| Previous changeset 7:1e74f16adaa1 (2016-06-26) Next changeset 9:f422ba2e9aa5 (2016-11-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 |
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modified:
blastxml_to_gapped_gff3.py gff3_rebase.py jbrowse-fromdir.xml jbrowse.py jbrowse.xml macros.xml readme.rst test-data/gencode/test-1.xml test-data/gencode/test.xml test-data/gff3/test.xml |
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added:
test-data/menus/test.xml |
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removed:
all_fasta.loc.sample test-data/frameshift/1.gff test-data/frameshift/test.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a all_fasta.loc.sample --- a/all_fasta.loc.sample Sun Jun 26 10:50:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -# |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a blastxml_to_gapped_gff3.py --- a/blastxml_to_gapped_gff3.py Sun Jun 26 10:50:15 2016 -0400 +++ b/blastxml_to_gapped_gff3.py Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -1,10 +1,12 @@ #!/usr/bin/perl +import argparse +import copy +import logging import re import sys -import copy -import argparse + from BCBio import GFF -import logging + logging.basicConfig(level=logging.INFO) log = logging.getLogger(name='blastxml2gff3') @@ -218,7 +220,6 @@ else: log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject)) - if strict_m: if ret == '=' or ret == 'X': ret = 'M' |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a gff3_rebase.py --- a/gff3_rebase.py Sun Jun 26 10:50:15 2016 -0400 +++ b/gff3_rebase.py Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -1,11 +1,13 @@ #!/usr/bin/env python -import sys -import logging -logging.basicConfig(level=logging.INFO) import argparse import copy +import logging +import sys + from BCBio import GFF from Bio.SeqFeature import FeatureLocation + +logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) __author__ = "Eric Rasche" |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a jbrowse-fromdir.xml --- a/jbrowse-fromdir.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/jbrowse-fromdir.xml Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -1,11 +1,10 @@ -<tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="0.4"> +<tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@WRAPPER_VERSION@"> <description>upgrades the bare data directory to a full JBrowse instance</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <version_command>python jbrowse.py --version</version_command> <command><![CDATA[ ## Create output directory mkdir -p $output.files_path && @@ -26,15 +25,12 @@ <outputs> <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/> </outputs> + <tests> + </tests> <help><![CDATA[ Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance. @ATTRIBUTION@ ]]></help> - <tests> - </tests> - <citations> - <citation type="doi">10.1101/gr.094607.109</citation> - </citations> + <expand macro="citations"/> </tool> - |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a jbrowse.py --- a/jbrowse.py Sun Jun 26 10:50:15 2016 -0400 +++ b/jbrowse.py Tue Nov 29 10:55:30 2016 -0500 |
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| b'@@ -1,17 +1,19 @@\n #!/usr/bin/env python\n-import os\n+import argparse\n import copy\n-import argparse\n-import subprocess\n import hashlib\n+import json\n+import logging\n+import os\n+import shutil\n import struct\n+import subprocess\n import tempfile\n-import shutil\n-import json\n+import xml.etree.ElementTree as ET\n+from collections import defaultdict\n+\n from Bio.Data import CodonTable\n-import xml.etree.ElementTree as ET\n-import logging\n-from collections import defaultdict\n+\n logging.basicConfig(level=logging.INFO)\n log = logging.getLogger(\'jbrowse\')\n \n@@ -79,11 +81,11 @@\n """,\n \'blast\': """\n var opacity = 0;\n- if(score == 0.0) {{\n+ if(score == 0.0) {\n opacity = 1;\n- }} else {{\n+ } else{\n opacity = (20 - Math.log10(score)) / 180;\n- }}\n+ }\n """\n }\n \n@@ -125,7 +127,7 @@\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-back\n- return struct.unpack(\'BBB\',hexstr.decode(\'hex\'))\n+ return struct.unpack(\'BBB\', hexstr.decode(\'hex\'))\n \n def min_max_gff(self, gff_file):\n min_val = None\n@@ -154,6 +156,31 @@\n self.brewer_colour_idx += 1\n return r, g, b\n \n+ def parse_menus(self, track):\n+ trackConfig = {\'menuTemplate\': [{}, {}, {}]}\n+\n+ if \'menu\' in track[\'menus\']:\n+ menu_list = [track[\'menus\'][\'menu\']]\n+ if isinstance(track[\'menus\'][\'menu\'], list):\n+ menu_list = track[\'menus\'][\'menu\']\n+\n+ for m in menu_list:\n+ tpl = {\n+ \'action\': m[\'action\'],\n+ \'label\': m.get(\'label\', \'{name}\'),\n+ \'iconClass\': m.get(\'iconClass\', \'dijitIconBookmark\'),\n+ }\n+ if \'url\' in m:\n+ tpl[\'url\'] = m[\'url\']\n+ if \'content\' in m:\n+ tpl[\'content\'] = m[\'content\']\n+ if \'title\' in m:\n+ tpl[\'title\'] = m[\'title\']\n+\n+ trackConfig[\'menuTemplate\'].append(tpl)\n+\n+ return trackConfig\n+\n def parse_colours(self, track, trackFormat, gff3=None):\n # Wiggle tracks have a bicolor pallete\n trackConfig = {\'style\': {}}\n@@ -166,7 +193,6 @@\n trackConfig[\'style\'][\'neg_color\'] = self.hex_from_rgb(*self._get_colours())\n trackConfig[\'style\'][\'pos_color\'] = self.hex_from_rgb(*self._get_colours())\n \n-\n # Wiggle tracks can change colour at a specified place\n bc_pivot = track[\'wiggle\'][\'bicolor_pivot\']\n if bc_pivot not in (\'mean\', \'zero\'):\n@@ -223,7 +249,7 @@\n auto_color = "\'%s\'" % self.hex_from_rgb(*self._get_colours())\n \n color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{\n- \'opacity\': self.OPACITY_MATH[algo].format(**{\'max\': max_val,\'min\': min_val}),\n+ \'opacity\': self.OPACITY_MATH[algo].format(**{\'max\': max_val, \'min\': min_val}),\n \'user_spec_color\': user_color,\n \'auto_gen_color\': auto_color,\n })\n@@ -240,14 +266,14 @@\n for dc in map(etree_to_dict, children):\n for k, v in dc.iteritems():\n dd[k].append(v)\n- d = {t.tag: {k:v[0] if len(v) == 1 else v for k, v in dd.iteritems()}}\n+ d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.iteritems()}}\n if t.attrib:\n d[t.tag].update((\'@\' + k, v) for k, v in t.attrib.iteritems())\n if t.text:\n text = t.text.strip()\n if children or t.attrib:\n if text:\n- d[t.tag][\'#text\'] = text\n+ d[t.tag][\'#text\'] = text\n else:\n d[t.tag] = text\n return d\n@@ -274,6 +300,7 @@\n self.genome_paths = genomes\n self.standalone = standalone\n '..b' \'perl\', self._jbrowse_bin(\'generate-names.pl\'),\n+ \'--hashBits\', \'16\'\n+ ]\n+\n+ tracks = \',\'.join(self.tracksToIndex)\n+\n+ if tracks:\n+ args += [\'--tracks\', tracks]\n+ else:\n+ # No tracks to index, index only the refseq\n+ args += [\'--tracks\', \'DNA\']\n+\n+ self.subprocess_check_call(args)\n \n def _add_json(self, json_data):\n \n@@ -343,7 +381,6 @@\n self.subprocess_check_call(cmd)\n os.unlink(tmp.name)\n \n-\n def _blastxml_to_gff3(self, xml, min_gap=10):\n gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)\n cmd = [\'python\', os.path.join(INSTALLED_TO, \'blastxml_to_gapped_gff3.py\'),\n@@ -389,6 +426,9 @@\n self.subprocess_check_call(cmd)\n os.unlink(gff3)\n \n+ if blastOpts.get(\'index\', \'false\') == \'true\':\n+ self.tracksToIndex.append("%s" % trackData[\'label\'])\n+\n def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):\n dest = os.path.join(\'data\', \'raw\', trackData[\'label\'] + \'.bw\')\n cmd = [\'ln\', data, dest]\n@@ -425,7 +465,6 @@\n "storeClass": "JBrowse/Store/SeqFeature/BAM",\n })\n \n-\n self._add_track_json(trackData)\n \n if bamOpts.get(\'auto_snp\', \'false\') == \'true\':\n@@ -433,7 +472,7 @@\n trackData2.update({\n "type": "JBrowse/View/Track/SNPCoverage",\n "key": trackData[\'key\'] + " - SNPs/Coverage",\n- "label": trackData[\'label\'] + "_autosnp",\n+ "label": trackData[\'label\'] + "_autosnp",\n })\n self._add_track_json(trackData2)\n \n@@ -468,7 +507,7 @@\n clientConfig = trackData[\'style\']\n del config[\'style\']\n \n- if \'match\' in gffOpts:\n+ if \'match\' in gffOpts:\n config[\'glyph\'] = \'JBrowse/View/FeatureGlyph/Segments\'\n cmd += [\'--type\', gffOpts[\'match\']]\n \n@@ -488,12 +527,14 @@\n \n self.subprocess_check_call(cmd)\n \n+ if gffOpts.get(\'index\', \'false\') == \'true\':\n+ self.tracksToIndex.append("%s" % trackData[\'label\'])\n \n def process_annotations(self, track):\n outputTrackConfig = {\n \'style\': {\n- \'label\': track[\'style\'].get(\'label\', \'description\'),\n- \'className\': track[\'style\'].get(\'className\', \'feature\'),\n+ \'label\': track[\'style\'].get(\'label\', \'description\'),\n+ \'className\': track[\'style\'].get(\'className\', \'feature\'),\n \'description\': track[\'style\'].get(\'description\', \'\'),\n },\n \'category\': track[\'category\'],\n@@ -516,11 +557,14 @@\n else:\n outputTrackConfig[key] = colourOptions[key]\n \n+ menus = self.cs.parse_menus(track[\'conf\'][\'options\'])\n+ outputTrackConfig.update(menus)\n+\n # import pprint; pprint.pprint(track)\n # import sys; sys.exit()\n if dataset_ext in (\'gff\', \'gff3\', \'bed\'):\n self.add_features(dataset_path, dataset_ext, outputTrackConfig,\n- track[\'conf\'][\'options\'][\'gff\'])\n+ track[\'conf\'][\'options\'][\'gff\'])\n elif dataset_ext == \'bigwig\':\n self.add_bigwig(dataset_path, outputTrackConfig,\n track[\'conf\'][\'options\'][\'wiggle\'])\n@@ -645,14 +689,14 @@\n try:\n # Only pertains to gff3 + blastxml. TODO?\n track_conf[\'style\'] = {t.tag: t.text for t in track.find(\'options/style\')}\n- except TypeError, te:\n+ except TypeError:\n track_conf[\'style\'] = {}\n pass\n track_conf[\'conf\'] = etree_to_dict(track.find(\'options\'))\n keys = jc.process_annotations(track_conf)\n \n-\n for key in keys:\n extra_data[\'visibility\'][track.attrib.get(\'visibility\', \'default_off\')].append(key)\n \n jc.add_final_data(extra_data)\n+ jc.generate_names()\n' |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a jbrowse.xml --- a/jbrowse.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/jbrowse.xml Tue Nov 29 10:55:30 2016 -0500 |
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| b'@@ -1,17 +1,16 @@\n-<tool id="jbrowse" name="JBrowse" version="0.5.2">\n+<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@">\n <description>genome browser</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements"/>\n <expand macro="stdio"/>\n- <version_command>python jbrowse.py --version</version_command>\n <command><![CDATA[\n \n #if $action.action_select == "create":\n- mkdir -p $output.files_path;\n+ mkdir -p $output.files_path &&\n #else:\n- cp -R $action.update_jbrowse.extra_files_path $output.files_path;\n+ cp -R $action.update_jbrowse.extra_files_path $output.files_path &&\n #end if\n \n ## Copy the XML file into the directory, mostly for debugging\n@@ -27,7 +26,7 @@\n #end if\n \n --outdir $output.files_path\n-$trackxml;\n+$trackxml &&\n \n #if str($standalone) == "Complete":\n mv $output.files_path/index.html $output;\n@@ -72,13 +71,13 @@\n <metadata>\n <gencode>$gencode</gencode>\n <genomes>\n- #if str($action.reference_genome.genome_type_select) == "indexed":\n- <genome>${action.reference_genome.genomes.fields.path}</genome>\n- #else\n- #for $genome in $action.reference_genome.genomes:\n- <genome>$genome</genome>\n- #end for\n- #end if\n+ #if str($reference_genome.genome_type_select) == "indexed":\n+ <genome>${reference_genome.genomes.fields.path}</genome>\n+ #else\n+ #for $genome in $reference_genome.genomes:\n+ <genome>$genome</genome>\n+ #end for\n+ #end if\n </genomes>\n <general>\n <defaultLocation>${jbgen.defaultLocation}</defaultLocation>\n@@ -145,6 +144,25 @@\n </scheme>\n #end if\n </scaling>\n+ <menus>\n+ #for $menu_item in $track.data_format.jbmenu.track_menu:\n+ <menu>\n+ <action>${menu_item.menu_action}</action>\n+ #if str($menu_item.menu_label) != "":\n+ <label>${menu_item.menu_label}</label>\n+ #end if\n+ #if str($menu_item.menu_title) != "":\n+ <title>${menu_item.menu_title}</title>\n+ #end if\n+ #if str($menu_item.menu_url) != "":\n+ <url>${menu_item.menu_url.replace("&", "&").replace("\\"", """)}</url>\n+ #end if\n+ #if str($menu_item.menu_icon) != "":\n+ <iconClass>${menu_item.menu_icon}</iconClass>\n+ #end if\n+ </menu>\n+ #end for\n+ </menus>\n #end if\n \n #if str($track.data_format.data_format_select) == "wiggle":\n@@ -194,6 +212,7 @@\n #end if\n <protein>${track.data_format.is_protein}</protein>\n <min_gap>${track.data_format.min_gap}</min_gap>\n+ <index>${track.data_format.index}</index>\n </blast>\n #else if str($track.data_format.data_format_select) == "gene_calls":\n <gff>\n@@ -201,6 +220,7 @@\n #if $track.data_format.match_part.match_part_select:\n <match>${track.data_format.match_part.name}</match>\n #end if\n+ <index>${track.data_format.index}</index>\n </gff>\n ## #else if str($track.data_format.data_format_select) == "sparql":\n ## <sparql>\n@@ -216,32 +236,40 @@\n #end for\n </tracks>\n </root>\n-]]>\n- </configfile>\n+]]></configfile>\n </configfiles>\n <inputs>\n- <conditional name="action" label="Action">\n- <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">\n- <option value="create">New JBrowse Instance</option>\n- <op'..b' <param name="match_part_select" value="false"/>\n+ </conditional>\n+ <section name="jbcolor_scale">\n+ <conditional name="color_score">\n+ <param name="color_score_select" value="none"/>\n+ </conditional>\n+ <conditional name="color">\n+ <param name="color_select" value="automatic"/>\n+ </conditional>\n+ </section>\n+ <section name="jbmenu">\n+ <repeat name="track_menu">\n+ <param name="menu_action" value="iframeDialog"/>\n+ <param name="menu_label" value="Some menu item"/>\n+ <param name="menu_title" value="Frame title"/>\n+ <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/>\n+ <param name="menu_icon" value="dijitIconNewTask"/>\n+ </repeat>\n+ <repeat name="track_menu">\n+ <param name="menu_action" value="newWindow"/>\n+ <param name="menu_label" value="Another menu item"/>\n+ <param name="menu_title" value="Frame title 2"/>\n+ <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/>\n+ </repeat>\n+ </section>\n+ </conditional>\n+ </repeat>\n+ <repeat name="data_tracks">\n+ <conditional name="data_format">\n+ <param name="data_format_select" value="gene_calls"/>\n+ <param name="annotation" value="gff3/1.gff"/>\n+ <param name="index" value="true"/>\n+ <conditional name="match_part">\n+ <param name="match_part_select" value="false"/>\n+ </conditional>\n+ <section name="jbcolor_scale">\n+ <conditional name="color_score">\n+ <param name="color_score_select" value="none"/>\n+ </conditional>\n+ <conditional name="color">\n+ <param name="color_select" value="automatic"/>\n+ </conditional>\n+ </section>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+\n+ <param name="uglyTestingHack" value="enabled" />\n+ <output name="output" file="menus/test.xml" lines_diff="6"/>\n+ </test>\n </tests>\n <help><![CDATA[\n JBrowse-in-Galaxy\n@@ -505,12 +737,6 @@\n JBrowse-in-Galaxy offers a highly configurable, workflow-compatible\n alternative to Trackster.\n \n-Overview\n---------\n-\n-JBrowse is a fast, embeddable genome browser built completely with\n-JavaScript and HTML5.\n-\n The JBrowse-in-Galaxy (JiG) tool was written to help build complex\n JBrowse installations straight from Galaxy, taking advantage of the\n latest Galaxy features such as dataset collections, sections, and colour\n@@ -587,7 +813,7 @@\n consists of top level ``match`` features, with a child ``match_part``\n feature, and is often used in displaying alignments. (See "Alignments"\n section on the `GFF3\n-specification <http://www.sequenceontology.org/gff3.shtml>`__ for more\n+specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more\n information). If the data is match/match part, you will need to specify\n the top level match feature name, as it can be one of a few different SO\n terms, and JiG does not yet have the ability to understand SO terms.\n@@ -755,8 +981,5 @@\n \n @ATTRIBUTION@\n ]]></help>\n- <citations>\n- <citation type="doi">10.1101/gr.094607.109</citation>\n- </citations>\n+ <expand macro="citations"/>\n </tool>\n-\n' |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a macros.xml --- a/macros.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/macros.xml Tue Nov 29 10:55:30 2016 -0500 |
| [ |
| b'@@ -2,10 +2,8 @@\n <macros>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.12.0">jbrowse</requirement>\n- <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>\n+ <requirement type="package" version="1.12.1">jbrowse</requirement>\n <requirement type="package" version="2.7">python</requirement>\n- <requirement type="package" version="5.18.1">perl</requirement>\n <requirement type="package" version="1.66">biopython</requirement>\n <requirement type="package" version="0.6.2">bcbiogff</requirement>\n <requirement type="package" version="1.2">samtools</requirement>\n@@ -13,7 +11,8 @@\n <yield/>\n </requirements>\n </xml>\n- <token name="@WRAPPER_VERSION@">1.0</token>\n+ <token name="@DATA_DIR@">\\$GALAXY_JBROWSE_SHARED_DIR</token>\n+ <token name="@WRAPPER_VERSION@">0.5.1</token>\n <xml name="stdio">\n <stdio>\n <exit_code range="1:"/>\n@@ -28,43 +27,6 @@\n This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche\n ]]>\n </token>\n- \n- <xml name="genome_selector"\n- token_help=""\n- token_label="Fasta sequences"\n- token_optional="False" >\n- <conditional name="reference_genome">\n- <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">\n- <option selected="True" value="indexed">Use a built-in genome</option>\n- <option value="history">Use a genome from history</option>\n- </param>\n- <when value="indexed">\n- <param \n- help="@HELP@"\n- label="@LABEL@"\n- name="genomes"\n- type="select"\n- optional="@OPTIONAL@"\n- >\n- <options from_data_table="all_fasta">\n- <filter column="2" type="sort_by" />\n- <validator message="No genomes are available for the selected input dataset" type="no_options" />\n- </options>\n- </param>\n- </when>\n- <when value="history">\n- <param \n- format="fasta"\n- label="@LABEL@"\n- help="@HELP@"\n- name="genomes"\n- type="data"\n- optional="@OPTIONAL@"\n- multiple="True" />\n- </when>\n- </conditional>\n- </xml>\n- \n <xml name="auto_manual_tk"\n token_cond_label="Color"\n token_cond_name="color"\n@@ -218,7 +180,7 @@\n <param type="select" label="JBrowse style.color function\'s score scaling" name="score_scaling"\n help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">\n <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>\n- <option value="logarithmic" selected="" >Logarithmic scaling</option>\n+ <option value="logarithmic">Logarithmic scaling</option>\n <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>\n </param>\n \n@@ -257,8 +219,8 @@\n </xml>\n <xml name="track_styling"\n token_classname="feature"\n- token_label="prodcut,name,id"\n- token_description="note"\n+ token_label="name,id"\n+ token_description="note,description"\n token_height="100px">\n <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">\n <param label="JBrowse style.className" type="text"\n@@ -283,7 +245,99 @@\n </section>\n </xml>\n \n+ <xml name="track_menu">\n+ <section name="jbmenu" titl'..b'ng the user away from JBrowse.</option>\n+ </param>\n+ <param label="Menu label"\n+ type="text"\n+ name="menu_label"\n+ help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">\n+ <expand macro="menu_sanitize" />\n+ </param>\n+ <param label="Menu title"\n+ type="text"\n+ name="menu_title"\n+ help="Will be displayed in the popup title bar if displayed ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">\n+ <expand macro="menu_sanitize" />\n+ </param>\n+ <param label="Menu url"\n+ type="text"\n+ name="menu_url"\n+ help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">\n+ <expand macro="menu_sanitize" />\n+ </param>\n+ <param label="Menu icon"\n+ type="select"\n+ name="menu_icon"\n+ help="Icon to display next to menu label">\n+ <option value="dijitIconBookmark" selected="true">Bookmark</option>\n+ <option value="dijitIconSave">Save</option>\n+ <option value="dijitIconPrint">Print</option>\n+ <option value="dijitIconCut">Cut</option>\n+ <option value="dijitIconCopy">Copy</option>\n+ <option value="dijitIconClear">Clear</option>\n+ <option value="dijitIconDelete">Delete</option>\n+ <option value="dijitIconUndo">Undo</option>\n+ <option value="dijitIconEdit">Edit</option>\n+ <option value="dijitIconNewTask">New Task</option>\n+ <option value="dijitIconEditTask">Edit Task</option>\n+ <option value="dijitIconEditProperty">Edit Property</option>\n+ <option value="dijitIconTask">Task</option>\n+ <option value="dijitIconFilter">Filter</option>\n+ <option value="dijitIconConfigure">Configure</option>\n+ <option value="dijitIconSearch">Search</option>\n+ <option value="dijitIconApplication">Application</option>\n+ <option value="dijitIconChart">Chart</option>\n+ <option value="dijitIconConnector">Connector</option>\n+ <option value="dijitIconDatabase">Database</option>\n+ <option value="dijitIconDocuments">Documents</option>\n+ <option value="dijitIconMail">Mail</option>\n+ <option value="dijitLeaf">Leaf</option>\n+ <option value="dijitIconFile">File</option>\n+ <option value="dijitIconFunction">Function</option>\n+ <option value="dijitIconKey">Key</option>\n+ <option value="dijitIconPackage">Package</option>\n+ <option value="dijitIconSample">Sample</option>\n+ <option value="dijitIconTable">Table</option>\n+ <option value="dijitIconUsers">Users</option>\n+ <option value="dijitIconFolderClosed">Folder Closed</option>\n+ <option value="dijitIconFolderOpen">Folder Open</option>\n+ <option value="dijitIconError">Error</option>\n+ </param>\n+ </repeat>\n+ </section>\n+ </xml>\n+\n+ <xml name="menu_sanitize">\n+ <sanitizer>\n+ <valid>\n+ <add value="{"/>\n+ <add value="}"/>\n+ <add value="!"/>\n+ <add value="?"/>\n+ <add value="&"/>\n+ <add value="+"/>\n+ <add value="="/>\n+ <add value="\'"/>\n+ <add value=\'"\'/>\n+ </valid>\n+ </sanitizer>\n+ </xml>\n+\n <xml name="input_conditional" token_label="Track Data" token_format="data">\n <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>\n </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1101/gr.094607.109</citation>\n+ </citations>\n+ </xml>\n </macros>\n' |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a readme.rst --- a/readme.rst Sun Jun 26 10:50:15 2016 -0400 +++ b/readme.rst Tue Nov 29 10:55:30 2016 -0500 |
| b |
| @@ -25,6 +25,9 @@ History ======= +- 0.5.1 Support for contextual menus. Conda tests. +- 0.5 Update existing instances on disk. Index names. Support HTML tracks + instead of Canvas. Support default tracks. General JBrowse optinos - 0.4 Support for dataset collections and customisation of tracks including labelling, colours, styling. Added support for genetic code selection. Fixed package installation recipe issues. |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/frameshift/1.gff --- a/test-data/frameshift/1.gff Sun Jun 26 10:50:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -##gff-version 3 -##sequence-region Merlin 1 172788 -Merlin GeneMark.hmm gene 10 20 . + . ID=Merlin_1;seqid=Merlin -Merlin GeneMark.hmm mRNA 10 20 . + . ID=Merlin_1_mRNA;Parent=Merlin_1 -Merlin GeneMark.hmm exon 10 20 . + . Parent=Merlin_1_mRNA -Merlin GeneMark.hmm CDS 10 20 1000 + 0 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA -Merlin GeneMark.hmm CDS 19 30 500 + 0 ID=Merlin_1_CDS ;Parent=Merlin_1_mRNA |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/frameshift/test.xml --- a/test-data/frameshift/test.xml Sun Jun 26 10:50:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,43 +0,0 @@ -<?xml version="1.0"?> -<root> - <metadata> - <gencode>11</gencode> - <genomes> - <genome>test-data/merlin.fa</genome> - </genomes> - <general> - <defaultLocation>Merlin:1-50</defaultLocation> - <trackPadding>40</trackPadding> - <shareLink>true</shareLink> - <aboutDescription></aboutDescription> - <show_tracklist>true</show_tracklist> - <show_nav>true</show_nav> - <show_overview>false</show_overview> - <show_menu>true</show_menu> - <hideGenomeOptions>false</hideGenomeOptions> - </general> - </metadata> - <tracks> - <track cat="Auto Coloured" format="gene_calls" visibility="default_on"> - <files> - <trackFile path="test-data/frameshift/1.gff" ext="gff3" label="Test Track"/> - </files> - <options> - <style> - <className>feature</className> - <description>feature</description> - <label>name,id</label> - <height>100px</height> - </style> - <gff> - </gff> - <scaling> - <method>ignore</method> - <scheme> - <color>__auto__</color> - </scheme> - </scaling> - </options> - </track> - </tracks> -</root> |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/gencode/test-1.xml --- a/test-data/gencode/test-1.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/test-data/gencode/test-1.xml Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -3,8 +3,20 @@ <metadata> <gencode>1</gencode> <genomes> - <genome>test-data/merlin.fa</genome> + <genome>/tmp/tmpPJZIQf/files/000/dataset_1.dat</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> </tracks> |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/gencode/test.xml --- a/test-data/gencode/test.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/test-data/gencode/test.xml Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -3,8 +3,20 @@ <metadata> <gencode>11</gencode> <genomes> - <genome>test-data/merlin.fa</genome> + <genome>/tmp/tmps5cL_a/files/000/dataset_3.dat</genome> </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> </metadata> <tracks> </tracks> |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/gff3/test.xml --- a/test-data/gff3/test.xml Sun Jun 26 10:50:15 2016 -0400 +++ b/test-data/gff3/test.xml Tue Nov 29 10:55:30 2016 -0500 |
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| b'@@ -3,226 +3,268 @@\n <metadata>\n <gencode>11</gencode>\n <genomes>\n- <genome>test-data/merlin.fa</genome>\n+ <genome>test-data/merlin.fa</genome>\n </genomes>\n <general>\n <defaultLocation></defaultLocation>\n- <trackPadding>40</trackPadding>\n+ <trackPadding>20</trackPadding>\n+\n <shareLink>true</shareLink>\n <aboutDescription></aboutDescription>\n <show_tracklist>true</show_tracklist>\n <show_nav>true</show_nav>\n- <show_overview>false</show_overview>\n+ <show_overview>true</show_overview>\n <show_menu>true</show_menu>\n <hideGenomeOptions>false</hideGenomeOptions>\n </general>\n </metadata>\n <tracks>\n- <track cat="Auto Coloured" format="gene_calls" visibility="default_on">\n+ <track cat="Auto Coloured" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>\n+ <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>\n+ <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>\n+ <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>\n+ <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>\n </files>\n \n <options>\n <style>\n <className>feature</className>\n- <description>feature</description>\n+ <description>note,description</description>\n <label>name,id</label>\n <height>100px</height>\n </style>\n+ <scaling>\n+ <method>ignore</method>\n+ <scheme>\n+ <color>__auto__</color>\n+ </scheme>\n+ </scaling>\n+ <menus>\n+ </menus>\n+\n <gff>\n+ <trackType>JBrowse/View/Track/CanvasFeatures</trackType>\n+ <index>false</index>\n </gff>\n- <scaling>\n- <method>ignore</method>\n- <scheme>\n- <color>__auto__</color>\n- </scheme>\n- </scaling>\n </options>\n </track>\n- <track cat="Ignore Scale" format="gene_calls">\n+ <track cat="Ignore Scale" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>\n+ <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>\n </files>\n \n <options>\n <style>\n <className>feature</className>\n- <description>feature</description>\n+ <description>note,description</description>\n <label>name,id</label>\n <height>100px</height>\n </style>\n+ <scaling>\n+ <method>ignore</method>\n+ <scheme>\n+ <color>#ff00ff</color>\n+ </scheme>\n+ </scaling>\n+ <menus>\n+ </menus>\n+\n <gff>\n+ <trackType>JBrowse/View/Track/CanvasFeatures</trackType>\n+ <index>false</index>\n </gff>\n- <scaling>\n- <method>ignore</method>\n- <scheme>\n- <color>#ff00ff</color>\n- </scheme>\n- '..b' <type>manual</type>\n+\n+ <min>0</min>\n+ <max>1000</max>\n+ </scales>\n+ <scheme>\n+ <type>opacity</type>\n+ <color>#ff0000</color>\n+ </scheme>\n+ </scaling>\n+ <menus>\n+ </menus>\n+\n <gff>\n+ <trackType>JBrowse/View/Track/CanvasFeatures</trackType>\n+ <index>false</index>\n </gff>\n- <scaling>\n- <method>score</method>\n- <algo>linear</algo>\n- <scales>\n- <type>manual</type>\n- <min>0</min>\n- <max>1000</max>\n- </scales>\n- <scheme>\n- <type>opacity</type>\n- <color>#ff0000</color>\n- </scheme>\n- </scaling>\n </options>\n </track>\n-\n-\n- <track cat="Realistic" format="gene_calls">\n+ <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>\n+ <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>\n </files>\n \n <options>\n <style>\n <className>feature</className>\n- <description>feature</description>\n+ <description>note,description</description>\n <label>name,id</label>\n <height>100px</height>\n </style>\n+ <scaling>\n+ <method>ignore</method>\n+ <scheme>\n+ <color>__auto__</color>\n+ </scheme>\n+ </scaling>\n+ <menus>\n+ </menus>\n+\n <gff>\n+ <trackType>JBrowse/View/Track/CanvasFeatures</trackType>\n+ <index>false</index>\n </gff>\n- <scaling>\n- <method>ignore</method>\n- <scheme>\n- <color>__auto__</color>\n- </scheme>\n- </scaling>\n </options>\n </track>\n- <track cat="Realistic" format="gene_calls">\n+ <track cat="Realistic" format="gene_calls" visibility="default_off">\n <files>\n- <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>\n+ <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>\n </files>\n \n <options>\n <style>\n <className>feature</className>\n- <description>feature</description>\n+ <description>note,description</description>\n <label>name,id</label>\n <height>100px</height>\n </style>\n+ <scaling>\n+ <method>ignore</method>\n+ <scheme>\n+ <color>__auto__</color>\n+ </scheme>\n+ </scaling>\n+ <menus>\n+ </menus>\n+\n <gff>\n+ <trackType>JBrowse/View/Track/CanvasFeatures</trackType>\n <match>cDNA_match</match>\n+ <index>false</index>\n </gff>\n- <scaling>\n- <method>ignore</method>\n- <scheme>\n- <type>opacity</type>\n- <color>__auto__</color>\n- </scheme>\n- </scaling>\n </options>\n </track>\n </tracks>\n' |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a test-data/menus/test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/menus/test.xml Tue Nov 29 10:55:30 2016 -0500 |
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| @@ -0,0 +1,91 @@ +<?xml version="1.0"?> +<root> + <metadata> + <gencode>11</gencode> + <genomes> + <genome>/tmp/tmplFZ5li/files/000/dataset_14.dat</genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + </metadata> + <tracks> + <track cat="With menu or index" format="gene_calls" visibility="default_off"> + <files> + <trackFile path="/tmp/tmplFZ5li/files/000/dataset_15.dat" ext="gff3" label="1.gff" /> + </files> + + <options> + <style> + <className>feature</className> + <description>note,description</description> + <label>name,id</label> + <height>100px</height> + </style> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + <menus> + <menu> + <action>iframeDialog</action> + <label>Some menu item</label> + <title>Frame title</title> + <url>https://example.com/#!/?id={name}&q={type}&z="{end}"</url> + <iconClass>dijitIconNewTask</iconClass> + </menu> + <menu> + <action>newWindow</action> + <label>Another menu item</label> + <title>Frame title 2</title> + <url>https://example.com/#!/?id={name}&q={type}&z="{end}"</url> + <iconClass>dijitIconBookmark</iconClass> + </menu> + </menus> + + <gff> + <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <index>false</index> + </gff> + </options> + </track> + <track cat="With menu or index" format="gene_calls" visibility="default_off"> + <files> + <trackFile path="/tmp/tmplFZ5li/files/000/dataset_15.dat" ext="gff3" label="1.gff" /> + </files> + + <options> + <style> + <className>feature</className> + <description>note,description</description> + <label>name,id</label> + <height>100px</height> + </style> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + <menus> + </menus> + + <gff> + <trackType>JBrowse/View/Track/CanvasFeatures</trackType> + <index>true</index> + </gff> + </options> + </track> + </tracks> +</root> |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Sun Jun 26 10:50:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> -<tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> -</tables> - |
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| diff -r 1e74f16adaa1 -r ad4b9d7eae6a tool_dependencies.xml --- a/tool_dependencies.xml Sun Jun 26 10:50:15 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="jbrowse" version="1.12.0"> - <repository changeset_revision="d65f12198038" name="package_jbrowse_1_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bundle_jbrowse" version="1.12.0"> - <repository changeset_revision="52153ec17769" name="package_perl_bundle_jbrowse_1_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="python" version="2.7"> - <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biopython" version="1.66"> - <repository changeset_revision="8433ee4531ff" name="package_biopython_1_66" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bcbiogff" version="0.6.2"> - <repository changeset_revision="8ee2210f6074" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pyyaml" version="3.11"> - <repository changeset_revision="99267d131c05" name="package_python_2_7_pyyaml_3_11" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |