\'].append((\n+ os.path.realpath(x.attrib[\'path\']),\n+ x.attrib[\'ext\'],\n+ x.attrib[\'label\'],\n+ metadata\n+ ))\n+ else:\n+ # For tracks without files (rest, sparql)\n+ track_conf[\'trackfiles\'].append((\n+ \'\', # N/A, no path for rest or sparql\n+ track.attrib[\'format\'],\n+ track.find(\'options/label\').text,\n+ {}\n+ ))\n+\n+ track_conf[\'category\'] = track.attrib[\'cat\']\n+ track_conf[\'format\'] = track.attrib[\'format\']\n+ track_conf[\'style\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style\')}\n+\n+ track_conf[\'style\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style\')}\n+\n+ track_conf[\'style_labels\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style_labels\')}\n+\n+ track_conf[\'conf\'] = etree_to_dict(track.find(\'options\'))\n+ keys = jc.process_annotations(track_conf)\n+\n+ for key in keys:\n+ default_session_data[\'visibility\'][track.attrib.get(\'visibility\', \'default_off\')].append(key)\n+\n+ default_session_data[\'style\'][key] = track_conf[\'style\'] # TODO do we need this anymore?\n+ default_session_data[\'style_labels\'][key] = track_conf[\'style_labels\']\n+\n+ default_session_data[\'defaultLocation\'] = root.find(\'metadata/general/defaultLocation\').text\n+ default_session_data[\'session_name\'] = root.find(\'metadata/general/session_name\').text\n+\n+ general_data = {\n+ \'analytics\': root.find(\'metadata/general/analytics\').text,\n+ \'primary_color\': root.find(\'metadata/general/primary_color\').text,\n+ \'secondary_color\': root.find(\'metadata/general/secondary_color\').text,\n+ \'tertiary_color\': root.find(\'metadata/general/tertiary_color\').text,\n+ \'quaternary_color\': root.find(\'metadata/general/quaternary_color\').text,\n+ \'font_size\': root.find(\'metadata/general/font_size\').text,\n+ }\n+\n+ jc.add_default_session(default_session_data)\n+ jc.add_general_configuration(general_data)\n+ jc.text_index()\n+\n' |
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| diff -r 247e17ce504b -r 1d86925dbb4c abjbrowse2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abjbrowse2.xml Mon Jan 22 11:52:19 2024 +0000 |
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| b'@@ -0,0 +1,1295 @@\n+<tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@">\n+ <description>genome browser</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <edam_topics>\n+ <edam_topic>topic_3307</edam_topic>\n+ <edam_topic>topic_0092</edam_topic>\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_0573</edam_operation>\n+ <edam_operation>operation_0564</edam_operation>\n+ </edam_operations>\n+ <xrefs>\n+ <xref type="bio.tools">jbrowse</xref>\n+ </xrefs>\n+ <expand macro="requirements"/>\n+ <version_command>python \'${__tool_directory__}/jbrowse2.py\' --version</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+mkdir -p $output.files_path &&\n+#if $action.action_select != "create":\n+ cp -R $action.update_jbrowse.extra_files_path/data $output.files_path/data &&\n+#end if\n+\n+## Copy the XML file into the directory, mostly for debugging\n+## but nice if users want to reproduce locally\n+cp $trackxml $output.files_path/galaxy.xml &&\n+\n+export JBROWSE2_SOURCE_DIR=\\$(dirname \\$(which jbrowse))/../opt/jbrowse2 &&\n+\n+## Once that\'s done, we run the python script to handle the real work\n+python \'$__tool_directory__/jbrowse2.py\'\n+\n+--jbrowse \\${JBROWSE2_SOURCE_DIR}\n+\n+--outdir $output.files_path\n+$trackxml &&\n+\n+cp $output.files_path/index.html $output;\n+\n+## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.\n+#if str($uglyTestingHack) == "enabled":\n+ cp $trackxml $output\n+#end if\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>\n+<root>\n+ <metadata>\n+ <genomes>\n+ #if str($reference_genome.genome_type_select) == "indexed":\n+ <genome path="${reference_genome.genomes.fields.path}" label="${reference_genome.genomes.fields.name}">\n+ <metadata />\n+ </genome>s\n+ #else\n+ <genome path="$reference_genome.genome" label="${reference_genome.genome.element_identifier}">\n+ <metadata>\n+ <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}"\n+ size="${reference_genome.genome.get_size(nice_size=True)}"\n+ edam_format="${reference_genome.genome.datatype.edam_format}"\n+ file_ext="${reference_genome.genome.ext}" />\n+ <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"\n+ #if $reference_genome.genome.history.user:\n+ user_email="${reference_genome.genome.history.user.email}"\n+ user_id="${reference_genome.genome.history.user_id}"\n+ display_name="${reference_genome.genome.history.get_display_name()}"/>\n+ #else\n+ user_email="anonymous"\n+ user_id="-1"\n+ display_name="Unnamed History"/>\n+ #end if\n+ <metadata\n+ #for (key, value) in $reference_genome.genome.get_metadata().items():\n+ #if "_types" not in $key:\n+ #if isinstance($value, list):\n+ #set value_str = "[%s]" % \',\'.join([str(val) for val in value])\n+ ${key}="$value_str"\n+ #else\n+ ${key}="${value}"\n+ #end if\n+ #end if\n+ #end for\n+ />\n+ <tool\n+ tool_id="${reference_genome.genome.creating_job.tool_id}"\n+ tool_version="${reference_genome.genome.creating_job.tool_version}"\n+ />\n+ </metadata>\n+ </genome>\n+ #end if\n+ </genomes>\n+ <gen'..b've upon this and provide more colour\n+scales. The Opacity option maps the highest scoring features to full\n+opacity, and everything else to lower ones.\n+\n+BAM Pileups\n+~~~~~~~~~~~\n+\n+We support BAM files and can automatically generate SNP tracks based on\n+that bam data.\n+\n+.. image:: bam.png\n+\n+This is *strongly discouraged* for high coverage density datasets.\n+Unfortunately there are no other configuration options exposed for bam\n+files.\n+\n+BlastXML\n+~~~~~~~~\n+\n+.. image:: blast.png\n+\n+JiG now supports both blastn and blastp datasets. JiG internally uses a\n+blastXML to gapped GFF3 tool to convert your blastxml datasets into a\n+format amenable to visualization in JBrowse. This tool is also\n+available separately from the IUC on the toolshed.\n+\n+**Minimum Gap Size** reflects how long a gap must be before it becomes a\n+real gap in the processed gff3 file. In the picture above, various sizes\n+of gaps can be seen. If the minimum gap size was set much higher, say\n+100nt, many of the smaller gaps would disappear, and the features on\n+both sides would be merged into one, longer feature. This setting is\n+inversely proportional to runtime and output file size. *Do not set this\n+to a low value for large datasets*. By setting this number lower, you\n+will have extremely large outputs and extremely long runtimes. The\n+default was configured based off of the author\'s experience, but the\n+author only works on small viruses. It is *strongly* recommended that\n+you filter your blast results before display, e.g. picking out the top\n+10 hits or so.\n+\n+**Protein blast search** option merely informs underlying tools that\n+they should adjust feature locations by 3x.\n+\n+Styling Options\n+^^^^^^^^^^^^^^^\n+\n+Please see the styling options for GFF3 datasets, they are identical.\n+\n+Feature Score Scaling & Coloring Options\n+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n+\n+Please see the score scaling and colouring options for GFF3 datasets,\n+they are identical. Remember to set your score scaling to "blast" method\n+if you do use it.\n+\n+Bigwig XY\n+~~~~~~~~~\n+\n+.. image:: bigwig.png\n+\n+**XYPlot**\n+\n+BigWig tracks can be displayed as a "density" plot which is continuous\n+line which varies in colour, or as an "XYplot." XYplots are preferable\n+for users to visually identify specific features in a bigwig track,\n+however density tracks are more visually compact.\n+\n+**Variance Band** is an option available to XYPlots, and can be seen in\n+the third and fourth tracks in the above picture. This overlays a mean\n+line, and 1 and 2 standard deviation areas.\n+\n+**Track Scaling** is different from colour scaling, instead it\n+configures how the track behaves inside of JBrowse. **Autoscaling\n+globally** means that JBrowse will determine the minimum and maximum for\n+the track, and fix the bounds of the viewport to that. E.g. if your\n+track ranges from 1-1000, and the region you\'re currently zoomed to only\n+goes from 0-50, then the viewport range will still show 1-1000. This is\n+good for global genomic context. However you may wish to consider\n+**autoscaling locally** instead. In the example of a region which varies\n+from 0-50, autoscaling locally would cause the individual track\'s\n+viewport to re-adjust and show just the 0-50 region. If neither of these\n+options are palatable, you may manually hardcode the minimum and\n+maximums for the track to scale to.\n+\n+Colour Options\n+^^^^^^^^^^^^^^\n+\n+BigWig tracks have two colours in JBrowse, a positive and a negative\n+colour.\n+\n+As always you may manually choose a colour, or let JiG choose for you.\n+\n+One of the more interesting options is the **Bicolor pivot**. This\n+option allows you to control the point at which JBrowse switches from\n+the positive colour to the negative. In the above graphic, you can see\n+this has been configured to "mean" for the first two (orange and blue)\n+tracks.\n+\n+VCFs/SNPs\n+~~~~~~~~~\n+\n+These tracks do not support any special configuration.\n+\n+@ATTRIBUTION@\n+]]></help>\n+ <expand macro="citations"/>\n+</tool>\n+\n' |
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| diff -r 247e17ce504b -r 1d86925dbb4c jbrowse2.py --- a/jbrowse2.py Sat Jan 20 10:04:08 2024 +0000 +++ b/jbrowse2.py Mon Jan 22 11:52:19 2024 +0000 |
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| @@ -1175,7 +1175,9 @@ refName = None if data.get("defaultLocation", ""): ddl = data["defaultLocation"] - loc_match = re.search(r"^(\w.+):(\d+)\.+(\d+)$", ddl) + loc_match = re.search( + r"^([^:]+):(\d+)\.+(\d+)$", ddl + ) # was re.search(r"^(\w.+):(\d+)\.+(\d+)$" if loc_match: refName = loc_match.group(1) start = int(loc_match.group(2)) @@ -1190,7 +1192,7 @@ start = 0 end = 10000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708 logging.info( - "@@@ no defaultlocation found for default session - suggest adding one!" + "@@@ no defaultlocation found for default session - please add one" ) if refName is not None: @@ -1211,7 +1213,7 @@ ) else: logging.info( - "@@@ no assembly name found default session - suggest adding one!" + "@@@ no contig name found for default session - please add one!" ) session_name = data.get("session_name", "New session") for key, value in mapped_chars.items(): |
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| diff -r 247e17ce504b -r 1d86925dbb4c macros.xml --- a/macros.xml Sat Jan 20 10:04:08 2024 +0000 +++ b/macros.xml Mon Jan 22 11:52:19 2024 +0000 |
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| @@ -28,7 +28,6 @@ <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC -This xml currently fails silently when profile=22.05 is set. ]]> </token> <xml name="genome_selector" @@ -139,7 +138,7 @@ <xml name="general_options"> <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> - <param label="Default location" type="text" name="defaultLocation" value="" help="Initial location to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/> + <param label="Subset to display to new users" type="text" name="defaultLocation" value="" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/> <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/> <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |