| Previous changeset 14:7c2e28e144f3 (2024-01-22) Next changeset 16:1fe91657bfd6 (2024-01-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty |
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modified:
jbrowse2.py jbrowse2.xml macros.xml readme.rst |
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removed:
Galaxy-History-jbrowse2samples.tar.gz abjbrowse2.py abjbrowse2.xml config.json.sample |
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| diff -r 7c2e28e144f3 -r cce8dacb240f Galaxy-History-jbrowse2samples.tar.gz |
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| Binary file Galaxy-History-jbrowse2samples.tar.gz has changed |
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| diff -r 7c2e28e144f3 -r cce8dacb240f abjbrowse2.py --- a/abjbrowse2.py Mon Jan 22 12:05:09 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1272 +0,0 @@\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'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- (\n- os.path.realpath(x.attrib["path"]),\n- x.attrib["ext"],\n- x.attrib["label"],\n- metadata,\n- )\n- )\n- else:\n- # For tracks without files (rest, sparql)\n- track_conf["trackfiles"].append(\n- (\n- "", # N/A, no path for rest or sparql\n- track.attrib["format"],\n- track.find("options/label").text,\n- {},\n- )\n- )\n-\n- track_conf["category"] = track.attrib["cat"]\n- track_conf["format"] = track.attrib["format"]\n- track_conf["style"] = {\n- item.tag: parse_style_conf(item) for item in track.find("options/style")\n- }\n-\n- track_conf["style"] = {\n- item.tag: parse_style_conf(item) for item in track.find("options/style")\n- }\n-\n- track_conf["style_labels"] = {\n- item.tag: parse_style_conf(item)\n- for item in track.find("options/style_labels")\n- }\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"][\n- track.attrib.get("visibility", "default_off")\n- ].append(key)\n-\n- default_session_data["style"][key] = track_conf[\n- "style"\n- ] # 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(\n- "metadata/general/defaultLocation"\n- ).text\n- default_session_data["session_name"] = root.find(\n- "metadata/general/session_name"\n- ).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' |
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| diff -r 7c2e28e144f3 -r cce8dacb240f abjbrowse2.xml --- a/abjbrowse2.xml Mon Jan 22 12:05:09 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1295 +0,0 @@\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 7c2e28e144f3 -r cce8dacb240f config.json.sample --- a/config.json.sample Mon Jan 22 12:05:09 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -{ - "configuration": { - "rpc": { - "defaultDriver": "WebWorkerRpcDriver", - "drivers": { - "MainThreadRpcDriver": {}, - "WebWorkerRpcDriver": {} - } - }, - "logoPath": { - "locationType": "UriLocation", - "uri": "" - } - }, - "plugins": [], - "assemblies": [], - "tracks": [], - "internetAccounts": [], - "aggregateTextSearchAdapters": [], - "connections": [], - "defaultSession": {} -} |
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| diff -r 7c2e28e144f3 -r cce8dacb240f jbrowse2.py --- a/jbrowse2.py Mon Jan 22 12:05:09 2024 +0000 +++ b/jbrowse2.py Thu Jan 25 07:39:41 2024 +0000 |
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| @@ -18,7 +18,7 @@ logging.basicConfig(level=logging.INFO) log = logging.getLogger("jbrowse") -JB2VER = "v2.10.0" +JB2VER = "v2.10.1" # version pinned for cloning TODAY = datetime.datetime.now().strftime("%Y-%m-%d") @@ -458,10 +458,10 @@ self.genome_name = ( genome_name # first one for all tracks - other than paf ) - if self.config_json.get("assemblies", None): - self.config_json["assemblies"] += assemblies - else: - self.config_json["assemblies"] = assemblies + if self.config_json.get("assemblies", None): + self.config_json["assemblies"] += assemblies + else: + self.config_json["assemblies"] = assemblies def make_assembly(self, fapath, gname): hashData = [ @@ -727,6 +727,14 @@ os.unlink(gff3) def add_bigwig(self, data, trackData): + """ "type": "LinearWiggleDisplay", + "configuration": {}, + "selectedRendering": "", + "resolution": 1, + "posColor": "rgb(228, 26, 28)", + "negColor": "rgb(255, 255, 51)", + "constraints": {} + """ url = "%s.bigwig" % trackData["label"] # slashes in names cause path trouble dest = os.path.join(self.outdir, url) @@ -756,7 +764,7 @@ trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) - logging.debug("#### wig trackData=%s" % str(trackData)) + logging.info("#### wig trackData=%s" % str(trackData)) def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): tId = trackData["label"] @@ -949,11 +957,11 @@ tname = trackData["name"] tId = trackData["label"] pgname = pafOpts["genome_label"] - if len(pgname.split() > 1): + if len(pgname.split()) > 1: pgname = pgname.split()[ 0 ] # trouble from spacey names in command lines avoidance - asstrack, gname = self.make_assembly(pafOpts["genome"], pgname) + asstrack = self.make_assembly(pafOpts["genome"], pgname) self.genome_names.append(pgname) if self.config_json.get("assemblies", None): self.config_json["assemblies"].append(asstrack) @@ -961,7 +969,6 @@ self.config_json["assemblies"] = [ asstrack, ] - url = "%s.paf" % (trackData["label"]) dest = "%s/%s" % (self.outdir, url) self.symlink_or_copy(os.path.realpath(data), dest) @@ -975,6 +982,16 @@ "pafLocation": {"uri": url}, "assemblyNames": [self.genome_name, pgname], }, + # "displays": [ + # { + # "type": "LinearSyntenyDisplay", + # "displayId": "%s-LinearSyntenyDisplay" % tId, + # }, + # { + # "type": "DotPlotDisplay", + # "displayId": "%s-DotPlotDisplay" % tId, + # }, + # ], } style_json = self._prepare_track_style(trackDict) trackDict["style"] = style_json @@ -1130,6 +1147,10 @@ ) elif dataset_ext == "vcf": self.add_vcf(dataset_path, outputTrackConfig) + elif dataset_ext == "paf": + self.add_paf( + dataset_path, outputTrackConfig, track["conf"]["options"]["synteny"] + ) else: log.warn("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields @@ -1177,7 +1198,7 @@ ddl = data["defaultLocation"] 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)) @@ -1407,6 +1428,15 @@ } track_conf["conf"] = etree_to_dict(track.find("options")) + track_conf["category"] = track.attrib["cat"] + track_conf["format"] = track.attrib["format"] + try: + # Only pertains to gff3 + blastxml. TODO? + track_conf["style"] = {t.tag: t.text for t in track.find("options/style")} + except TypeError: + track_conf["style"] = {} + pass + track_conf["conf"] = etree_to_dict(track.find("options")) keys = jc.process_annotations(track_conf) if keys: @@ -1422,34 +1452,26 @@ default_session_data["style_labels"][key] = track_conf.get( "style_labels", None ) - - default_session_data["defaultLocation"] = root.find( - "metadata/general/defaultLocation" - ).text - default_session_data["session_name"] = root.find( - "metadata/general/session_name" - ).text - - general_data = { - "analytics": root.find("metadata/general/analytics").text, - "primary_color": root.find("metadata/general/primary_color").text, - "secondary_color": root.find("metadata/general/secondary_color").text, - "tertiary_color": root.find("metadata/general/tertiary_color").text, - "quaternary_color": root.find("metadata/general/quaternary_color").text, - "font_size": root.find("metadata/general/font_size").text, - } - track_conf["category"] = track.attrib["cat"] - track_conf["format"] = track.attrib["format"] - try: - # Only pertains to gff3 + blastxml. TODO? - track_conf["style"] = {t.tag: t.text for t in track.find("options/style")} - except TypeError: - track_conf["style"] = {} - pass - track_conf["conf"] = etree_to_dict(track.find("options")) - jc.add_general_configuration(general_data) - jc.config_json["tracks"] = jc.tracksToAdd + default_session_data["defaultLocation"] = root.find( + "metadata/general/defaultLocation" + ).text + default_session_data["session_name"] = root.find( + "metadata/general/session_name" + ).text + general_data = { + "analytics": root.find("metadata/general/analytics").text, + "primary_color": root.find("metadata/general/primary_color").text, + "secondary_color": root.find("metadata/general/secondary_color").text, + "tertiary_color": root.find("metadata/general/tertiary_color").text, + "quaternary_color": root.find("metadata/general/quaternary_color").text, + "font_size": root.find("metadata/general/font_size").text, + } + jc.add_general_configuration(general_data) + trackconf = jc.config_json.get("tracks", None) + if trackconf: + jc.config_json["tracks"].update(jc.tracksToAdd) + else: + jc.config_json["tracks"] = jc.tracksToAdd jc.write_config() jc.add_default_session(default_session_data) - # jc.text_index() not sure what broke here. |
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| diff -r 7c2e28e144f3 -r cce8dacb240f jbrowse2.xml --- a/jbrowse2.xml Mon Jan 22 12:05:09 2024 +0000 +++ b/jbrowse2.xml Thu Jan 25 07:39:41 2024 +0000 |
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| @@ -33,7 +33,7 @@ #if str($reference_genome.genome_type_select) == "indexed": <genome path="${reference_genome.genomes.fields.path}" label="${reference_genome.genomes.fields.name}"> <metadata /> - </genome>s + </genome> #else <genome path="$reference_genome.genome" label="${reference_genome.genome.element_identifier}"> <metadata> @@ -297,12 +297,12 @@ </when> <when value="synteny"> - <param label="Other genome sequence" + <param label="Comparison genome sequence" help="Paf must use this as the reference to map the real reference sequence" format="fasta" name="synteny_genome" type="data" /> - <expand macro="input_conditional" label="Synteny data" format="paf" /> + <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/> <expand macro="track_visibility" /> </when> |
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| diff -r 7c2e28e144f3 -r cce8dacb240f macros.xml --- a/macros.xml Mon Jan 22 12:05:09 2024 +0000 +++ b/macros.xml Thu Jan 25 07:39:41 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.10.0</token> + <token name="@TOOL_VERSION@">2.10.1</token> <xml name = "edamInc"> <edam_topics> <edam_topic>topic_3307</edam_topic> |
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| diff -r 7c2e28e144f3 -r cce8dacb240f readme.rst --- a/readme.rst Mon Jan 22 12:05:09 2024 +0000 +++ b/readme.rst Thu Jan 25 07:39:41 2024 +0000 |
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| @@ -38,11 +38,15 @@ - 2.10.0+galaxy2 - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0 + - was working well enough for VGP when previous PR discovered + - too late to backport all the fixes + - working default session and some other ideas copied instead. - seems to work well with defaults. - need to document and implement track settings by running the browser locally. - works well enough to be useful in workflows such as TreeValGal. - JB2 seems to set defaults wisely. - not yet ideal for users who need fine grained track control. + - synteny works. Wrapper License (MIT/BSD Style) |